From ngoto at pub.open-bio.org Fri Dec 2 02:01:40 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Fri Dec 2 01:56:19 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio test_alignment.rb,1.4,1.5
Message-ID: <200512020701.jB271eVL024738@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory pub.open-bio.org:/tmp/cvs-serv24705/test/unit/bio
Modified Files:
test_alignment.rb
Log Message:
* consensus_iupac now returns only standard bases
'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v', 'h', 'd', 'b', 'n',
or nil (in SiteMethods#consensus_iupac) or '?' (or missing_char, in
EnumerableExtension#consensus_iupac).
Note that consensus_iupac now does not return u and invalid letters
not defined in IUPAC standard even if all bases are equal.
* added more tests to test_alignment.rb
Index: test_alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_alignment.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** test_alignment.rb 25 Nov 2005 16:53:32 -0000 1.4
--- test_alignment.rb 2 Dec 2005 07:01:38 -0000 1.5
***************
*** 138,142 ****
end #class TestAlignmentPropertyMethods
!
class TestAlignmentSite < Test::Unit::TestCase
--- 138,145 ----
end #class TestAlignmentPropertyMethods
! # This is a unit test of Bio::Alignment::Site class and
! # Bio::Alignment::SiteMethods module.
! # Since Bio::Alignment::Site includes Bio::Alignment::SiteMethods,
! # we can test both at a time.
class TestAlignmentSite < Test::Unit::TestCase
***************
*** 239,243 ****
--- 242,414 ----
end #class TestAlignmentSite
+ class TestAlignmentSequenceArray < Test::Unit::TestCase
+ def test_each_seq
+ expected_results = [ 'atg', 'aag', 'acg' ]
+ a = Alignment::SequenceArray[ *expected_results ]
+ a.each_seq do |x|
+ assert_equal(expected_results.shift, x)
+ end
+ assert(expected_results.empty?)
+ end
+
+ def test_seqclass_default
+ a = Alignment::SequenceArray.new
+ assert_equal(String, a.seqclass)
+ end
+
+ def test_seqclass
+ a = Alignment::SequenceArray[ Bio::Sequence::NA.new('atg') ]
+ assert_equal(Bio::Sequence::NA, a.seqclass)
+ end
+
+ def test_seqclass=()
+ a = Alignment::SequenceArray.new
+ assert_equal(String, a.seqclass)
+ a << Bio::Sequence::NA.new('a')
+ assert_equal(Bio::Sequence::NA, a.seqclass)
+ a.seqclass = Bio::Sequence::AA
+ assert_equal(Bio::Sequence::AA, a.seqclass)
+ end
+
+ def test_alignment_length
+ a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
+ assert_equal(4, a.alignment_length)
+ end
+
+ def test_private_alignment_site
+ a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
+ assert_equal(Alignment::Site[ '-', 't', 't', 't', '-' ],
+ a.instance_eval { _alignment_site(1) })
+ end
+ def test_alignment_site
+ a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
+ assert_equal(Alignment::Site[ '-', 't', 't', 't', '-' ],
+ a.__send__(:_alignment_site, 1))
+ end
+
+ def test_each_site
+ expected_results = [
+ Alignment::Site[ 'a', 'a', 'a', 'a', '-' ],
+ Alignment::Site[ '-', 't', 't', 't', '-' ],
+ Alignment::Site[ '-', '-', 'g', 'g', '-' ],
+ Alignment::Site[ '-', '-', 'c', '-', '-' ]
+ ]
+ a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
+ a.each_site do |site|
+ assert_equal(expected_results.shift, site)
+ end
+ assert(expected_results.empty?)
+ end
+
+ def test_each_site_step
+ expected_results = [
+ Alignment::Site[ '-', 't', 't', 't', '-' ], # site 1
+ Alignment::Site[ '-', 'a', 'g', 't', '-' ], # site 3
+ ]
+ a = Alignment::SequenceArray[ 'a', 'atgatc', 'atggcc', 'atgtga', '' ]
+ a.each_site_step(1, 4, 2) do |site|
+ assert_equal(expected_results.shift, site)
+ end
+ assert(expected_results.empty?)
+ end
+
+ def test_alignment_collect
+ a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
+ assert_equal(Alignment::SequenceArray[ 'a', 'au', 'augc', 'aug', '' ],
+ a.alignment_collect { |x| x.gsub(/t/, 'u') })
+ end
+
+ def test_alignment_window
+ a = Alignment::SequenceArray[ 'a', 'at', 'atgca', 'atg', '' ]
+ assert_equal(Alignment::SequenceArray[ '', 't', 'tgc', 'tg', '' ],
+ a.alignment_window(1, 3))
+ end
+
+ def test_each_window
+ expected_results = [
+ Alignment::SequenceArray[ 'atg', 'tcg', '' ], # 0..2
+ Alignment::SequenceArray[ 'gca', 'gat', '' ], # 2..4
+ Alignment::SequenceArray[ 'atg', 'tgc', '' ], # 4..6
+ Alignment::SequenceArray[ 'c', 'a', '' ] # 7..7
+ ]
+ a = Alignment::SequenceArray[ 'atgcatgc', 'tcgatgca', '' ]
+ r = a.each_window(3, 2) do |x|
+ assert_equal(expected_results.shift, x)
+ end
+ assert_equal(expected_results.shift, r)
+ assert(expected_results.empty?)
+ end
+
+ def test_collect_each_site
+ a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
+ assert_equal(["aaaa-", "-ttt-", "--gg-", "--c--" ],
+ a.collect_each_site { |x| x.join('') })
+ end
+
+ def test_consensus_each_site_default
+ expected_results = [
+ Alignment::Site[ 'a', 'a', 'a', 'a', 'a' ],
+ Alignment::Site[ 'a', 'c', 'g', 't', '-' ]
+ ]
+
+ a = Alignment::SequenceArray[ 'aa', 'ac', 'ag', 'at', 'a-' ]
+ result = a.consensus_each_site do |site|
+ assert_equal(expected_results.shift, site)
+ 'x'
+ end
+ assert_equal('xx', result)
+ assert(expected_results.empty?)
+ end
+
+ def test_consensus_each_site_gap_mode_1
+ expected_results = [
+ Alignment::Site[ 'a', 'a', 'a', 'a', 'a' ]
+ ]
+
+ a = Alignment::SequenceArray[ 'aa', 'ac', 'ag', 'at', 'a-' ]
+ result = a.consensus_each_site(:gap_mode => 1) do |site|
+ assert_equal(expected_results.shift, site)
+ 'x'
+ end
+ assert_equal('x-', result)
+ assert(expected_results.empty?)
+ end
+
+ def test_consensus_each_site_gap_mode_minus1
+ expected_results = [
+ Alignment::Site[ 'a', 'a', 'a', 'a', 'a' ],
+ Alignment::Site[ 'a', 'c', 'g', 't' ]
+ ]
+
+ a = Alignment::SequenceArray[ 'aa', 'ac', 'ag', 'at', 'a-' ]
+ result = a.consensus_each_site(:gap_mode => -1) do |site|
+ assert_equal(expected_results.shift, site)
+ 'x'
+ end
+ assert_equal('xx', result)
+ assert(expected_results.empty?)
+ end
+
+ def test_consensus_string_default
+ a = Alignment::SequenceArray[ 'ata', 'aac', 'aag', 'aat' ]
+ assert_equal('a??', a.consensus_string)
+ end
+
+ def test_consensus_string_half
+ a = Alignment::SequenceArray[ 'ata', 'aac', 'aag', 'aat' ]
+ assert_equal('aa?', a.consensus_string(0.5))
+ end
+
+ def test_consensus_iupac
+ a = Alignment::SequenceArray[
+ 'acgtaaaccgaaacaz',
+ 'acgtaaaccgccggcz',
+ 'acgtcgtgttgtttgz',
+ 'acgtcgtgttaaactz' ]
+ assert_equal('acgtmrwsykvhdbn?', a.consensus_iupac)
+ end
+
+ end #class TestAlignmentSequenceArray
From ngoto at pub.open-bio.org Fri Dec 2 02:01:40 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Fri Dec 2 01:56:20 2005
Subject: [BioRuby-cvs] bioruby/lib/bio alignment.rb,1.12,1.13
Message-ID: <200512020701.jB271eVL024736@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv24705/lib/bio
Modified Files:
alignment.rb
Log Message:
* consensus_iupac now returns only standard bases
'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v', 'h', 'd', 'b', 'n',
or nil (in SiteMethods#consensus_iupac) or '?' (or missing_char, in
EnumerableExtension#consensus_iupac).
Note that consensus_iupac now does not return u and invalid letters
not defined in IUPAC standard even if all bases are equal.
* added more tests to test_alignment.rb
Index: alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/alignment.rb,v
retrieving revision 1.12
retrieving revision 1.13
diff -C2 -d -r1.12 -r1.13
*** alignment.rb 25 Nov 2005 16:50:39 -0000 1.12
--- alignment.rb 2 Dec 2005 07:01:37 -0000 1.13
***************
*** 228,232 ****
a = self.collect { |x| x.downcase }.sort.uniq
if a.size == 1 then
! a[0]
elsif r = IUPAC_NUC.find { |x| (a - x).size <= 0 } then
r[0]
--- 228,239 ----
a = self.collect { |x| x.downcase }.sort.uniq
if a.size == 1 then
! case a[0]
! when 'a', 'c', 'g', 't'
! a[0]
! when 'u'
! 't'
! else
! IUPAC_NUC.find { |x| a[0] == x[0] } ? a[0] : nil
! end
elsif r = IUPAC_NUC.find { |x| (a - x).size <= 0 } then
r[0]
***************
*** 329,333 ****
# For Array or Hash objects, you'd better using
# ArrayExtension or HashExtension modules, respectively.
! # They have built-in 'each_seq' method.
#
module EnumerableExtension
--- 336,341 ----
# For Array or Hash objects, you'd better using
# ArrayExtension or HashExtension modules, respectively.
! # They would have built-in each_seq method and/or
! # some methods would be redefined.
#
module EnumerableExtension
***************
*** 336,340 ****
# Iterates over each sequences.
# Yields a sequence.
! # It acts same as Enumerable#each.
#
# You would redefine the method suitable for the class/object.
--- 344,348 ----
# Iterates over each sequences.
# Yields a sequence.
! # It acts the same as Enumerable#each.
#
# You would redefine the method suitable for the class/object.
***************
*** 380,383 ****
--- 388,395 ----
# If the position is out of range, it returns the site
# of which all are gaps.
+ #
+ # It is a private method.
+ # Only difference from public alignment_site method is
+ # it does not do set_all_property(get_all_property).
def _alignment_site(position)
site = Site.new
***************
*** 433,437 ****
end
! # Iterates over each sequence and each results running block
# are collected and returns a new alignment as a
# Bio::Alignment::SequenceArray object.
--- 445,449 ----
end
! # Iterates over each sequence and results running blocks
# are collected and returns a new alignment as a
# Bio::Alignment::SequenceArray object.
From ngoto at pub.open-bio.org Fri Dec 2 07:01:30 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Fri Dec 2 06:56:20 2005
Subject: [BioRuby-cvs] bioruby/lib/bio alignment.rb,1.13,1.14
Message-ID: <200512021201.jB2C1UVL025772@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv25760/lib/bio
Modified Files:
alignment.rb
Log Message:
fixed bugs in EnumerableExtension#alignment_rstrip! and #remove_all_gaps!.
Index: alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/alignment.rb,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** alignment.rb 2 Dec 2005 07:01:37 -0000 1.13
--- alignment.rb 2 Dec 2005 12:01:28 -0000 1.14
***************
*** 735,739 ****
each_site_step(len - 1, 0, -1) do |a|
a.remove_gaps!
! if a.empty then
newlen -= 1
else
--- 735,739 ----
each_site_step(len - 1, 0, -1) do |a|
a.remove_gaps!
! if a.empty? then
newlen -= 1
else
***************
*** 743,747 ****
return nil if newlen >= len
each_seq do |s|
! s[len..-1] = '' if s.length > len
end
self
--- 743,747 ----
return nil if newlen >= len
each_seq do |s|
! s[newlen..-1] = '' if s.length > newlen
end
self
***************
*** 792,796 ****
ret = nil
each_seq do |s|
! ret ||= s.gsub!(gap_regexp, '')
end
ret ? self : nil
--- 792,797 ----
ret = nil
each_seq do |s|
! x = s.gsub!(gap_regexp, '')
! ret ||= x
end
ret ? self : nil
From ngoto at pub.open-bio.org Fri Dec 2 08:01:51 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Fri Dec 2 07:56:28 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio test_alignment.rb,1.5,1.6
Message-ID: <200512021301.jB2D1pVL025886@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory pub.open-bio.org:/tmp/cvs-serv25876/test/unit/bio
Modified Files:
test_alignment.rb
Log Message:
* TestAlignmentSequenceArray are changed to TestAlignmentEnumerableExtension.
* Added more tests
Index: test_alignment.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_alignment.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** test_alignment.rb 2 Dec 2005 07:01:38 -0000 1.5
--- test_alignment.rb 2 Dec 2005 13:01:49 -0000 1.6
***************
*** 242,249 ****
end #class TestAlignmentSite
! class TestAlignmentSequenceArray < Test::Unit::TestCase
def test_each_seq
expected_results = [ 'atg', 'aag', 'acg' ]
! a = Alignment::SequenceArray[ *expected_results ]
a.each_seq do |x|
assert_equal(expected_results.shift, x)
--- 242,254 ----
end #class TestAlignmentSite
! # This is sample class for testing Bio::Alignment::EnumerableExtension.
! class A < Array
! include Alignment::EnumerableExtension
! end
!
! class TestAlignmentEnumerableExtension < Test::Unit::TestCase
def test_each_seq
expected_results = [ 'atg', 'aag', 'acg' ]
! a = A[ *expected_results ]
a.each_seq do |x|
assert_equal(expected_results.shift, x)
***************
*** 253,267 ****
def test_seqclass_default
! a = Alignment::SequenceArray.new
assert_equal(String, a.seqclass)
end
def test_seqclass
! a = Alignment::SequenceArray[ Bio::Sequence::NA.new('atg') ]
assert_equal(Bio::Sequence::NA, a.seqclass)
end
def test_seqclass=()
! a = Alignment::SequenceArray.new
assert_equal(String, a.seqclass)
a << Bio::Sequence::NA.new('a')
--- 258,272 ----
def test_seqclass_default
! a = A.new
assert_equal(String, a.seqclass)
end
def test_seqclass
! a = A[ Bio::Sequence::NA.new('atg') ]
assert_equal(Bio::Sequence::NA, a.seqclass)
end
def test_seqclass=()
! a = A.new
assert_equal(String, a.seqclass)
a << Bio::Sequence::NA.new('a')
***************
*** 272,281 ****
def test_alignment_length
! a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
assert_equal(4, a.alignment_length)
end
def test_private_alignment_site
! a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
assert_equal(Alignment::Site[ '-', 't', 't', 't', '-' ],
a.instance_eval { _alignment_site(1) })
--- 277,286 ----
def test_alignment_length
! a = A[ 'a', 'at', 'atgc', 'atg', '' ]
assert_equal(4, a.alignment_length)
end
def test_private_alignment_site
! a = A[ 'a', 'at', 'atgc', 'atg', '' ]
assert_equal(Alignment::Site[ '-', 't', 't', 't', '-' ],
a.instance_eval { _alignment_site(1) })
***************
*** 283,287 ****
def test_alignment_site
! a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
assert_equal(Alignment::Site[ '-', 't', 't', 't', '-' ],
a.__send__(:_alignment_site, 1))
--- 288,292 ----
def test_alignment_site
! a = A[ 'a', 'at', 'atgc', 'atg', '' ]
assert_equal(Alignment::Site[ '-', 't', 't', 't', '-' ],
a.__send__(:_alignment_site, 1))
***************
*** 295,299 ****
Alignment::Site[ '-', '-', 'c', '-', '-' ]
]
! a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
a.each_site do |site|
assert_equal(expected_results.shift, site)
--- 300,304 ----
Alignment::Site[ '-', '-', 'c', '-', '-' ]
]
! a = A[ 'a', 'at', 'atgc', 'atg', '' ]
a.each_site do |site|
assert_equal(expected_results.shift, site)
***************
*** 307,311 ****
Alignment::Site[ '-', 'a', 'g', 't', '-' ], # site 3
]
! a = Alignment::SequenceArray[ 'a', 'atgatc', 'atggcc', 'atgtga', '' ]
a.each_site_step(1, 4, 2) do |site|
assert_equal(expected_results.shift, site)
--- 312,316 ----
Alignment::Site[ '-', 'a', 'g', 't', '-' ], # site 3
]
! a = A[ 'a', 'atgatc', 'atggcc', 'atgtga', '' ]
a.each_site_step(1, 4, 2) do |site|
assert_equal(expected_results.shift, site)
***************
*** 315,319 ****
def test_alignment_collect
! a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
assert_equal(Alignment::SequenceArray[ 'a', 'au', 'augc', 'aug', '' ],
a.alignment_collect { |x| x.gsub(/t/, 'u') })
--- 320,324 ----
def test_alignment_collect
! a = A[ 'a', 'at', 'atgc', 'atg', '' ]
assert_equal(Alignment::SequenceArray[ 'a', 'au', 'augc', 'aug', '' ],
a.alignment_collect { |x| x.gsub(/t/, 'u') })
***************
*** 321,325 ****
def test_alignment_window
! a = Alignment::SequenceArray[ 'a', 'at', 'atgca', 'atg', '' ]
assert_equal(Alignment::SequenceArray[ '', 't', 'tgc', 'tg', '' ],
a.alignment_window(1, 3))
--- 326,330 ----
def test_alignment_window
! a = A[ 'a', 'at', 'atgca', 'atg', '' ]
assert_equal(Alignment::SequenceArray[ '', 't', 'tgc', 'tg', '' ],
a.alignment_window(1, 3))
***************
*** 333,337 ****
Alignment::SequenceArray[ 'c', 'a', '' ] # 7..7
]
! a = Alignment::SequenceArray[ 'atgcatgc', 'tcgatgca', '' ]
r = a.each_window(3, 2) do |x|
assert_equal(expected_results.shift, x)
--- 338,342 ----
Alignment::SequenceArray[ 'c', 'a', '' ] # 7..7
]
! a = A[ 'atgcatgc', 'tcgatgca', '' ]
r = a.each_window(3, 2) do |x|
assert_equal(expected_results.shift, x)
***************
*** 342,346 ****
def test_collect_each_site
! a = Alignment::SequenceArray[ 'a', 'at', 'atgc', 'atg', '' ]
assert_equal(["aaaa-", "-ttt-", "--gg-", "--c--" ],
a.collect_each_site { |x| x.join('') })
--- 347,351 ----
def test_collect_each_site
! a = A[ 'a', 'at', 'atgc', 'atg', '' ]
assert_equal(["aaaa-", "-ttt-", "--gg-", "--c--" ],
a.collect_each_site { |x| x.join('') })
***************
*** 353,357 ****
]
! a = Alignment::SequenceArray[ 'aa', 'ac', 'ag', 'at', 'a-' ]
result = a.consensus_each_site do |site|
assert_equal(expected_results.shift, site)
--- 358,362 ----
]
! a = A[ 'aa', 'ac', 'ag', 'at', 'a-' ]
result = a.consensus_each_site do |site|
assert_equal(expected_results.shift, site)
***************
*** 367,371 ****
]
! a = Alignment::SequenceArray[ 'aa', 'ac', 'ag', 'at', 'a-' ]
result = a.consensus_each_site(:gap_mode => 1) do |site|
assert_equal(expected_results.shift, site)
--- 372,376 ----
]
! a = A[ 'aa', 'ac', 'ag', 'at', 'a-' ]
result = a.consensus_each_site(:gap_mode => 1) do |site|
assert_equal(expected_results.shift, site)
***************
*** 382,386 ****
]
! a = Alignment::SequenceArray[ 'aa', 'ac', 'ag', 'at', 'a-' ]
result = a.consensus_each_site(:gap_mode => -1) do |site|
assert_equal(expected_results.shift, site)
--- 387,391 ----
]
! a = A[ 'aa', 'ac', 'ag', 'at', 'a-' ]
result = a.consensus_each_site(:gap_mode => -1) do |site|
assert_equal(expected_results.shift, site)
***************
*** 392,416 ****
def test_consensus_string_default
! a = Alignment::SequenceArray[ 'ata', 'aac', 'aag', 'aat' ]
assert_equal('a??', a.consensus_string)
end
def test_consensus_string_half
! a = Alignment::SequenceArray[ 'ata', 'aac', 'aag', 'aat' ]
assert_equal('aa?', a.consensus_string(0.5))
end
def test_consensus_iupac
! a = Alignment::SequenceArray[
'acgtaaaccgaaacaz',
'acgtaaaccgccggcz',
'acgtcgtgttgtttgz',
! 'acgtcgtgttaaactz' ]
assert_equal('acgtmrwsykvhdbn?', a.consensus_iupac)
end
! end #class TestAlignmentSequenceArray
--- 397,568 ----
def test_consensus_string_default
! a = A[ 'ata', 'aac', 'aag', 'aat' ]
assert_equal('a??', a.consensus_string)
end
def test_consensus_string_half
! a = A[ 'ata', 'aac', 'aag', 'aat' ]
assert_equal('aa?', a.consensus_string(0.5))
end
def test_consensus_iupac
! a = A[
'acgtaaaccgaaacaz',
'acgtaaaccgccggcz',
'acgtcgtgttgtttgz',
! 'acgtcgtgttaaactz'
! ]
assert_equal('acgtmrwsykvhdbn?', a.consensus_iupac)
end
! def test_match_line_amino
! a = A[
! 'M-SNNNQMMHF-CASSSSSNNFH-AW',
! 'M-TEHDHIIYY-STATTGNDEVF-FW',
! 'M-AQQERLLHW-AVGNPNDEQLY-HW',
! 'M-SKKQKVFYF-CASKADEQHIH-LW',
! 'M-TNNNQMMHY-STASSSQHRMF-QW',
! 'M-AEHDHIIYW-AVGTTGKKKFY-YW'
! #* ::::::::: ........... *
! ]
! assert_equal('* ::::::::: ........... *', a.match_line_amino)
! end
!
! def test_match_line_nuc
! a = A[ 'aaa', 'aa-','aac', 'at-' ]
! assert_equal('* ', a.match_line_nuc)
! end
!
! def test_match_line
! a = A[
! Sequence::AA.new('MNSA'),
! Sequence::AA.new('MHTL'),
! Sequence::AA.new('MQNV'),
! Sequence::AA.new('MKKW'),
! ]
! assert_equal('*:. ', a.match_line)
! assert_equal('*:. ', a.match_line(:type => :aa))
! assert_equal('* ', a.match_line(:type => :na))
! end
!
! def test_convert_match
! a = A[
! 'aaaa',
! 'accc',
! 'acac',
! 'actc'
! ]
! a.convert_match
! assert_equal(A[ 'aaaa', '.ccc', '.c.c', '.ctc' ], a)
! end
!
! def test_convert_unmatch
! a = A[ 'aaaa', '.ccc', '.c.c', '.ctc' ]
! a.convert_unmatch
! assert_equal(A[ 'aaaa', 'accc', 'acac', 'actc' ], a)
! end
!
! def test_alignment_normalize!
! a = A[ 'a', 'atg', 'atgc', '' ]
! a.alignment_normalize!
! assert_equal(A[ 'a---', 'atg-', 'atgc', '----'], a)
! end
!
! def test_alignment_rstrip!
! a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
! assert(a.alignment_rstrip!)
! assert_equal(A[ '--aaa', '--t-t', '---g-', '--t' ], a)
! end
!
! def test_alignment_rstrip_nil
! a = A[ 'aa', '-a', 'a-' ]
! assert_nil(a.alignment_rstrip!)
! assert_equal(A[ 'aa', '-a', 'a-' ], a)
! end
!
! def test_alignment_lstrip!
! a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
! assert(a.alignment_lstrip!)
! assert_equal(A[ 'aaa--', 't-t--', '-g---', 't' ], a)
! end
!
! def test_alignment_lstrip_nil
! a = A[ 'aa', '-a', 'a-' ]
! assert_nil(a.alignment_lstrip!)
! assert_equal(A[ 'aa', '-a', 'a-' ], a)
! end
!
! def test_alignment_strip!
! a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
! assert(a.alignment_strip!)
! assert_equal(A[ 'aaa', 't-t', '-g-', 't' ], a)
! end
!
! def test_alignment_strip_nil
! a = A[ 'aa', '-a', 'a-' ]
! assert_nil(a.alignment_strip!)
! assert_equal(A[ 'aa', '-a', 'a-' ], a)
! end
!
! def test_remove_all_gaps!
! a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
! assert(a.remove_all_gaps!)
! assert_equal(A[ 'aaa', 'tt', 'g', 't' ], a)
! end
!
! # test of alignment_slice.
! # Please also refer alignment_window.
! def test_alignment_slice
! a = A[ 'a', 'at', 'atgca', 'atg', '' ]
! assert_equal(Alignment::SequenceArray[ '', 't', 'tgc', 'tg', nil ],
! a.alignment_slice(1, 3))
! end
+ def test_alignment_subseq
+ a = A[ Sequence.new('a'), Sequence.new('at'), Sequence.new('atgca'),
+ Sequence.new('atg'), Sequence.new('') ]
+ assert_equal(Alignment::SequenceArray[ Sequence.new(''),
+ Sequence.new('t'), Sequence.new('tgc'),
+ Sequence.new('tg'), nil ],
+ a.alignment_subseq(2,4))
+ end
+ def test_alignment_concat
+ a = A[ 'aaa', 'c', 'gg', 't' ]
+ a.alignment_concat(A[ 'ttt', 'gg', 'aa', 'cc', 'aa' ])
+ assert_equal(A[ 'aaattt', 'cgg', 'ggaa', 'tcc' ], a)
+ a.alignment_concat([ 'c', 't' ])
+ assert_equal(A[ 'aaatttc', 'cggt', 'ggaa', 'tcc' ], a)
+ end
+ end #class TestAlignmentEnumerableExtension
+
+ class TestAlignmentClustalWFormatter < Test::Unit::TestCase
+ def setup
+ @obj = Object.new
+ @obj.extend(Alignment::ClustalWFormatter)
+ end
+
+ def test_have_same_name_true
+ assert_equal([ 0, 1 ], @obj.instance_eval {
+ have_same_name?([ 'ATP ATG', 'ATP ATA', 'BBB' ]) })
+ end
+
+ def test_have_same_name_false
+ assert_equal(false, @obj.instance_eval {
+ have_same_name?([ 'GTP ATG', 'ATP ATA', 'BBB' ]) })
+ end
+
+ def test_avoid_same_name
+ assert_equal([ 'ATP_ATG', 'ATP_ATA', 'BBB' ],
+ @obj.instance_eval {
+ avoid_same_name([ 'ATP ATG', 'ATP ATA', 'BBB' ]) })
+ end
+ def test_avoid_same_name_numbering
+ assert_equal([ '0_ATP', '1_ATP', '2_BBB' ],
+ @obj.instance_eval {
+ avoid_same_name([ 'ATP', 'ATP', 'BBB' ]) })
+ end
+
+ end #class TestAlignmentClustalWFormatter
From k at pub.open-bio.org Tue Dec 6 07:29:03 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Tue Dec 6 07:23:21 2005
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd.ja,1.16,1.17
Message-ID: <200512061229.jB6CT3VL019934@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/doc
In directory pub.open-bio.org:/tmp/cvs-serv19930
Modified Files:
Tutorial.rd.ja
Log Message:
* added BioRuby shell documentation
Index: Tutorial.rd.ja
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd.ja,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** Tutorial.rd.ja 24 Sep 2005 14:58:21 -0000 1.16
--- Tutorial.rd.ja 6 Dec 2005 12:29:00 -0000 1.17
***************
*** 3,37 ****
$Id$
! Copyright (C) 2001-2003 KATAYAMA Toshiaki
! 英語版翻訳: Naohisa Goto
! 英語版監訳: PjotrPrins
! Wikiでご覧になっている方へ: この文書はBioRubyのCVSレポジトリにて管理
! しています。Wikiで編集しても、別途CVSにも反映させないと変更内容が失わ
! れてしまいます。連絡方法は(()) をご覧ください。
[...1028 lines suppressed...]
- == Using BioPerl from Ruby
-
- (...)
-
- == 必要なライブラリのインストール
-
- 現在のところ、BioRubyの使用には追加の外部ライブラリや拡張モジュールは必要
- ありません(Ruby 1.8.0以降の場合)。(ただし、XMLParseやBDBなど、いくつかの
- 拡張モジュールをインストールすることで、一部の機能がスピードアップしたり
- 機能が増える場合があります。)
-
- とはいえ、将来的には必要になるかもしれませんので、BioRubyのウェブサイトや
- 付属文書をチェックしてみてください。
-
- Rubyの拡張ライブラリをインストールするには、基本的にはその配布物に付属の
- READMEなどの文章を注意深く読んで、そこに書いてある事を手動で行う必要が
- あります。(将来的には、gems が標準になってより簡単になるかもしれません。)
=end
--- 2029,2032 ----
From k at pub.open-bio.org Wed Dec 7 00:12:09 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Wed Dec 7 00:06:13 2005
Subject: [BioRuby-cvs] bioruby/lib/bio shell.rb,1.10,1.11
Message-ID: <200512070512.jB75C9VL027055@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv26999/lib/bio
Modified Files:
shell.rb
Log Message:
* lib/bioruby.rb is added for easy bioruby script startup after the discussion
with Tanka-san (.bioruby/script.rb will use this)
* access.rb plugin is moved under the plugin directory as a entry.rb
* Core is changed to Ghost :)
Index: shell.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** shell.rb 28 Nov 2005 07:06:32 -0000 1.10
--- shell.rb 7 Dec 2005 05:12:06 -0000 1.11
***************
*** 36,40 ****
require 'bio/shell/core'
require 'bio/shell/session'
! require 'bio/shell/access'
require 'bio/shell/plugin/seq'
require 'bio/shell/plugin/midi'
--- 36,40 ----
require 'bio/shell/core'
require 'bio/shell/session'
! require 'bio/shell/plugin/entry'
require 'bio/shell/plugin/seq'
require 'bio/shell/plugin/midi'
***************
*** 44,48 ****
require 'bio/shell/plugin/keggapi'
! extend Core
extend Private
--- 44,48 ----
require 'bio/shell/plugin/keggapi'
! extend Ghost
extend Private
From k at pub.open-bio.org Wed Dec 7 00:12:08 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Wed Dec 7 00:06:20 2005
Subject: [BioRuby-cvs] bioruby/bin bioruby,1.9,1.10
Message-ID: <200512070512.jB75C8VL027047@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/bin
In directory pub.open-bio.org:/tmp/cvs-serv26999/bin
Modified Files:
bioruby
Log Message:
* lib/bioruby.rb is added for easy bioruby script startup after the discussion
with Tanka-san (.bioruby/script.rb will use this)
* access.rb plugin is moved under the plugin directory as a entry.rb
* Core is changed to Ghost :)
Index: bioruby
===================================================================
RCS file: /home/repository/bioruby/bioruby/bin/bioruby,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** bioruby 28 Nov 2005 07:03:28 -0000 1.9
--- bioruby 7 Dec 2005 05:12:06 -0000 1.10
***************
*** 59,63 ****
# change prompt for bioruby
! $_ = Bio::Shell::Core::ESC_SEQ
IRB.conf[:PROMPT][:BIORUBY_COLOR] = {
:PROMPT_I => "bio#{$_[:ruby]}ruby#{$_[:none]}> ",
--- 59,63 ----
# change prompt for bioruby
! $_ = Bio::Shell.esc_seq
IRB.conf[:PROMPT][:BIORUBY_COLOR] = {
:PROMPT_I => "bio#{$_[:ruby]}ruby#{$_[:none]}> ",
From k at pub.open-bio.org Wed Dec 7 00:12:08 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Wed Dec 7 00:06:20 2005
Subject: [BioRuby-cvs] bioruby/lib bioruby.rb,NONE,1.1
Message-ID: <200512070512.jB75C8VL027049@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib
In directory pub.open-bio.org:/tmp/cvs-serv26999/lib
Added Files:
bioruby.rb
Log Message:
* lib/bioruby.rb is added for easy bioruby script startup after the discussion
with Tanka-san (.bioruby/script.rb will use this)
* access.rb plugin is moved under the plugin directory as a entry.rb
* Core is changed to Ghost :)
--- NEW FILE: bioruby.rb ---
#
# = bioruby.rb - Loading all BioRuby modules and setup for shell programming
#
# Copyright:: Copyright (C) 2005
# Toshiaki Katayama
# License:: LGPL
#
# $Id: bioruby.rb,v 1.1 2005/12/07 05:12:06 k Exp $
#
#--
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
#++
#
require 'bio/shell'
include Bio::Shell
Bio::Shell.setup
From k at pub.open-bio.org Wed Dec 7 00:12:09 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Wed Dec 7 00:06:31 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/shell/plugin codon.rb, 1.8,
1.9 entry.rb, 1.3, 1.4
Message-ID: <200512070512.jB75C9VL027063@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv26999/lib/bio/shell/plugin
Modified Files:
codon.rb entry.rb
Log Message:
* lib/bioruby.rb is added for easy bioruby script startup after the discussion
with Tanka-san (.bioruby/script.rb will use this)
* access.rb plugin is moved under the plugin directory as a entry.rb
* Core is changed to Ghost :)
Index: codon.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/codon.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** codon.rb 28 Nov 2005 12:07:42 -0000 1.8
--- codon.rb 7 Dec 2005 05:12:07 -0000 1.9
***************
*** 31,47 ****
class ColoredCodonTable
- Color = Bio::Shell::Core::ESC_SEQ
-
- @@colors = {
- :text => Color[:none],
- :aa => Color[:green],
- :start => Color[:red],
- :stop => Color[:red],
- :basic => Color[:cyan],
- :polar => Color[:blue],
- :acidic => Color[:magenta],
- :nonpolar => Color[:yellow],
- }
-
@@properties = {
:basic => %w( H K R ),
--- 31,34 ----
***************
*** 58,61 ****
--- 45,49 ----
@cuhash = cuhash
if Bio::Shell.config[:color]
+ setup_colors
generate_colored_text
else
***************
*** 65,68 ****
--- 53,71 ----
attr_reader :table
+ def setup_colors
+ esc_seq = Bio::Shell.esc_seq
+
+ @colors = {
+ :text => esc_seq[:none],
+ :aa => esc_seq[:green],
+ :start => esc_seq[:red],
+ :stop => esc_seq[:red],
+ :basic => esc_seq[:cyan],
+ :polar => esc_seq[:blue],
+ :acidic => esc_seq[:magenta],
+ :nonpolar => esc_seq[:yellow],
+ }
+ end
+
def generate_mono_text
@table.each do |codon, aa|
***************
*** 94,116 ****
if aa == '*'
! color_code = "#{@@colors[:stop]}STOP"
if @cuhash
! color_aa = "#{@@colors[:stop]}#{aa}"
else
color_aa = ''
end
else
! color_code = "#{@@colors[property]}#{@aacode[aa]}"
if @table.start_codon?(codon)
if @cuhash
! color_aa = "#{@@colors[:aa]}#{aa}"
else
! color_aa = "#{@@colors[:start]}#{aa}"
end
else
if @cuhash
! color_aa = "#{@@colors[property]}#{aa}"
else
! color_aa = "#{@@colors[:aa]}#{aa}"
end
end
--- 97,119 ----
if aa == '*'
! color_code = "#{@colors[:stop]}STOP"
if @cuhash
! color_aa = "#{@colors[:stop]}#{aa}"
else
color_aa = ''
end
else
! color_code = "#{@colors[property]}#{@aacode[aa]}"
if @table.start_codon?(codon)
if @cuhash
! color_aa = "#{@colors[:aa]}#{aa}"
else
! color_aa = "#{@colors[:start]}#{aa}"
end
else
if @cuhash
! color_aa = "#{@colors[property]}#{aa}"
else
! color_aa = "#{@colors[:aa]}#{aa}"
end
end
***************
*** 119,134 ****
if @cuhash
percent = @cuhash[codon].to_s.rjust(6)
! eval("@#{codon} = '#{color_aa}#{@@colors[:text]}#{percent}'")
else
! eval("@#{codon} = ' #{color_code} #{color_aa}#{@@colors[:text]} '")
end
end
@hydrophilic = [
! "#{@@colors[:basic]}basic#{@@colors[:text]},",
! "#{@@colors[:polar]}polar#{@@colors[:text]},",
! "#{@@colors[:acidic]}acidic#{@@colors[:text]}"
].join(" ")
! @hydrophobic = "#{@@colors[:nonpolar]}nonpolar"
end
--- 122,137 ----
if @cuhash
percent = @cuhash[codon].to_s.rjust(6)
! eval("@#{codon} = '#{color_aa}#{@colors[:text]}#{percent}'")
else
! eval("@#{codon} = ' #{color_code} #{color_aa}#{@colors[:text]} '")
end
end
@hydrophilic = [
! "#{@colors[:basic]}basic#{@colors[:text]},",
! "#{@colors[:polar]}polar#{@colors[:text]},",
! "#{@colors[:acidic]}acidic#{@colors[:text]}"
].join(" ")
! @hydrophobic = "#{@colors[:nonpolar]}nonpolar"
end
***************
*** 175,179 ****
text = header + table
end
! text.gsub(/^\s+#/, @@colors[:text])
end
--- 178,182 ----
text = header + table
end
! text.gsub(/^\s+#/, @colors[:text])
end
Index: entry.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/entry.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** entry.rb 28 Nov 2005 12:07:42 -0000 1.3
--- entry.rb 7 Dec 2005 05:12:07 -0000 1.4
***************
*** 1,4 ****
#
! # = bio/shell/access.rb - database access module
#
# Copyright:: Copyright (C) 2005
--- 1,4 ----
#
! # = bio/shell/plugin/entry.rb - extract entry and sequence
#
# Copyright:: Copyright (C) 2005
From k at pub.open-bio.org Wed Dec 7 00:12:09 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Wed Dec 7 00:06:43 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/shell core.rb,1.14,1.15
Message-ID: <200512070512.jB75C9VL027059@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/shell
In directory pub.open-bio.org:/tmp/cvs-serv26999/lib/bio/shell
Modified Files:
core.rb
Log Message:
* lib/bioruby.rb is added for easy bioruby script startup after the discussion
with Tanka-san (.bioruby/script.rb will use this)
* access.rb plugin is moved under the plugin directory as a entry.rb
* Core is changed to Ghost :)
Index: core.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/core.rb,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** core.rb 28 Nov 2005 07:03:28 -0000 1.14
--- core.rb 7 Dec 2005 05:12:07 -0000 1.15
***************
*** 1,4 ****
#
! # = bio/shell/core.rb - internal methods for BioRuby shell
#
# Copyright:: Copyright (C) 2005
--- 1,4 ----
#
! # = bio/shell/core.rb - internal methods for the BioRuby shell
#
# Copyright:: Copyright (C) 2005
***************
*** 27,31 ****
#
! module Bio::Shell::Core
CONFIG = "config"
--- 27,31 ----
#
! module Bio::Shell::Ghost
CONFIG = "config"
***************
*** 56,59 ****
--- 56,63 ----
}
+ def esc_seq
+ ESC_SEQ
+ end
+
### save/restore the environment
***************
*** 263,267 ****
def config_message(str = nil)
! str ||= Bio::Shell::Core::MESSAGE
@config[:message] = str
end
--- 267,271 ----
def config_message(str = nil)
! str ||= MESSAGE
@config[:message] = str
end
***************
*** 437,444 ****
File.open(file, "w") do |f|
f.print "#!/usr/bin/env ruby\n\n"
! f.print "require 'bio/shell'\n\n"
! f.print "include Bio::Shell\n\n"
! f.print "Bio::Shell.setup\n\n"
! f.puts Readline::HISTORY.to_a[@script_begin..@script_end]
end
puts "done"
--- 441,447 ----
File.open(file, "w") do |f|
f.print "#!/usr/bin/env ruby\n\n"
! f.print "require 'bioruby'\n\n"
! f.print Readline::HISTORY.to_a[@script_begin..@script_end]
! f.print "\n\n"
end
puts "done"
From k at pub.open-bio.org Wed Dec 7 02:24:17 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Wed Dec 7 02:18:24 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/shell/plugin codon.rb,1.9,1.10
Message-ID: <200512070724.jB77OHVL027374@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv27370/lib/bio/shell/plugin
Modified Files:
codon.rb
Log Message:
* codontables is chagned to return hash
Index: codon.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/codon.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** codon.rb 7 Dec 2005 05:12:07 -0000 1.9
--- codon.rb 7 Dec 2005 07:24:15 -0000 1.10
***************
*** 196,202 ****
def codontables
! Bio::CodonTable::DEFINITIONS.sort.each do |i, definition|
puts "#{i}\t#{definition}"
end
end
--- 196,204 ----
def codontables
! tables = Bio::CodonTable::DEFINITIONS
! tables.sort.each do |i, definition|
puts "#{i}\t#{definition}"
end
+ return tables
end
From k at pub.open-bio.org Wed Dec 7 02:31:42 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Wed Dec 7 02:25:46 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/shell/plugin codon.rb,1.10,1.11
Message-ID: <200512070731.jB77VgVL027418@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv27409/lib/bio/shell/plugin
Modified Files:
codon.rb
Log Message:
* fixed a bug introduced by the previous patch to separate Bio::Shell::Core
(realized that setup_color is also needed for mono mode)
Index: codon.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/codon.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** codon.rb 7 Dec 2005 07:24:15 -0000 1.10
--- codon.rb 7 Dec 2005 07:31:40 -0000 1.11
***************
*** 44,49 ****
@number = number
@cuhash = cuhash
if Bio::Shell.config[:color]
- setup_colors
generate_colored_text
else
--- 44,49 ----
@number = number
@cuhash = cuhash
+ setup_colors
if Bio::Shell.config[:color]
generate_colored_text
else
From k at pub.open-bio.org Wed Dec 7 02:50:47 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Wed Dec 7 02:44:49 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/shell session.rb,1.10,1.11
Message-ID: <200512070750.jB77olVL027479@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/shell
In directory pub.open-bio.org:/tmp/cvs-serv27465/lib/bio/shell
Modified Files:
session.rb
Log Message:
* less command is changed to use config
Index: session.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/session.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** session.rb 28 Nov 2005 12:07:42 -0000 1.10
--- session.rb 7 Dec 2005 07:50:44 -0000 1.11
***************
*** 123,127 ****
def less(file)
! pager = ENV['PAGER'] || "less"
system("#{pager} #{file}")
end
--- 123,127 ----
def less(file)
! pager = Bio::Shell.config[:pager] || ENV['PAGER'] || "less"
system("#{pager} #{file}")
end
From k at pub.open-bio.org Wed Dec 7 05:54:25 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Wed Dec 7 05:48:27 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/shell core.rb,1.15,1.16
Message-ID: <200512071054.jB7AsPVL028151@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/shell
In directory pub.open-bio.org:/tmp/cvs-serv28147/lib/bio/shell
Modified Files:
core.rb
Log Message:
* minor fix (reverted)
Index: core.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/core.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** core.rb 7 Dec 2005 05:12:07 -0000 1.15
--- core.rb 7 Dec 2005 10:54:23 -0000 1.16
***************
*** 442,446 ****
f.print "#!/usr/bin/env ruby\n\n"
f.print "require 'bioruby'\n\n"
! f.print Readline::HISTORY.to_a[@script_begin..@script_end]
f.print "\n\n"
end
--- 442,446 ----
f.print "#!/usr/bin/env ruby\n\n"
f.print "require 'bioruby'\n\n"
! f.puts Readline::HISTORY.to_a[@script_begin..@script_end]
f.print "\n\n"
end
From k at pub.open-bio.org Wed Dec 7 06:23:53 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Wed Dec 7 06:17:55 2005
Subject: [BioRuby-cvs] bioruby/lib/bio db.rb,0.30,0.31
Message-ID: <200512071123.jB7BNrVL028264@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv28253/lib/bio
Modified Files:
db.rb
Log Message:
* fixed to check empty or incomplete string (e.g. empty entry)
Index: db.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db.rb,v
retrieving revision 0.30
retrieving revision 0.31
diff -C2 -d -r0.30 -r0.31
*** db.rb 30 Oct 2005 17:15:05 -0000 0.30
--- db.rb 7 Dec 2005 11:23:51 -0000 0.31
***************
*** 211,226 ****
# space and stripeed.
def truncate(str)
! return str.gsub(/\s+/, ' ').strip
end
# Returns a tag name of the field as a String.
def tag_get(str)
! return str[0,@tagsize].strip
end
# Returns a String of the field without a tag name.
def tag_cut(str)
! str[0,@tagsize] = ''
! return str
end
--- 211,237 ----
# space and stripeed.
def truncate(str)
! if str
! str.gsub(/\s+/, ' ').strip
! else
! ""
! end
end
# Returns a tag name of the field as a String.
def tag_get(str)
! if str
! str[0,@tagsize].strip
! else
! ""
! end
end
# Returns a String of the field without a tag name.
def tag_cut(str)
! if str
! str[0,@tagsize] = ''
! else
! ""
! end
end
From k at pub.open-bio.org Wed Dec 7 06:23:53 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Wed Dec 7 06:17:55 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/db/genbank common.rb, 1.8,
1.9 genbank.rb, 0.37, 0.38
Message-ID: <200512071123.jB7BNrVL028268@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/db/genbank
In directory pub.open-bio.org:/tmp/cvs-serv28253/lib/bio/db/genbank
Modified Files:
common.rb genbank.rb
Log Message:
* fixed to check empty or incomplete string (e.g. empty entry)
Index: genbank.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/genbank.rb,v
retrieving revision 0.37
retrieving revision 0.38
diff -C2 -d -r0.37 -r0.38
*** genbank.rb 14 Nov 2005 05:43:43 -0000 0.37
--- genbank.rb 7 Dec 2005 11:23:51 -0000 0.38
***************
*** 32,36 ****
class Locus
def initialize(locus_line)
! if locus_line.length > 75 # after Rel 126.0
@entry_id = locus_line[12..27].strip
@length = locus_line[29..39].to_i
--- 32,38 ----
class Locus
def initialize(locus_line)
! if locus_line.empty?
! # do nothing (just for empty or incomplete entry string)
! elsif locus_line.length > 75 # after Rel 126.0
@entry_id = locus_line[12..27].strip
@length = locus_line[29..39].to_i
Index: common.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/genbank/common.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** common.rb 14 Nov 2005 05:43:43 -0000 1.8
--- common.rb 7 Dec 2005 11:23:51 -0000 1.9
***************
*** 54,62 ****
def acc_version
! versions.first
end
def accession
! acc_version.split(/\./).first
end
--- 54,62 ----
def acc_version
! versions.first.to_s
end
def accession
! acc_version.split(/\./).first.to_s
end
***************
*** 92,95 ****
--- 92,96 ----
unless @data['SOURCE']
name, org = get('SOURCE').split('ORGANISM')
+ org ||= ""
if org[/\S+;/]
organism = $`
***************
*** 137,141 ****
authors = truncate(tag_cut(field))
authors = authors.split(/, /)
! authors[-1] = authors[-1].split(/\s+and\s+/)
authors = authors.flatten.map { |a| a.sub(/,/, ', ') }
hash['authors'] = authors
--- 138,142 ----
authors = truncate(tag_cut(field))
authors = authors.split(/, /)
! authors[-1] = authors[-1].split(/\s+and\s+/) if authors[-1]
authors = authors.flatten.map { |a| a.sub(/,/, ', ') }
hash['authors'] = authors
***************
*** 237,240 ****
--- 238,242 ----
unless @data['ORIGIN']
ori, seqstr = get('ORIGIN').split("\n", 2)
+ seqstr ||= ""
@data['ORIGIN'] = truncate(tag_cut(ori))
@data['SEQUENCE'] = seqstr.tr("0-9 \t\n\r\/", '')
From k at pub.open-bio.org Wed Dec 7 06:40:47 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Wed Dec 7 06:35:00 2005
Subject: [BioRuby-cvs] bioruby/doc Tutorial.rd.ja,1.17,1.18
Message-ID: <200512071140.jB7BelVL028330@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/doc
In directory pub.open-bio.org:/tmp/cvs-serv28316/doc
Modified Files:
Tutorial.rd.ja
Log Message:
* clean up
Index: Tutorial.rd.ja
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Tutorial.rd.ja,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** Tutorial.rd.ja 6 Dec 2005 12:29:00 -0000 1.17
--- Tutorial.rd.ja 7 Dec 2005 11:40:45 -0000 1.18
***************
*** 41,44 ****
--- 41,54 ----
のような感じでバージョンが表示されます。バージョン 1.8.2 以降をお勧めします。
+ Ruby 標準装備のクラスやメソッドについては、Ruby のリファレンスマニュアルを
+ 参照してください。
+
+ * (())
+
+ コマンドラインでヘルプを参照するには、Ruby 標準添付の ri コマンドや、
+ 日本語版の refe コマンドが便利です。
[...1082 lines suppressed...]
出力形式を扱うようにしています。しかし、このフォーマットでは得られる
データが限られるので、"-m 7" の XML 形式の出力を使うことをお勧めします。
- (Ruby 1.8.0以降を使用すれば、特別な外部ライブラリを別途インストール
- しなくても大丈夫です。Ruby 1.6.X では XMLParser または REXMLを別途
- インストールしてください。)
すでに見たように Bio::Fasta::Report と Bio::Blast::Report の Hit オブジェ
--- 1634,1645 ----
をそれぞれ指定します。
! ところで、BLAST では "-m 7" オプションによる XML 出力フォーマッットの方が
! 得られる情報が豊富なため、Bio::Blast は Ruby 用の XML ライブラリである
! XMLParser または REXML が使用可能な場合は、XML 出力を利用します。
! 両方使用可能な場合、XMLParser のほうが高速なので優先的に使用されます。
! なお、Ruby 1.8.0 以降では REXML は Ruby 本体に標準添付されています。
! もし XML ライブラリがインストールされていない場合は "-m 8" のタブ区切りの
出力形式を扱うようにしています。しかし、このフォーマットでは得られる
データが限られるので、"-m 7" の XML 形式の出力を使うことをお勧めします。
すでに見たように Bio::Fasta::Report と Bio::Blast::Report の Hit オブジェ
From k at pub.open-bio.org Sat Dec 10 13:14:24 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sat Dec 10 13:08:14 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/data na.rb,0.18,0.19
Message-ID: <200512101814.jBAIEOVL014132@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/data
In directory pub.open-bio.org:/tmp/cvs-serv14128/lib/bio/data
Modified Files:
na.rb
Log Message:
* to_re method is improved for the efficiency especially for longer sequence
Index: na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/data/na.rb,v
retrieving revision 0.18
retrieving revision 0.19
diff -C2 -d -r0.18 -r0.19
*** na.rb 25 Nov 2005 15:59:29 -0000 0.18
--- na.rb 10 Dec 2005 18:14:22 -0000 0.19
***************
*** 177,188 ****
def to_re(seq, rna = false)
! str = ""
! seq.to_s.downcase.each_byte do |base|
! if re = NAMES[base.chr]
! str += re
! else
! str += "."
! end
! end
if rna
str.tr!("t", "u")
--- 177,184 ----
def to_re(seq, rna = false)
! str = seq.to_s
! str.gsub!(/[^atgcu]/) { |base|
! NAMES[base] || '.'
! }
if rna
str.tr!("t", "u")
From nakao at pub.open-bio.org Sun Dec 11 09:59:27 2005
From: nakao at pub.open-bio.org (Mitsuteru C. Nakao)
Date: Sun Dec 11 09:53:17 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio/io test_ddbjxml.rb,NONE,1.1
Message-ID: <200512111459.jBBExRVL025284@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio/io
In directory pub.open-bio.org:/tmp/cvs-serv25274/test/unit/bio/io
Added Files:
test_ddbjxml.rb
Log Message:
* Newly added.
--- NEW FILE: test_ddbjxml.rb ---
#
# test/unit/bio/io/test_ddbjxml.rb - Unit test for DDBJ XML.
#
# Copyright (C) 2005 Mitsuteru Nakao
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: test_ddbjxml.rb,v 1.1 2005/12/11 14:59:25 nakao Exp $
#
require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)
require 'test/unit'
require 'bio/io/ddbjxml'
module Bio
class TestDDBJXMLConstants < Test::Unit::TestCase
def test_constants
constants = ["DDBJ", "TxSearch", "ClustalW", "PML", "Gib", "Fasta", "BASE_URI", "SRS", "Gtop", "GetEntry", "Blast"].sort
assert_equal(constants, Bio::DDBJ::XML.constants.sort)
end
def test_base_url
assert_equal("http://xml.nig.ac.jp/wsdl/", Bio::DDBJ::XML::BASE_URI)
end
def test_blast_server_rul
assert_equal("http://xml.nig.ac.jp/wsdl/Blast.wsdl", Bio::DDBJ::XML::Blast::SERVER_URI)
end
def test_clustalw_server_url
assert_equal("http://xml.nig.ac.jp/wsdl/ClustalW.wsdl", Bio::DDBJ::XML::ClustalW::SERVER_URI)
end
def test_ddbj_server_url
assert_equal("http://xml.nig.ac.jp/wsdl/DDBJ.wsdl", Bio::DDBJ::XML::DDBJ::SERVER_URI)
end
def test_fasta_server_url
assert_equal("http://xml.nig.ac.jp/wsdl/Fasta.wsdl", Bio::DDBJ::XML::Fasta::SERVER_URI)
end
def test_getentry_server_url
assert_equal("http://xml.nig.ac.jp/wsdl/GetEntry.wsdl", Bio::DDBJ::XML::GetEntry::SERVER_URI)
end
def test_gib_server_url
assert_equal("http://xml.nig.ac.jp/wsdl/Gib.wsdl", Bio::DDBJ::XML::Gib::SERVER_URI)
end
def test_gtop_server_url
assert_equal("http://xml.nig.ac.jp/wsdl/Gtop.wsdl", Bio::DDBJ::XML::Gtop::SERVER_URI)
end
def test_pml_server_url
assert_equal("http://xml.nig.ac.jp/wsdl/PML.wsdl", Bio::DDBJ::XML::PML::SERVER_URI)
end
def test_srs_server_url
assert_equal("http://xml.nig.ac.jp/wsdl/SRS.wsdl", Bio::DDBJ::XML::SRS::SERVER_URI)
end
def test_txsearch_server_url
assert_equal("http://xml.nig.ac.jp/wsdl/TxSearch.wsdl", Bio::DDBJ::XML::TxSearch::SERVER_URI)
end
end
end
From k at pub.open-bio.org Sun Dec 11 20:44:56 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 11 20:38:29 2005
Subject: [BioRuby-cvs] bioruby README,1.10,1.11
Message-ID: <200512120144.jBC1iuVL026521@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby
In directory pub.open-bio.org:/tmp/cvs-serv26517
Modified Files:
README
Log Message:
* fixed typo
Index: README
===================================================================
RCS file: /home/repository/bioruby/bioruby/README,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** README 26 Sep 2005 00:48:04 -0000 1.10
--- README 12 Dec 2005 01:44:54 -0000 1.11
***************
*** 165,169 ****
require_gem 'bio'
! == LICENCE
BioRuby can be freely distributed under the GNU LGPL licence.
--- 165,169 ----
require_gem 'bio'
! == LICENSE
BioRuby can be freely distributed under the GNU LGPL licence.
From k at pub.open-bio.org Sun Dec 11 21:06:38 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 11 21:00:10 2005
Subject: [BioRuby-cvs] bioruby README,1.11,1.12
Message-ID: <200512120206.jBC26cVL026578@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby
In directory pub.open-bio.org:/tmp/cvs-serv26574
Modified Files:
README
Log Message:
* fixed one more typo;)
Index: README
===================================================================
RCS file: /home/repository/bioruby/bioruby/README,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** README 12 Dec 2005 01:44:54 -0000 1.11
--- README 12 Dec 2005 02:06:35 -0000 1.12
***************
*** 167,171 ****
== LICENSE
! BioRuby can be freely distributed under the GNU LGPL licence.
Note that, install.rb included in the BioRuby package comes from
--- 167,171 ----
== LICENSE
! BioRuby can be freely distributed under the GNU LGPL license.
Note that, install.rb included in the BioRuby package comes from
From ngoto at pub.open-bio.org Fri Dec 16 14:23:05 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Fri Dec 16 14:16:07 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb atom.rb, 1.2, 1.3 pdb.rb, 1.3,
1.4
Message-ID: <200512161923.jBGJN5VL014379@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory pub.open-bio.org:/tmp/cvs-serv14367/d
Modified Files:
atom.rb pdb.rb
Log Message:
grave changes
It does not work correctly now.
Index: atom.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/atom.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** atom.rb 8 Sep 2005 01:22:11 -0000 1.2
--- atom.rb 16 Dec 2005 19:23:02 -0000 1.3
***************
*** 56,124 ****
end #class Coordinate
! #Atom class
class Atom
-
include Utils
include Comparable
- attr_accessor :serial, :element, :alt_loc, :x, :y, :z,
- :occ, :bfac, :residue
-
- def initialize(serial, element, alt_loc, x, y, z,
- occ, bfac, residue = nil)
-
- @serial = serial
- @element = element
- @alt_loc = alt_loc
- @x = x
- @y = y
- @z = z
- @occ = occ
- @bfac = bfac
-
- @residue = residue
-
- end
-
#Returns a Coordinate class instance of the xyz positions
def xyz
! Coordinate[@x,@y,@z]
end
#Returns an array of the xyz positions
def to_a
! [@x,@y,@z]
end
#Sorts based on serial numbers
def <=>(other)
! return @serial <=> other.serial
end
#Stringifies to PDB format
def to_s
! if @element.length < 4
! elementOutput = " " << "%-3s" % @element
! else
! elementOutput = @element
! end
! if @residue.hetatm
! "HETATM%5s %s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f" % [ @serial, elementOutput, @alt_loc, @residue.resName, @residue.chain.id, @residue.resSeq, @residue.iCode, @x, @y, @z, @occ, @bfac ]
else
! "ATOM %5s %s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f" % [ @serial, elementOutput, @alt_loc, @residue.resName, @residue.chain.id, @residue.resSeq, @residue.iCode, @x, @y, @z, @occ, @bfac ]
end
end
-
- end
-
- end
-
- end
-
- =begin
! = Bio::PDB::Atom
! A class for atom data - each ATOM line is parsed into an Atom object
! =end
--- 56,110 ----
end #class Coordinate
! # Bio::PDB::Atom is a class for atom data.
! # Each ATOM line is parsed into an Atom object.
! Atom = Struct.new(:serial, :element, :alt_loc, :x, :y, :z,
! :occ, :bfac, :residue)
class Atom
include Utils
include Comparable
#Returns a Coordinate class instance of the xyz positions
def xyz
! Coordinate[ x, y, z ]
end
#Returns an array of the xyz positions
def to_a
! [ x, y, z ]
end
#Sorts based on serial numbers
def <=>(other)
! return serial <=> other.serial
end
#Stringifies to PDB format
def to_s
! if element.length < 4
! elementOutput = sprintf(" %-3s", element)
else
! elementOutput = element
end
+ sprintf("%-6s%5s %s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f",
+ record_type,
+ serial, elementOutput, alt_loc, residue.resName,
+ residue.chain.id, residue.resSeq, residue.iCode,
+ x, y, z, occ, bfac)
end
! def record_type
! 'ATOM'
! end
! end #class Atom
! # Bio::PDB::HetAtm is a class for HETATM data.
! # Each HETATM line is parsed into an HetAtm object.
! # Since HetAtm inherits Atom class, please refer Atom class for usage.
! class HetAtm < Atom
! def record_type
! 'HETATM'
! end
! end #class HetAtm
! end #class PDB
! end #class Bio
Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** pdb.rb 26 Sep 2005 13:00:08 -0000 1.3
--- pdb.rb 16 Dec 2005 19:23:03 -0000 1.4
***************
*** 33,37 ****
#This is the main PDB class which takes care of parsing, annotations
#and is the entry way to the co-ordinate data held in models
! class PDB < DB
include Utils
--- 33,37 ----
#This is the main PDB class which takes care of parsing, annotations
#and is the entry way to the co-ordinate data held in models
! class PDB #< DB
[...2079 lines suppressed...]
***************
*** 1179,1186 ****
end
! atom = Atom.new(serial,name,altLoc,
! x,y,z,
! occupancy,tempFactor,
! newResidue)
newResidue.addAtom(atom)
--- 1231,1238 ----
end
! atom = atomclass.new(serial,name,altLoc,
! x,y,z,
! occupancy,tempFactor,
! newResidue)
newResidue.addAtom(atom)
From ngoto at pub.open-bio.org Fri Dec 16 14:23:05 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Fri Dec 16 14:16:08 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/db pdb.rb,1.4,1.5
Message-ID: <200512161923.jBGJN5VL014382@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv14367
Modified Files:
pdb.rb
Log Message:
grave changes
It does not work correctly now.
Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** pdb.rb 8 Mar 2004 07:32:35 -0000 1.4
--- pdb.rb 16 Dec 2005 19:23:03 -0000 1.5
***************
*** 25,29 ****
# definition of the PDB class
module Bio
! class PDB < DB
end #class PDB
end #module Bio
--- 25,29 ----
# definition of the PDB class
module Bio
! class PDB #< DB
end #class PDB
end #module Bio
From ngoto at pub.open-bio.org Sun Dec 18 10:09:48 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Sun Dec 18 10:03:06 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb atom.rb, 1.3, 1.4 pdb.rb, 1.4,
1.5 residue.rb, 1.2, 1.3
Message-ID: <200512181509.jBIF9mVL028188@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory pub.open-bio.org:/tmp/cvs-serv28178
Modified Files:
atom.rb pdb.rb residue.rb
Log Message:
more changes
(does not correctly work now!)
Index: atom.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/atom.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** atom.rb 16 Dec 2005 19:23:02 -0000 1.3
--- atom.rb 18 Dec 2005 15:09:46 -0000 1.4
***************
*** 93,99 ****
end
! def record_type
'ATOM'
end
end #class Atom
--- 93,102 ----
end
! def record_name
'ATOM'
end
+ def record_type
+ record_name
+ end
end #class Atom
***************
*** 102,106 ****
# Since HetAtm inherits Atom class, please refer Atom class for usage.
class HetAtm < Atom
! def record_type
'HETATM'
end
--- 105,109 ----
# Since HetAtm inherits Atom class, please refer Atom class for usage.
class HetAtm < Atom
! def record_name
'HETATM'
end
Index: residue.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/residue.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** residue.rb 26 Sep 2005 13:00:08 -0000 1.2
--- residue.rb 18 Dec 2005 15:09:46 -0000 1.3
***************
*** 88,92 ****
#Adds an atom to this residue
def addAtom(atom)
! raise "Expecting Bio::PDB::Atom" if not atom.is_a? Bio::PDB::Atom
@atoms.push(atom)
self
--- 88,92 ----
#Adds an atom to this residue
def addAtom(atom)
! raise "Expecting ATOM or HETATM" unless atom.is_a? Bio::PDB::Record::ATOM
@atoms.push(atom)
self
Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** pdb.rb 16 Dec 2005 19:23:03 -0000 1.4
--- pdb.rb 18 Dec 2005 15:09:46 -0000 1.5
***************
*** 51,55 ****
module Pdb_Integer
def self.new(str)
! str.strip.to_i
end
end
--- 51,55 ----
module Pdb_Integer
def self.new(str)
! str.to_i
end
[...1773 lines suppressed...]
! newResidue = Residue.new(f.resName, f.resSeq, f.iCode,
chain)
chain.addResidue(newResidue)
else
! newResidue = Residue.new(f.resName, f.resSeq, f.iCode,
! chain, true)
chain.addLigand(newResidue)
end
! atom = f
! f.residue = newResidue
newResidue.addAtom(atom)
cResidue = newResidue
!
end
end
!
! when 'MODEL'
if cModel.model_serial
self.addModel(cModel)
From k at pub.open-bio.org Sun Dec 18 10:37:21 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 10:30:45 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio/shell/plugin test_seq.rb, 1.2,
1.3
Message-ID: <200512181537.jBIFbLVL028322@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv28318/test/unit/bio/shell/plugin
Modified Files:
test_seq.rb
Log Message:
* fixed tests (not yet completed)
Index: test_seq.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/shell/plugin/test_seq.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_seq.rb 23 Nov 2005 11:40:45 -0000 1.2
--- test_seq.rb 18 Dec 2005 15:37:19 -0000 1.3
***************
*** 35,109 ****
def test_naseq
str = 'ACGT'
! assert_equal(Bio::Sequence::NA, naseq(str).class)
! assert_equal(Bio::Sequence::NA.new(str), naseq(str))
! assert_equal('acgt', naseq(str))
end
def test_aaseq
str = 'WD'
! assert_equal(Bio::Sequence::AA, aaseq(str).class)
! assert_equal(Bio::Sequence::AA.new('WD'), aaseq(str))
! assert_equal('WD', aaseq(str))
! end
!
! def test_revseq
! str = 'acgta'
! assert_equal('tacgt', revseq(str))
! end
!
! def test_translate
! str = 'ATGATG'
! assert_equal(Bio::Sequence::AA.new('MM'), translate(str))
end
! def test_seq_report_na
! str = 'ACGT'
! output = ''
! assert_equal(output, seq_report(str))
! end
! def test_seq_report_aa
! str = 'WD'
! output = ''
! assert_equal(output, seq_report(str))
! end
! def test_na_report
! naseq = 'ACGT'
! output =<1, \"c\"=>1, \"g\"=>1, \"t\"=>1}
! molecular weight : 1245.88148
! complemnet weight : 1245.88148
! protein weight : 119.12
//
END
! assert_equal(output, na_report(naseq))
end
! def test_aa_report
aaseq = 'WD'
output =<1, \"D\"=>1}
! protein weight : 319.315
! amino acid codes : [\"Trp\", \"Asp\"]
! amino acid names : [\"tryptophan\", \"aspartic acid\"]
//
END
! assert_equal(output, aa_report(aaseq))
end
! def test_double_helix
seq = 'ACGTACGTACGTACGT'
output = <3' sequence : atgcatgcatgc
! 3'->5' sequence : gcatgcatgcat
! Translation 1 : MHAC
! Translation 2 : CMH
! Translation 3 : ACM
! Translation -1 : ACMH
! Translation -2 : HAC
! Translation -3 : MHA
! Length : 12 bp
! GC percent : 50 %
! Composition : a - 3 ( 25.00 %)
! c - 3 ( 25.00 %)
! g - 3 ( 25.00 %)
! t - 3 ( 25.00 %)
! Codon usage :
+ *---------------------------------------------*
+ | | 2nd | |
+ | 1st |-------------------------------| 3rd |
+ | | U | C | A | G | |
+ |-------+-------+-------+-------+-------+-----|
+ | U U |F 0.0%|S 0.0%|Y 0.0%|C 0.0%| u |
+ | U U |F 0.0%|S 0.0%|Y 0.0%|C 25.0%| c |
+ | U U |L 0.0%|S 0.0%|* 0.0%|* 0.0%| a |
+ | UUU |L 0.0%|S 0.0%|* 0.0%|W 0.0%| g |
+ |-------+-------+-------+-------+-------+-----|
+ | CCCC |L 0.0%|P 0.0%|H 25.0%|R 0.0%| u |
+ | C |L 0.0%|P 0.0%|H 0.0%|R 0.0%| c |
+ | C |L 0.0%|P 0.0%|Q 0.0%|R 0.0%| a |
+ | CCCC |L 0.0%|P 0.0%|Q 0.0%|R 0.0%| g |
+ |-------+-------+-------+-------+-------+-----|
+ | A |I 0.0%|T 0.0%|N 0.0%|S 0.0%| u |
+ | A A |I 0.0%|T 0.0%|N 0.0%|S 0.0%| c |
+ | AAAAA |I 0.0%|T 0.0%|K 0.0%|R 0.0%| a |
+ | A A |M 25.0%|T 0.0%|K 0.0%|R 0.0%| g |
+ |-------+-------+-------+-------+-------+-----|
+ | GGGG |V 0.0%|A 0.0%|D 0.0%|G 0.0%| u |
+ | G |V 0.0%|A 0.0%|D 0.0%|G 0.0%| c |
+ | G GGG |V 0.0%|A 25.0%|E 0.0%|G 0.0%| a |
+ | GG G |V 0.0%|A 0.0%|E 0.0%|G 0.0%| g |
+ *---------------------------------------------*
! Molecular weight : 3701.61444
! Protein weight : 460.565
//
END
! assert_equal(output, seqstat(naseq))
end
! def test_aa_seqstat
aaseq = 'WD'
output =<C sequence : WD
! Length : 2 aa
! Composition : D Asp - 1 ( 50.00 %) aspartic acid
! W Trp - 1 ( 50.00 %) tryptophan
! Protein weight : 319.315
//
END
! assert_equal(output, seqstat(aaseq))
end
! def test_doublehelix
seq = 'ACGTACGTACGTACGT'
output = <
Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv28562/lib/bio/shell/plugin
Modified Files:
keggapi.rb
Log Message:
* added some notes
Index: keggapi.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/keggapi.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** keggapi.rb 30 Nov 2005 02:01:04 -0000 1.7
--- keggapi.rb 18 Dec 2005 15:47:33 -0000 1.8
***************
*** 119,122 ****
--- 119,142 ----
=begin
+
+ == BioRuby extensions
+
+ --- get_all_best_best_neighbors_by_gene(genes_id)
+ --- get_all_best_neighbors_by_gene(genes_id)
+ --- get_all_reverse_best_neighbors_by_gene(genes_id)
+ --- get_all_paralogs_by_gene(genes_id)
+ --- get_all_genes_by_motifs(motif_id_list)
+ --- get_all_oc_members_by_gene(genes_id)
+ --- get_all_pc_members_by_gene(genes_id)
+ --- get_all_genes_by_organism(org)
+ --- get_all_linkdb_by_entry(entry_id, db)
+ --- save_image(url, filename = nil)
+ --- get_entries(ary = [])
+ --- get_aaseqs(ary = [])
+ --- get_naseqs(ary = [])
+ --- get_definitions(ary = [])
+
+ == Original KEGG API methods
+
--- get_linkdb_by_entry(entry_id, db, start, max_results)
--- get_best_best_neighbors_by_gene(genes_id, start, max_results)
***************
*** 164,166 ****
--- 184,187 ----
--- get_number_of_genes_by_organism(org)
--- convert_mol_to_kcf(mol_text)
+
=end
From k at pub.open-bio.org Sun Dec 18 10:50:08 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 10:43:04 2005
Subject: [BioRuby-cvs] bioruby/lib/bio location.rb,0.21,0.22
Message-ID: <200512181550.jBIFo8VL028682@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv28673/lib/bio
Modified Files:
location.rb
Log Message:
* minor change (error message format)
Index: location.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/location.rb,v
retrieving revision 0.21
retrieving revision 0.22
diff -C2 -d -r0.21 -r0.22
*** location.rb 30 Oct 2005 22:59:56 -0000 0.21
--- location.rb 18 Dec 2005 15:50:06 -0000 0.22
***************
*** 280,284 ****
e = $2.to_i
if e - s < 0
! # raise "[Error] invalid range : #{location}"
$stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
end
--- 280,284 ----
e = $2.to_i
if e - s < 0
! # raise "Error: invalid range : #{location}"
$stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
end
***************
*** 287,291 ****
e = $2.to_i
if e - s != 1
! # raise "[Error] invalid range : #{location}"
$stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
end
--- 287,291 ----
e = $2.to_i
if e - s != 1
! # raise "Error: invalid range : #{location}"
$stderr.puts "[Warning] invalid range : #{location}" if $DEBUG
end
***************
*** 296,300 ****
;
else
! raise "[Error] unknown location format : #{location}"
end
--- 296,300 ----
;
else
! raise "Error: unknown location format : #{location}"
end
From k at pub.open-bio.org Sun Dec 18 10:58:42 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 10:55:25 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/mafft report.rb,1.7,1.8
Message-ID: <200512181558.jBIFwgVL028868@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl/mafft
In directory pub.open-bio.org:/tmp/cvs-serv28824/appl/mafft
Modified Files:
report.rb
Log Message:
* s/Licence/License/
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft/report.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** report.rb 1 Nov 2005 05:32:24 -0000 1.7
--- report.rb 18 Dec 2005 15:58:40 -0000 1.8
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2003 GOTO Naohisa
! # Licence:: LGPL
#
#--
--- 3,7 ----
#
# Copyright:: Copyright (C) 2003 GOTO Naohisa
! # License:: LGPL
#
#--
From k at pub.open-bio.org Sun Dec 18 10:58:43 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 10:55:37 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/sosui report.rb,1.8,1.9
Message-ID: <200512181558.jBIFwhVL028882@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl/sosui
In directory pub.open-bio.org:/tmp/cvs-serv28824/appl/sosui
Modified Files:
report.rb
Log Message:
* s/Licence/License/
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sosui/report.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** report.rb 31 Oct 2005 17:01:50 -0000 1.8
--- report.rb 18 Dec 2005 15:58:41 -0000 1.9
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2003 Mitsuteru C. Nakao
! # Licence:: LGPL
#
# $Id$
--- 3,7 ----
#
# Copyright:: Copyright (C) 2003 Mitsuteru C. Nakao
! # License:: LGPL
#
# $Id$
From k at pub.open-bio.org Sun Dec 18 10:58:44 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 10:56:18 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/io fetch.rb, 1.3, 1.4 registry.rb,
1.15, 1.16
Message-ID: <200512181558.jBIFwiVL028905@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory pub.open-bio.org:/tmp/cvs-serv28824/io
Modified Files:
fetch.rb registry.rb
Log Message:
* s/Licence/License/
Index: registry.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/registry.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** registry.rb 27 Nov 2005 19:55:39 -0000 1.15
--- registry.rb 18 Dec 2005 15:58:42 -0000 1.16
***************
*** 4,8 ****
# Copyright:: Copyright (C) 2002, 2003, 2004, 2005
# Toshiaki Katayama
! # Licence:: LGPL
#
# $Id$
--- 4,8 ----
# Copyright:: Copyright (C) 2002, 2003, 2004, 2005
# Toshiaki Katayama
! # License:: LGPL
#
# $Id$
Index: fetch.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/fetch.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** fetch.rb 28 Nov 2005 02:02:38 -0000 1.3
--- fetch.rb 18 Dec 2005 15:58:42 -0000 1.4
***************
*** 4,8 ****
# Copyright:: Copyright (C) 2002, 2005
# Toshiaki Katayama
! # Licence:: LGPL
#
# $Id$
--- 4,8 ----
# Copyright:: Copyright (C) 2002, 2005
# Toshiaki Katayama
! # License:: LGPL
#
# $Id$
From k at pub.open-bio.org Sun Dec 18 10:58:43 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 10:56:50 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/targetp report.rb,1.6,1.7
Message-ID: <200512181558.jBIFwhVL028890@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl/targetp
In directory pub.open-bio.org:/tmp/cvs-serv28824/appl/targetp
Modified Files:
report.rb
Log Message:
* s/Licence/License/
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/targetp/report.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** report.rb 31 Oct 2005 18:00:16 -0000 1.6
--- report.rb 18 Dec 2005 15:58:41 -0000 1.7
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2003 Mitsuteru C. Nakao
! # Licence:: LGPL
#
# $Id$
--- 3,7 ----
#
# Copyright:: Copyright (C) 2003 Mitsuteru C. Nakao
! # License:: LGPL
#
# $Id$
From k at pub.open-bio.org Sun Dec 18 10:58:43 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 10:56:51 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/sim4 report.rb,1.6,1.7
Message-ID: <200512181558.jBIFwhVL028878@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl/sim4
In directory pub.open-bio.org:/tmp/cvs-serv28824/appl/sim4
Modified Files:
report.rb
Log Message:
* s/Licence/License/
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sim4/report.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** report.rb 1 Nov 2005 05:32:23 -0000 1.6
--- report.rb 18 Dec 2005 15:58:40 -0000 1.7
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2004 GOTO Naohisa
! # Licence:: LGPL
#
#--
--- 3,7 ----
#
# Copyright:: Copyright (C) 2004 GOTO Naohisa
! # License:: LGPL
#
#--
From k at pub.open-bio.org Sun Dec 18 10:58:43 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 10:56:52 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/spidey report.rb,1.7,1.8
Message-ID: <200512181558.jBIFwhVL028886@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl/spidey
In directory pub.open-bio.org:/tmp/cvs-serv28824/appl/spidey
Modified Files:
report.rb
Log Message:
* s/Licence/License/
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/spidey/report.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** report.rb 1 Nov 2005 05:32:24 -0000 1.7
--- report.rb 18 Dec 2005 15:58:41 -0000 1.8
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2004 GOTO Naohisa
! # Licence:: LGPL
#
#--
--- 3,7 ----
#
# Copyright:: Copyright (C) 2004 GOTO Naohisa
! # License:: LGPL
#
#--
From k at pub.open-bio.org Sun Dec 18 10:58:41 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 10:56:53 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blast wublast.rb,1.4,1.5
Message-ID: <200512181559.jBIFwfVL028853@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl/blast
In directory pub.open-bio.org:/tmp/cvs-serv28824/appl/blast
Modified Files:
wublast.rb
Log Message:
* s/Licence/License/
Index: wublast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast/wublast.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** wublast.rb 1 Nov 2005 05:32:23 -0000 1.4
--- wublast.rb 18 Dec 2005 15:58:39 -0000 1.5
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2003 GOTO Naohisa
! # Licence:: LGPL
#
#--
--- 3,7 ----
#
# Copyright:: Copyright (C) 2003 GOTO Naohisa
! # License:: LGPL
#
#--
From k at pub.open-bio.org Sun Dec 18 11:28:48 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 11:21:37 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio/shell/plugin test_seq.rb, 1.3,
1.4
Message-ID: <200512181628.jBIGSmVL029196@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv29192/test/unit/bio/shell/plugin
Modified Files:
test_seq.rb
Log Message:
* changed to use require 'bioruby' instead of require 'bio/shell'; include Bio::Shell
Index: test_seq.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/shell/plugin/test_seq.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** test_seq.rb 18 Dec 2005 15:37:19 -0000 1.3
--- test_seq.rb 18 Dec 2005 16:28:46 -0000 1.4
***************
*** 26,35 ****
require 'test/unit'
! require 'bio/shell'
module Bio
class TestShellPluginSeq < Test::Unit::TestCase
- include Bio::Shell
def test_naseq
--- 26,36 ----
require 'test/unit'
! require 'bioruby'
module Bio
class TestShellPluginSeq < Test::Unit::TestCase
+ # include Bio::Shell
+ # Bio::Shell.instance_variable_set :@config, {}
def test_naseq
From nakao at pub.open-bio.org Sun Dec 18 11:50:23 2005
From: nakao at pub.open-bio.org (Mitsuteru C. Nakao)
Date: Sun Dec 18 11:43:13 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl test_fasta.rb,NONE,1.1
Message-ID: <200512181650.jBIGoNVL029315@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio/appl
In directory pub.open-bio.org:/tmp/cvs-serv29305/test/unit/bio/appl
Added Files:
test_fasta.rb
Log Message:
* Newly added.
--- NEW FILE: test_fasta.rb ---
#
# test/unit/bio/appl/test_fasta.rb - Unit test for Bio::Fasta
#
# Copyright (C) 2005 Mitsuteru Nakao
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: test_fasta.rb,v 1.1 2005/12/18 16:50:20 nakao Exp $
#
require 'pathname'
libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib'))).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)
require 'test/unit'
require 'bio/appl/fasta'
module Bio
class TestFastaInitialize < Test::Unit::TestCase
def test_new_1
program = 'string'
db = 'string'
option = ['-e', '0.001']
server = 'local'
assert_raise(ArgumentError) { Bio::Fasta.new() }
assert_raise(ArgumentError) { Bio::Fasta.new(program) }
assert(Bio::Fasta.new(program, db))
assert(Bio::Fasta.new(program, db, option))
assert(Bio::Fasta.new(program, db, option, server))
assert_raise(ArgumentError) { Bio::Fasta.new(program, db, option, server, nil) }
end
def test_option_backward_compatibility
fasta = Bio::Fasta.new('program', 'db', "-e 10")
assert_equal([ '-Q', '-H', '-m','10', '-e', '10'], fasta.options)
end
def test_option
fasta = Bio::Fasta.new('program', 'db', ["-e", "10"])
assert_equal([ '-Q', '-H', '-m','10', '-e', '10'], fasta.options)
end
end
class TestFasta < Test::Unit::TestCase
def setup
program = 'ssearch'
db = 'nr'
option = ['-e', '10']
@obj = Bio::Fasta.new(program, db, option)
end
def test_program
assert_equal('ssearch', @obj.program)
@obj.program = 'lalign'
assert_equal('lalign', @obj.program)
end
def test_db
assert_equal('nr', @obj.db)
@obj.db = 'refseq'
assert_equal('refseq', @obj.db)
end
def test_options
assert_equal(["-Q", "-H", "-m", "10", "-e", "10"], @obj.options)
@obj.options = ['-Q', '-H', '-m', '8']
assert_equal(['-Q', '-H', '-m', '8'], @obj.options)
end
def test_server
assert_equal('local', @obj.server)
@obj.server = 'genomenet'
assert_equal('genomenet', @obj.server)
end
def test_ktup
assert_equal(nil, @obj.ktup)
@obj.ktup = 6
assert_equal(6, @obj.ktup)
end
def test_matrix
assert_equal(nil, @obj.matrix)
@obj.matrix = 'PAM120'
assert_equal('PAM120', @obj.matrix)
end
def test_output
assert_equal('', @obj.output)
# assert_raise(NoMethodError) { @obj.output = "" }
end
def test_option
option = ['-M'].to_s
assert(@obj.option = option)
assert_equal(option, @obj.option)
end
def test_format
assert_equal(10, @obj.format)
end
def test_format_arg_str
assert(@obj.format = '1')
assert_equal(1, @obj.format)
end
def test_format_arg_integer
assert(@obj.format = 2)
assert_equal(2, @obj.format)
end
end
class TestFastaQuery < Test::Unit::TestCase
def test_self_parser
end
def test_self_local
# test/functional/bio/test_fasta.rb
end
def test_self_remote
# test/functional/bio/test_fasta.rb
end
def test_query
end
end
end
From k at pub.open-bio.org Sun Dec 18 11:50:58 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 11:43:49 2005
Subject: [BioRuby-cvs] bioruby/lib/bio pathway.rb,1.33,1.34
Message-ID: <200512181650.jBIGowVL029335@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv29285/lib/bio
Modified Files:
pathway.rb
Log Message:
* rolled back to the previous version until bugs caused by the specification change are fixed
Index: pathway.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/pathway.rb,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** pathway.rb 4 Nov 2005 17:39:44 -0000 1.33
--- pathway.rb 18 Dec 2005 16:50:56 -0000 1.34
***************
*** 1,21 ****
#
! # = bio/pathway.rb - Binary relations and Graph algorithms
! #
! # Copyright:: Copyright (c) 2001, 2005
! # Toshiaki Katayama ,
! # Shuichi Kawashima ,
! # Nobuya Tanaka
! # License:: LGPL
! #
! # $Id$
[...1506 lines suppressed...]
+
+ --- Bio::Relation#eql?(rel)
+ --- Bio::Relation#hash
+
+ Method eql? is an alias of the === method and is used with hash method
+ to make uniq arry of the Bio::Relation objects.
+
+ a1 = Bio::Relation.new('a', 'b', 1)
+ a2 = Bio::Relation.new('b', 'a', 1)
+ a3 = Bio::Relation.new('b', 'c', 1)
+ p [ a1, a2, a3 ].uniq
+
+ --- Bio::Relation#<=>(rel)
+
+ Used by the each method to compare with another Bio::Relation object.
+ This method is only usable when the edge objects have the property of
+ the module Comparable.
+
+ =end
+
From k at pub.open-bio.org Sun Dec 18 11:50:58 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 11:43:52 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio test_pathway.rb,1.2,1.3
Message-ID: <200512181650.jBIGowVL029339@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory pub.open-bio.org:/tmp/cvs-serv29285/test/unit/bio
Modified Files:
test_pathway.rb
Log Message:
* rolled back to the previous version until bugs caused by the specification change are fixed
Index: test_pathway.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_pathway.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_pathway.rb 24 Sep 2005 03:12:55 -0000 1.2
--- test_pathway.rb 18 Dec 2005 16:50:56 -0000 1.3
***************
*** 1,4 ****
#
! # test/unit/bio/tc_pathway.rb - Unit test for Bio::Pathway
#
# Copyright (C) 2004 Moses Hohman
--- 1,4 ----
#
! # test/bio/tc_pathway.rb - Unit test for Bio::Pathway
#
# Copyright (C) 2004 Moses Hohman
***************
*** 22,26 ****
require 'pathname'
! libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)
--- 22,26 ----
require 'pathname'
! libpath = Pathname.new(File.join(File.dirname(__FILE__), [".."]*2, "lib")).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)
***************
*** 29,483 ****
class Float
! NaN = 0/0.0
! Infinity = 1/0.0
end
class Array
! def sum
! inject { | sum, val | sum += val }
! end
end
module Bio
! class Pathway
! # bug in subgraph: does not include nodes w/o edges
! def subgraph(list = nil)
! if list
! @label.clear
! list.each { |node| @label[node] = true }
! end
! sub_graph = Pathway.new([], @undirected)
! @graph.each do |from, hash|
! next unless @label[from]
! sub_graph.graph[from] = {}
! hash.each do |to, relation|
! next unless @label[to]
! sub_graph.graph[from][to] = relation
! end
! end
! sub_graph
! end
! # bug in cliquishness: subgraph of neighbors does not include nodes w/o edges
! def subgraph_adjacency_matrix(nodes)
! adjacency_matrix = to_matrix(0).to_a
! node_indices = nodes.collect { |x| @index[x] }
! subgraph = adjacency_matrix.values_at(*(node_indices))
! subgraph.collect! { |row| row.values_at(*(node_indices)) }
! end
! # bug in cliquishness: subgraph of neighbors does not include nodes w/o edges
! # Throws exception if graph is directed
! def cliquishness(node)
! raise "Cannot calculate cliquishness in directed graph" if not undirected?
! neighbors = @graph[node].keys
! return Float::NaN if neighbors.size==0
! return 1 if neighbors.size==1
! # divide by two to avoid double-counting
! num_neighbor_edges = subgraph_adjacency_matrix(neighbors).flatten.sum/2
! num_complete_edges = neighbors.size*(neighbors.size-1)/2
! num_neighbor_edges.to_f / num_complete_edges.to_f
end
- end
! class TestMyGraph < Test::Unit::TestCase
! def test_cliquishness
! graph = Pathway.new([
! Relation.new(1, 3, 1),
! Relation.new(2, 3, 1),
! Relation.new(1, 5, 1),
! Relation.new(2, 6, 1),
! Relation.new(3, 6, 1),
! Relation.new(4, 6, 1),
! Relation.new(5, 6, 1),
! ], true)
! assert_equal(0, graph.cliquishness(1), "1's cliquishness wrong")
! assert_equal(1, graph.cliquishness(2), "2's cliquishness wrong")
! assert_in_delta(0.33, graph.cliquishness(3), 0.01, "3's cliquishness wrong")
! assert_equal(1, graph.cliquishness(4), "4's cliquishness wrong")
! assert_equal(0, graph.cliquishness(5), "5's cliquishness wrong")
! assert_in_delta(0.16, graph.cliquishness(6), 0.01, "6's cliquishness wrong")
end
- end
! class TestRelation < Test::Unit::TestCase
! def test_comparison_operator
! r1 = Relation.new('a', 'b', 1)
! r2 = Relation.new('b', 'a', 1)
! r3 = Relation.new('b', 'a', 2)
! r4 = Relation.new('a', 'b', 1)
! assert(r1 === r2, "r1 === r2 not true, === not symmetric wrt nodes")
! assert(!(r1 === r3), "r1 === r3 not false, === does not take edge into account")
! assert(r1 === r4, "r1 === r4 not true, === is not reflexive wrt nodes")
! assert_equal([r1, r3], [ r1, r2, r3, r4 ].uniq, "uniq did not have expected effect")
! assert(r1.eql?(r2), "r1 not eql r2")
! assert(!r3.eql?(r2), "r3 eql to r2")
end
- end
! class TestSampleGraph < Test::Unit::TestCase
!
! # Sample Graph :
! # +----------------+
! # | |
! # v |
! # +---------(q)-->(t)------->(y)<----(r)
! # | | | ^ |
! # v | v | |
! # +--(s)<--+ | (x)<---+ (u)<-----+
! # | | | | |
! # v | | v |
! # (v)----->(w)<---+ (z)----+
! def setup
! @data = [
! [ 'q', 's', 1, ],
! [ 'q', 't', 1, ],
! [ 'q', 'w', 1, ],
! [ 'r', 'u', 1, ],
! [ 'r', 'y', 1, ],
! [ 's', 'v', 1, ],
! [ 't', 'x', 1, ],
! [ 't', 'y', 1, ],
! [ 'u', 'y', 1, ],
! [ 'v', 'w', 1, ],
! [ 'w', 's', 1, ],
! [ 'x', 'z', 1, ],
! [ 'y', 'q', 1, ],
! [ 'z', 'x', 1, ],
! ]
! @graph = Pathway.new(@data.collect { |x| Relation.new(*x) })
! end
! def test_to_matrix
! assert_equal(Matrix[
! [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
! [0, 0, 0, 0, 0, 0, 0, 1, 0, 0],
! [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
! [0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
! [0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
! [0, 1, 0, 0, 0, 0, 0, 1, 1, 0],
! [0, 0, 0, 1, 0, 0, 0, 0, 0, 1],
! [1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
! [0, 0, 1, 1, 0, 0, 0, 0, 0, 0],
! [0, 0, 0, 1, 0, 0, 0, 0, 0, 0]
! ], @graph.to_matrix(0), "matrix wrong")
! assert_equal({"v"=>0,"w"=>1,"x"=>2,"y"=>3,"z"=>4,"q"=>5,"r"=>6,"s"=>7,"t"=>8,"u"=>9}, @graph.index, "node --> matrix index order wrong")
! end
! def test_dump_matrix
! dumped = "[" +
! "# v, w, x, y, z, q, r, s, t, u\n" +
! " [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],\n" + # v
! " [0, 0, 0, 0, 0, 0, 0, 1, 0, 0],\n" + # w
! " [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],\n" + # x
! " [0, 0, 0, 0, 0, 1, 0, 0, 0, 0],\n" + # y
! " [0, 0, 1, 0, 0, 0, 0, 0, 0, 0],\n" + # z
! " [0, 1, 0, 0, 0, 0, 0, 1, 1, 0],\n" + # q
! " [0, 0, 0, 1, 0, 0, 0, 0, 0, 1],\n" + # r
! " [1, 0, 0, 0, 0, 0, 0, 0, 0, 0],\n" + # s
! " [0, 0, 1, 1, 0, 0, 0, 0, 0, 0],\n" + # t
! " [0, 0, 0, 1, 0, 0, 0, 0, 0, 0]\n]" # u
! assert_equal(dumped, @graph.dump_matrix(0))
! end
! def test_dump_list
! dumped = "v => w (1)\n" +
! "w => s (1)\n" +
! "x => z (1)\n" +
! "y => q (1)\n" +
! "z => x (1)\n" +
! "q => w (1), s (1), t (1)\n" +
! "r => y (1), u (1)\n" +
! "s => v (1)\n" +
! "t => x (1), y (1)\n" +
! "u => y (1)\n"
! assert_equal(dumped, @graph.dump_list)
! end
! def test_extract_subgraph_by_label
! hash = { 'q' => "L1", 's' => "L2", 'v' => "L3", 'w' => "L4" }
! @graph.label = hash
! dumped = "v => w (1)\n" +
! "w => s (1)\n" +
! "q => w (1), s (1)\n" +
! "s => v (1)\n"
! assert_equal(dumped, @graph.subgraph.dump_list)
! end
! def test_extract_subgraph_by_list
! dumped = "x => z (1)\n" +
! "y => q (1)\n" +
! "z => x (1)\n" +
! "q => t (1)\n" +
! "t => x (1), y (1)\n"
! assert_equal(dumped, @graph.subgraph(['q', 't', 'x', 'y', 'z']).dump_list)
! end
! def test_extract_subgraph_retains_disconnected_nodes
! assert_equal(4, @graph.subgraph(['r', 's', 'v', 'w']).nodes, "wrong number of nodes")
! end
! # Sample Graph :
! # +----------------+
! # | |
! # v |
! # +---------(q)-->(t)------->(y)<----(r)
! # | | | ^ |
! # v | v | |
! # +--(s)<--+ | (x)<---+ (u)<-----+
! # | | | | |
! # v | | v |
! # (v)----->(w)<---+ (z)----+
! def test_cliquishness_raises_exception_for_directed_graph
! assert_raises (RuntimeError) { @graph.cliquishness('q') }
! end
! def test_undirected_cliquishness
! @graph.undirected
! assert_in_delta(0.33, @graph.cliquishness('q'), 0.01)
! end
! def test_small_world_aka_node_degree_histogram
! expected = {1=>7, 2=>2, 3=>1}
! expected.default = 0
! assert_equal(expected, @graph.small_world)
! end
! # Sample Graph :
! # +----------------+
! # | |
! # v |
! # +---------(q)-->(t)------->(y)<----(r)
! # | | | ^ |
! # v | v | |
! # +--(s)<--+ | (x)<---+ (u)<-----+
! # | | | | |
! # v | | v |
! # (v)----->(w)<---+ (z)----+
! def test_breadth_first_search
! distances, predecessors = @graph.breadth_first_search('q')
! assert_equal({
! "v"=>2,
! "w"=>1,
! "x"=>2,
! "y"=>2,
! "z"=>3,
! "q"=>0,
! "s"=>1,
! "t"=>1}, distances, "distances wrong")
! assert_equal({
! "v"=>"s",
! "w"=>"q",
! "x"=>"t",
! "y"=>"t",
! "z"=>"x",
! "q"=>nil,
! "s"=>"q",
! "t"=>"q"}, predecessors, "predecessors wrong")
! end
! def test_bfs_shortest_path
! step, path = @graph.bfs_shortest_path('y', 'w')
! assert_equal(2, step, "wrong # of steps")
! assert_equal(["y", "q", "w"], path, "wrong path")
! end
! def test_depth_first_search
! timestamp, tree, back, cross, forward = @graph.depth_first_search
! assert_equal({
! "v"=>[1, 6],
! "w"=>[2, 5],
! "x"=>[7, 10],
! "y"=>[11, 16],
! "z"=>[8, 9],
! "q"=>[12, 15],
! "r"=>[17, 20],
! "s"=>[3, 4],
! "t"=>[13, 14],
! "u"=>[18, 19]}, timestamp, "timestamps wrong")
! assert_equal({
! "w"=>"v",
! "z"=>"x",
! "q"=>"y",
! "s"=>"w",
! "t"=>"q",
! "u"=>"r"}, tree, "tree edges wrong")
! assert_equal({
! "z"=>"x",
! "s"=>"v",
! "t"=>"y"}, back, "back edges wrong")
! assert_equal({
! "q"=>"s",
! "r"=>"y",
! "t"=>"x",
! "u"=>"y"}, cross, "cross edges wrong")
! assert_equal({}, forward, "forward edges wrong")
! end
! # Sample Graph :
! # +----------------+
! # | |
! # v |
! # +---------(q)-->(t)------->(y)<----(r)
! # | | | ^ |
! # v | v | |
! # +--(s)<--+ | (x)<---+ (u)<-----+
! # | | | | |
! # v | | v |
! # (v)----->(w)<---+ (z)----+
! def test_dijkstra
! distances, predecessors = @graph.dijkstra('q')
! assert_equal({
! "v"=>2,
! "w"=>1,
! "x"=>2,
! "y"=>2,
! "z"=>3,
! "q"=>0,
! "r"=>Float::Infinity,
! "s"=>1,
! "t"=>1,
! "u"=>Float::Infinity}, distances, "distances wrong")
! assert_equal({
! "v"=>"s",
! "w"=>"q",
! "x"=>"t",
! "y"=>"t",
! "z"=>"x",
! "q"=>nil,
! "r"=>nil,
! "s"=>"q",
! "t"=>"q",
! "u"=>nil}, predecessors, "predecessors wrong")
! end
! def test_bellman_ford
! distances, predecessors = @graph.bellman_ford('q')
! assert_equal({
! "v"=>2,
! "w"=>1,
! "x"=>2,
! "y"=>2,
! "z"=>3,
! "q"=>0,
! "r"=>Float::Infinity,
! "s"=>1,
! "t"=>1,
! "u"=>Float::Infinity}, distances, "distances wrong")
! assert_equal({
! "v"=>"s",
! "w"=>"q",
! "x"=>"t",
! "y"=>"t",
! "z"=>"x",
! "q"=>nil,
! "r"=>nil,
! "s"=>"q",
! "t"=>"q",
! "u"=>nil}, predecessors, "predecessors wrong")
end
- end
! class TestTopologicalSort < Test::Unit::TestCase
! #
! # Professor Bumstead topologically sorts his clothing when getting dressed.
! #
! # "undershorts" "socks"
! # | | |
! # v | v "watch"
! # "pants" --+-------> "shoes"
! # |
! # v
! # "belt" <----- "shirt" ----> "tie" ----> "jacket"
! # | ^
! # `---------------------------------------'
! #
! def test_dfs_topological_sort
! dag = Pathway.new([
! Relation.new("undershorts", "pants", true),
! Relation.new("undershorts", "shoes", true),
! Relation.new("socks", "shoes", true),
! Relation.new("watch", "watch", true),
! Relation.new("pants", "belt", true),
! Relation.new("pants", "shoes", true),
! Relation.new("shirt", "belt", true),
! Relation.new("shirt", "tie", true),
! Relation.new("tie", "jacket", true),
! Relation.new("belt", "jacket", true),
! ])
! sorted = dag.dfs_topological_sort
! assert(sorted.index("socks") < sorted.index("shoes"), "socks >= shoes")
! assert(sorted.index("undershorts") < sorted.index("pants"), "undershorts >= pants")
! assert(sorted.index("undershorts") < sorted.index("shoes"), "undershorts >= shoes")
! assert(sorted.index("pants") < sorted.index("shoes"), "pants >= shoes")
! assert(sorted.index("pants") < sorted.index("belt"), "pants >= belt")
! assert(sorted.index("shirt") < sorted.index("belt"), "shirt >= belt")
! assert(sorted.index("shirt") < sorted.index("tie"), "shirt >= tie")
! assert(sorted.index("belt") < sorted.index("jacket"), "belt >= jacket")
! assert(sorted.index("tie") < sorted.index("jacket"), "tie >= jacket")
end
- end
! #TODO: verify the below
! class TestWeightedGraph < Test::Unit::TestCase
! # 'a' --> 'b'
! # | 1 | 3
! # |5 v
! # `----> 'c'
! def setup
! r1 = Relation.new('a', 'b', 1)
! r2 = Relation.new('a', 'c', 5)
! r3 = Relation.new('b', 'c', 3)
! @w_graph = Pathway.new([r1, r2, r3])
! end
! def test_dijkstra_on_weighted_graph
! distances, predecessors = @w_graph.dijkstra('a')
! assert_equal({
! "a"=>0,
! "b"=>1,
! "c"=>4}, distances, "distances wrong")
! assert_equal({
! "a"=>nil,
! "b"=>"a",
! "c"=>"b"}, predecessors, "predecessors wrong")
! end
! def test_bellman_ford_on_negative_weighted_graph
!
! # ,-- 'a' --> 'b'
! # | | 1 | 3
! # | |5 v
! # | `----> 'c'
! # | ^
! # |2 | -5
! # `--> 'd' ----'
!
! r4 = Relation.new('a', 'd', 2)
! r5 = Relation.new('d', 'c', -5)
! @w_graph.append(r4)
! @w_graph.append(r5)
! distances, predecessors = @w_graph.bellman_ford('a')
! assert_equal({
! "a"=>0,
! "b"=>1,
! "c"=>-3,
! "d"=>2}, distances, "distances wrong")
! assert_equal({
! "a"=>nil,
! "b"=>"a",
! "c"=>"d",
! "d"=>"a"}, predecessors, "predecessors wrong")
end
- end
end
--- 29,485 ----
class Float
! NaN = 0/0.0
! Infinity = 1/0.0
end
class Array
! def sum
! inject { | sum, val | sum += val }
! end
end
module Bio
! class Pathway
! # bug in subgraph: does not include nodes w/o edges
! def subgraph(list = nil)
! if list
! @label.clear
! list.each { |node| @label[node] = true }
! end
! sub_graph = Pathway.new([], @undirected)
! @graph.each do |from, hash|
! next unless @label[from]
! sub_graph.graph[from] = {}
! hash.each do |to, relation|
! next unless @label[to]
! sub_graph.graph[from][to] = relation
! end
! end
! sub_graph
! end
! # bug in cliquishness: subgraph of neighbors does not include nodes w/o edges
! def subgraph_adjacency_matrix(nodes)
! adjacency_matrix = to_matrix(0).to_a
! node_indices = nodes.collect { |x| @index[x] }
! subgraph = adjacency_matrix.values_at(*(node_indices))
! subgraph.collect! { |row| row.values_at(*(node_indices)) }
! end
! # bug in cliquishness: subgraph of neighbors does not include nodes w/o edges
! # Throws exception if graph is directed
! def cliquishness(node)
! raise "Cannot calculate cliquishness in directed graph" if not undirected?
! neighbors = @graph[node].keys
! return Float::NaN if neighbors.size==0
! return 1 if neighbors.size==1
! # divide by two to avoid double-counting
! num_neighbor_edges = subgraph_adjacency_matrix(neighbors).flatten.sum/2
! num_complete_edges = neighbors.size*(neighbors.size-1)/2
! num_neighbor_edges.to_f / num_complete_edges.to_f
! end
end
! class TestMyGraph < Test::Unit::TestCase
! def test_cliquishness
! graph = Pathway.new([
! Relation.new(1, 3, 1),
! Relation.new(2, 3, 1),
! Relation.new(1, 5, 1),
! Relation.new(2, 6, 1),
! Relation.new(3, 6, 1),
! Relation.new(4, 6, 1),
! Relation.new(5, 6, 1),
! ], true)
! assert_equal(0, graph.cliquishness(1), "1's cliquishness wrong")
! assert_equal(1, graph.cliquishness(2), "2's cliquishness wrong")
! assert_in_delta(0.33, graph.cliquishness(3), 0.01, "3's cliquishness wrong")
! assert_equal(1, graph.cliquishness(4), "4's cliquishness wrong")
! assert_equal(0, graph.cliquishness(5), "5's cliquishness wrong")
! assert_in_delta(0.16, graph.cliquishness(6), 0.01, "6's cliquishness wrong")
! end
end
! class TestRelation < Test::Unit::TestCase
! def test_comparison_operator
! r1 = Relation.new('a', 'b', 1)
! r2 = Relation.new('b', 'a', 1)
! r3 = Relation.new('b', 'a', 2)
! r4 = Relation.new('a', 'b', 1)
! assert(r1 === r2, "r1 === r2 not true, === not symmetric wrt nodes")
! assert(!(r1 === r3), "r1 === r3 not false, === does not take edge into account")
! assert(r1 === r4, "r1 === r4 not true, === is not reflexive wrt nodes")
! assert_equal([r1, r3], [ r1, r2, r3, r4 ].uniq, "uniq did not have expected effect")
! assert(r1.eql?(r2), "r1 not eql r2")
! assert(!r3.eql?(r2), "r3 eql to r2")
! end
end
! class TestSampleGraph < Test::Unit::TestCase
!
! # Sample Graph :
! # +----------------+
! # | |
! # v |
! # +---------(q)-->(t)------->(y)<----(r)
! # | | | ^ |
! # v | v | |
! # +--(s)<--+ | (x)<---+ (u)<-----+
! # | | | | |
! # v | | v |
! # (v)----->(w)<---+ (z)----+
! def setup
! @data = [
! [ 'q', 's', 1, ],
! [ 'q', 't', 1, ],
! [ 'q', 'w', 1, ],
! [ 'r', 'u', 1, ],
! [ 'r', 'y', 1, ],
! [ 's', 'v', 1, ],
! [ 't', 'x', 1, ],
! [ 't', 'y', 1, ],
! [ 'u', 'y', 1, ],
! [ 'v', 'w', 1, ],
! [ 'w', 's', 1, ],
! [ 'x', 'z', 1, ],
! [ 'y', 'q', 1, ],
! [ 'z', 'x', 1, ],
! ]
! @graph = Pathway.new(@data.collect { |x| Relation.new(*x) })
! end
! def test_to_matrix
! assert_equal(Matrix[
! [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],
! [0, 0, 0, 0, 0, 0, 0, 1, 0, 0],
! [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
! [0, 0, 0, 0, 0, 1, 0, 0, 0, 0],
! [0, 0, 1, 0, 0, 0, 0, 0, 0, 0],
! [0, 1, 0, 0, 0, 0, 0, 1, 1, 0],
! [0, 0, 0, 1, 0, 0, 0, 0, 0, 1],
! [1, 0, 0, 0, 0, 0, 0, 0, 0, 0],
! [0, 0, 1, 1, 0, 0, 0, 0, 0, 0],
! [0, 0, 0, 1, 0, 0, 0, 0, 0, 0]
! ], @graph.to_matrix(0), "matrix wrong")
! assert_equal({"v"=>0,"w"=>1,"x"=>2,"y"=>3,"z"=>4,"q"=>5,"r"=>6,"s"=>7,"t"=>8,"u"=>9}, @graph.index, "node --> matrix index order wrong")
! end
! def test_dump_matrix
! dumped = "[" +
! "# v, w, x, y, z, q, r, s, t, u\n" +
! " [0, 1, 0, 0, 0, 0, 0, 0, 0, 0],\n" + # v
! " [0, 0, 0, 0, 0, 0, 0, 1, 0, 0],\n" + # w
! " [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],\n" + # x
! " [0, 0, 0, 0, 0, 1, 0, 0, 0, 0],\n" + # y
! " [0, 0, 1, 0, 0, 0, 0, 0, 0, 0],\n" + # z
! " [0, 1, 0, 0, 0, 0, 0, 1, 1, 0],\n" + # q
! " [0, 0, 0, 1, 0, 0, 0, 0, 0, 1],\n" + # r
! " [1, 0, 0, 0, 0, 0, 0, 0, 0, 0],\n" + # s
! " [0, 0, 1, 1, 0, 0, 0, 0, 0, 0],\n" + # t
! " [0, 0, 0, 1, 0, 0, 0, 0, 0, 0]\n]" # u
! assert_equal(dumped, @graph.dump_matrix(0))
! end
! def test_dump_list
! dumped = "v => w (1)\n" +
! "w => s (1)\n" +
! "x => z (1)\n" +
! "y => q (1)\n" +
! "z => x (1)\n" +
! "q => w (1), s (1), t (1)\n" +
! "r => y (1), u (1)\n" +
! "s => v (1)\n" +
! "t => x (1), y (1)\n" +
! "u => y (1)\n"
! assert_equal(dumped, @graph.dump_list)
! end
! def test_extract_subgraph_by_label
! hash = { 'q' => "L1", 's' => "L2", 'v' => "L3", 'w' => "L4" }
! @graph.label = hash
! dumped =
! "v => w (1)\n" +
! "w => s (1)\n" +
! "q => w (1), s (1)\n" +
! "s => v (1)\n"
! assert_equal(dumped, @graph.subgraph.dump_list)
! end
! def test_extract_subgraph_by_list
! dumped =
! "x => z (1)\n" +
! "y => q (1)\n" +
! "z => x (1)\n" +
! "q => t (1)\n" +
! "t => x (1), y (1)\n"
! assert_equal(dumped, @graph.subgraph(['q', 't', 'x', 'y', 'z']).dump_list)
! end
! def test_extract_subgraph_retains_disconnected_nodes
! assert_equal(4, @graph.subgraph(['r', 's', 'v', 'w']).nodes, "wrong number of nodes")
! end
! # Sample Graph :
! # +----------------+
! # | |
! # v |
! # +---------(q)-->(t)------->(y)<----(r)
! # | | | ^ |
! # v | v | |
! # +--(s)<--+ | (x)<---+ (u)<-----+
! # | | | | |
! # v | | v |
! # (v)----->(w)<---+ (z)----+
! def test_cliquishness_raises_exception_for_directed_graph
! assert_raises (RuntimeError) { @graph.cliquishness('q') }
! end
! def test_undirected_cliquishness
! @graph.undirected
! assert_in_delta(0.33, @graph.cliquishness('q'), 0.01)
! end
! def test_small_world_aka_node_degree_histogram
! expected = {1=>7, 2=>2, 3=>1}
! expected.default = 0
! assert_equal(expected, @graph.small_world)
! end
! # Sample Graph :
! # +----------------+
! # | |
! # v |
! # +---------(q)-->(t)------->(y)<----(r)
! # | | | ^ |
! # v | v | |
! # +--(s)<--+ | (x)<---+ (u)<-----+
! # | | | | |
! # v | | v |
! # (v)----->(w)<---+ (z)----+
! def test_breadth_first_search
! distances, predecessors = @graph.breadth_first_search('q')
! assert_equal({
! "v"=>2,
! "w"=>1,
! "x"=>2,
! "y"=>2,
! "z"=>3,
! "q"=>0,
! "s"=>1,
! "t"=>1}, distances, "distances wrong")
! assert_equal({
! "v"=>"s",
! "w"=>"q",
! "x"=>"t",
! "y"=>"t",
! "z"=>"x",
! "q"=>nil,
! "s"=>"q",
! "t"=>"q"}, predecessors, "predecessors wrong")
! end
! def test_bfs_shortest_path
! step, path = @graph.bfs_shortest_path('y', 'w')
! assert_equal(2, step, "wrong # of steps")
! assert_equal(["y", "q", "w"], path, "wrong path")
! end
! def test_depth_first_search
! timestamp, tree, back, cross, forward = @graph.depth_first_search
! assert_equal({
! "v"=>[1, 6],
! "w"=>[2, 5],
! "x"=>[7, 10],
! "y"=>[11, 16],
! "z"=>[8, 9],
! "q"=>[12, 15],
! "r"=>[17, 20],
! "s"=>[3, 4],
! "t"=>[13, 14],
! "u"=>[18, 19]}, timestamp, "timestamps wrong")
! assert_equal({
! "w"=>"v",
! "z"=>"x",
! "q"=>"y",
! "s"=>"w",
! "t"=>"q",
! "u"=>"r"}, tree, "tree edges wrong")
! assert_equal({
! "z"=>"x",
! "s"=>"v",
! "t"=>"y"}, back, "back edges wrong")
! assert_equal({
! "q"=>"s",
! "r"=>"y",
! "t"=>"x",
! "u"=>"y"}, cross, "cross edges wrong")
! assert_equal({}, forward, "forward edges wrong")
! end
! # Sample Graph :
! # +----------------+
! # | |
! # v |
! # +---------(q)-->(t)------->(y)<----(r)
! # | | | ^ |
! # v | v | |
! # +--(s)<--+ | (x)<---+ (u)<-----+
! # | | | | |
! # v | | v |
! # (v)----->(w)<---+ (z)----+
! def test_dijkstra
! distances, predecessors = @graph.dijkstra('q')
! assert_equal({
! "v"=>2,
! "w"=>1,
! "x"=>2,
! "y"=>2,
! "z"=>3,
! "q"=>0,
! "r"=>Float::Infinity,
! "s"=>1,
! "t"=>1,
! "u"=>Float::Infinity}, distances, "distances wrong")
! assert_equal({
! "v"=>"s",
! "w"=>"q",
! "x"=>"t",
! "y"=>"t",
! "z"=>"x",
! "q"=>nil,
! "r"=>nil,
! "s"=>"q",
! "t"=>"q",
! "u"=>nil}, predecessors, "predecessors wrong")
! end
! def test_bellman_ford
! distances, predecessors = @graph.bellman_ford('q')
! assert_equal({
! "v"=>2,
! "w"=>1,
! "x"=>2,
! "y"=>2,
! "z"=>3,
! "q"=>0,
! "r"=>Float::Infinity,
! "s"=>1,
! "t"=>1,
! "u"=>Float::Infinity}, distances, "distances wrong")
! assert_equal({
! "v"=>"s",
! "w"=>"q",
! "x"=>"t",
! "y"=>"t",
! "z"=>"x",
! "q"=>nil,
! "r"=>nil,
! "s"=>"q",
! "t"=>"q",
! "u"=>nil}, predecessors, "predecessors wrong")
! end
end
! class TestTopologicalSort < Test::Unit::TestCase
! #
! # Professor Bumstead topologically sorts his clothing when getting dressed.
! #
! # "undershorts" "socks"
! # | | |
! # v | v "watch"
! # "pants" --+-------> "shoes"
! # |
! # v
! # "belt" <----- "shirt" ----> "tie" ----> "jacket"
! # | ^
! # `---------------------------------------'
! #
! def test_dfs_topological_sort
! dag = Pathway.new([
! Relation.new("undershorts", "pants", true),
! Relation.new("undershorts", "shoes", true),
! Relation.new("socks", "shoes", true),
! Relation.new("watch", "watch", true),
! Relation.new("pants", "belt", true),
! Relation.new("pants", "shoes", true),
! Relation.new("shirt", "belt", true),
! Relation.new("shirt", "tie", true),
! Relation.new("tie", "jacket", true),
! Relation.new("belt", "jacket", true),
! ])
! sorted = dag.dfs_topological_sort
! assert(sorted.index("socks") < sorted.index("shoes"), "socks >= shoes")
! assert(sorted.index("undershorts") < sorted.index("pants"), "undershorts >= pants")
! assert(sorted.index("undershorts") < sorted.index("shoes"), "undershorts >= shoes")
! assert(sorted.index("pants") < sorted.index("shoes"), "pants >= shoes")
! assert(sorted.index("pants") < sorted.index("belt"), "pants >= belt")
! assert(sorted.index("shirt") < sorted.index("belt"), "shirt >= belt")
! assert(sorted.index("shirt") < sorted.index("tie"), "shirt >= tie")
! assert(sorted.index("belt") < sorted.index("jacket"), "belt >= jacket")
! assert(sorted.index("tie") < sorted.index("jacket"), "tie >= jacket")
! end
end
! #TODO: verify the below
! class TestWeightedGraph < Test::Unit::TestCase
! # 'a' --> 'b'
! # | 1 | 3
! # |5 v
! # `----> 'c'
! def setup
! r1 = Relation.new('a', 'b', 1)
! r2 = Relation.new('a', 'c', 5)
! r3 = Relation.new('b', 'c', 3)
! @w_graph = Pathway.new([r1, r2, r3])
! end
! def test_dijkstra_on_weighted_graph
! distances, predecessors = @w_graph.dijkstra('a')
! assert_equal({
! "a"=>0,
! "b"=>1,
! "c"=>4}, distances, "distances wrong")
! assert_equal({
! "a"=>nil,
! "b"=>"a",
! "c"=>"b"}, predecessors, "predecessors wrong")
! end
! def test_bellman_ford_on_negative_weighted_graph
!
! # ,-- 'a' --> 'b'
! # | | 1 | 3
! # | |5 v
! # | `----> 'c'
! # | ^
! # |2 | -5
! # `--> 'd' ----'
!
! r4 = Relation.new('a', 'd', 2)
! r5 = Relation.new('d', 'c', -5)
! @w_graph.append(r4)
! @w_graph.append(r5)
! distances, predecessors = @w_graph.bellman_ford('a')
! assert_equal({
! "a"=>0,
! "b"=>1,
! "c"=>-3,
! "d"=>2}, distances, "distances wrong")
! assert_equal({
! "a"=>nil,
! "b"=>"a",
! "c"=>"d",
! "d"=>"a"}, predecessors, "predecessors wrong")
! end
end
end
From nakao at pub.open-bio.org Sun Dec 18 11:51:20 2005
From: nakao at pub.open-bio.org (Mitsuteru C. Nakao)
Date: Sun Dec 18 11:44:11 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/io soapwsdl.rb,1.2,1.3
Message-ID: <200512181651.jBIGpKVL029377@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory pub.open-bio.org:/tmp/cvs-serv29367/lib/bio/io
Modified Files:
soapwsdl.rb
Log Message:
* Added RDoc.
Index: soapwsdl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/soapwsdl.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** soapwsdl.rb 23 Oct 2005 10:41:00 -0000 1.2
--- soapwsdl.rb 18 Dec 2005 16:51:18 -0000 1.3
***************
*** 1,6 ****
#
! # bio/io/soapwsdl.rb - SOAP/WSDL interface class
#
! # Copyright (C) 2004 KATAYAMA Toshiaki
#
# This library is free software; you can redistribute it and/or
--- 1,41 ----
#
! # = bio/io/soapwsdl.rb - SOAP/WSDL interface class
#
! # Copyright:: Copyright (C) 2004
! # KATAYAMA Toshiaki
! # License:: LGPL
! #
! # $Id$
! #
! # SOAP/WSDL
! #
! #
! # == Examples
! #
! # class API < Bio::SOAPWSDL
! # def initialize
! # @wsdl = 'http://example.com/example.wsdl'
! # @log = File.new("soap_log", 'w')
! # create_driver
! # end
! # end
! #
! # == Use HTTP proxy
! #
! # You need to set following two environmental variables
! # (case might be insensitive) as required by SOAP4R.
! #
! # --- soap_use_proxy
! # Set the value of this variable to 'on'.
! #
! # --- http_proxy
! # Set the URL of your proxy server (http://myproxy.com:8080 etc.).
! #
! # === Example
! #
! # % export soap_use_proxy=on
! # % export http_proxy=http://localhost:8080
! #
! #--
#
# This library is free software; you can redistribute it and/or
***************
*** 18,22 ****
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! # $Id$
#
--- 53,57 ----
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! #++
#
***************
*** 30,33 ****
--- 65,75 ----
class SOAPWSDL
+ # WSDL URL
+ attr_reader :wsdl
+
+ # log IO
+ attr_reader :log
+
+
def initialize(wsdl = nil)
@wsdl = wsdl
***************
*** 35,39 ****
create_driver
end
! attr_reader :wsdl, :log
def create_driver
--- 77,81 ----
create_driver
end
!
def create_driver
***************
*** 45,49 ****
--- 87,94 ----
@driver.generate_explicit_type = true # Ruby obj <-> SOAP obj
end
+ private :create_driver
+
+ # Set a WSDL URL.
def wsdl=(url)
@wsdl = url
***************
*** 51,54 ****
--- 96,101 ----
end
+
+ # Set log IO
def log=(io)
@log = io
***************
*** 56,80 ****
end
def method_missing(*arg)
@driver.send(*arg)
end
end # SOAP
end # Bio
-
- =begin
-
- To use HTTP proxy, you need to set following two environmental variables
- (case might be insensitive) as required by SOAP4R.
-
- --- soap_use_proxy
-
- Set the value of this variable to 'on'.
-
- --- http_proxy
-
- Set the URL of your proxy server (http://myproxy.com:8080 etc.).
-
- =end
--- 103,114 ----
end
+
def method_missing(*arg)
@driver.send(*arg)
end
+ private :method_missing
end # SOAP
end # Bio
From k at pub.open-bio.org Sun Dec 18 10:58:42 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 11:46:20 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/blat report.rb,1.5,1.6
Message-ID: <200512181559.jBIFwgVL028857@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl/blat
In directory pub.open-bio.org:/tmp/cvs-serv28824/appl/blat
Modified Files:
report.rb
Log Message:
* s/Licence/License/
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blat/report.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** report.rb 1 Nov 2005 05:32:24 -0000 1.5
--- report.rb 18 Dec 2005 15:58:39 -0000 1.6
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2004 GOTO Naohisa
! # Licence:: LGPL
#
#--
--- 3,7 ----
#
# Copyright:: Copyright (C) 2004 GOTO Naohisa
! # License:: LGPL
#
#--
From k at pub.open-bio.org Sun Dec 18 10:58:43 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 11:46:21 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/tmhmm report.rb,1.5,1.6
Message-ID: <200512181558.jBIFwhVL028894@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl/tmhmm
In directory pub.open-bio.org:/tmp/cvs-serv28824/appl/tmhmm
Modified Files:
report.rb
Log Message:
* s/Licence/License/
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/tmhmm/report.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** report.rb 6 Nov 2005 16:10:07 -0000 1.5
--- report.rb 18 Dec 2005 15:58:41 -0000 1.6
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2003 Mitsuteru C. Nakao
! # Licence:: LGPL
#
# $Id$
--- 3,7 ----
#
# Copyright:: Copyright (C) 2003 Mitsuteru C. Nakao
! # License:: LGPL
#
# $Id$
From k at pub.open-bio.org Sun Dec 18 10:58:41 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 11:46:21 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/bl2seq report.rb,1.5,1.6
Message-ID: <200512181559.jBIFwfVL028849@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl/bl2seq
In directory pub.open-bio.org:/tmp/cvs-serv28824/appl/bl2seq
Modified Files:
report.rb
Log Message:
* s/Licence/License/
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/bl2seq/report.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** report.rb 1 Nov 2005 05:32:23 -0000 1.5
--- report.rb 18 Dec 2005 15:58:39 -0000 1.6
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2005 GOTO Naohisa
! # Licence:: LGPL
#
#--
--- 3,7 ----
#
# Copyright:: Copyright (C) 2005 GOTO Naohisa
! # License:: LGPL
#
#--
From k at pub.open-bio.org Sun Dec 18 10:58:42 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 11:46:22 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/genscan report.rb,1.7,1.8
Message-ID: <200512181558.jBIFwgVL028866@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl/genscan
In directory pub.open-bio.org:/tmp/cvs-serv28824/appl/genscan
Modified Files:
report.rb
Log Message:
* s/Licence/License/
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/genscan/report.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** report.rb 6 Nov 2005 18:24:41 -0000 1.7
--- report.rb 18 Dec 2005 15:58:40 -0000 1.8
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2003 Mitsuteru C. Nakao
! # Licence:: LGPL
#
# $Id$
--- 3,7 ----
#
# Copyright:: Copyright (C) 2003 Mitsuteru C. Nakao
! # License:: LGPL
#
# $Id$
From k at pub.open-bio.org Sun Dec 18 10:58:42 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 11:46:25 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl/clustalw report.rb,1.8,1.9
Message-ID: <200512181558.jBIFwgVL028864@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl/clustalw
In directory pub.open-bio.org:/tmp/cvs-serv28824/appl/clustalw
Modified Files:
report.rb
Log Message:
* s/Licence/License/
Index: report.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw/report.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** report.rb 1 Nov 2005 05:32:23 -0000 1.8
--- report.rb 18 Dec 2005 15:58:40 -0000 1.9
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2003 GOTO Naohisa
! # Licence:: LGPL
#
#--
--- 3,7 ----
#
# Copyright:: Copyright (C) 2003 GOTO Naohisa
! # License:: LGPL
#
#--
From k at pub.open-bio.org Sun Dec 18 10:58:42 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 11:46:27 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl clustalw.rb, 1.9, 1.10 mafft.rb,
1.8, 1.9 sim4.rb, 1.4, 1.5
Message-ID: <200512181558.jBIFwgVL028860@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory pub.open-bio.org:/tmp/cvs-serv28824/appl
Modified Files:
clustalw.rb mafft.rb sim4.rb
Log Message:
* s/Licence/License/
Index: sim4.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/sim4.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** sim4.rb 1 Nov 2005 05:32:23 -0000 1.4
--- sim4.rb 18 Dec 2005 15:58:40 -0000 1.5
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2004 GOTO Naohisa
! # Licence:: LGPL
#
#--
--- 3,7 ----
#
# Copyright:: Copyright (C) 2004 GOTO Naohisa
! # License:: LGPL
#
#--
Index: clustalw.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** clustalw.rb 1 Nov 2005 05:32:23 -0000 1.9
--- clustalw.rb 18 Dec 2005 15:58:40 -0000 1.10
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2003 GOTO Naohisa
! # Licence:: LGPL
#
#--
--- 3,7 ----
#
# Copyright:: Copyright (C) 2003 GOTO Naohisa
! # License:: LGPL
#
#--
Index: mafft.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft.rb,v
retrieving revision 1.8
retrieving revision 1.9
diff -C2 -d -r1.8 -r1.9
*** mafft.rb 1 Nov 2005 05:32:23 -0000 1.8
--- mafft.rb 18 Dec 2005 15:58:40 -0000 1.9
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2003 GOTO Naohisa
! # Licence:: LGPL
#
#--
--- 3,7 ----
#
# Copyright:: Copyright (C) 2003 GOTO Naohisa
! # License:: LGPL
#
#--
From k at pub.open-bio.org Sun Dec 18 10:58:44 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 11:46:30 2005
Subject: [BioRuby-cvs]
bioruby/lib/bio/db aaindex.rb, 1.15, 1.16 gff.rb, 1.4,
1.5 litdb.rb, 0.6, 0.7 nbrf.rb, 1.6, 1.7
Message-ID: <200512181558.jBIFwiVL028898@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv28824/db
Modified Files:
aaindex.rb gff.rb litdb.rb nbrf.rb
Log Message:
* s/Licence/License/
Index: litdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/litdb.rb,v
retrieving revision 0.6
retrieving revision 0.7
diff -C2 -d -r0.6 -r0.7
*** litdb.rb 7 Nov 2005 14:28:12 -0000 0.6
--- litdb.rb 18 Dec 2005 15:58:41 -0000 0.7
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2001 KATAYAMA Toshiaki
! # Licence:: LGPL
#
# $Id$
--- 3,7 ----
#
# Copyright:: Copyright (C) 2001 KATAYAMA Toshiaki
! # License:: LGPL
#
# $Id$
Index: aaindex.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/aaindex.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** aaindex.rb 8 Nov 2005 02:13:44 -0000 1.15
--- aaindex.rb 18 Dec 2005 15:58:41 -0000 1.16
***************
*** 3,7 ****
#
# Copyright:: Copyright (C) 2001 KAWASHIMA Shuichi
! # Licence:: LGPL
#
# $Id$
--- 3,7 ----
#
# Copyright:: Copyright (C) 2001 KAWASHIMA Shuichi
! # License:: LGPL
#
# $Id$
Index: nbrf.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/nbrf.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** nbrf.rb 1 Nov 2005 05:32:24 -0000 1.6
--- nbrf.rb 18 Dec 2005 15:58:41 -0000 1.7
***************
*** 4,8 ****
# Copyright:: Copyright (C) 2001-2003 GOTO Naohisa
# Copyright (C) 2001-2002 KATAYAMA Toshiaki
! # Licence:: LGPL
#
#--
--- 4,8 ----
# Copyright:: Copyright (C) 2001-2003 GOTO Naohisa
# Copyright (C) 2001-2002 KATAYAMA Toshiaki
! # License:: LGPL
#
#--
Index: gff.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/gff.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** gff.rb 7 Nov 2005 13:19:17 -0000 1.4
--- gff.rb 18 Dec 2005 15:58:41 -0000 1.5
***************
*** 2,9 ****
# = bio/db/gff.rb - GFF format class
#
! # Copyright:: Copyright (C) 2003 KATAYAMA Toshiaki
! # Licence:: LGPL
#
! # $Id$
#
# == Description
--- 2,10 ----
# = bio/db/gff.rb - GFF format class
#
! # Copyright:: Copyright (C) 2003, 2005
! # Toshiaki Katayama
! # License:: LGPL
#
! # $Id$
#
# == Description
***************
*** 11,15 ****
--- 12,19 ----
#
# == Example
+ #
+ #
# == References
+ #
# * http://www.sanger.ac.uk/Software/formats/GFF/
#
***************
*** 35,122 ****
module Bio
! # = GFF
! class GFF
! # Returns
! attr_accessor :records
! #
! def initialize(str = '')
! @records = Array.new
! str.each_line do |line|
! @records << Record.new(line)
! end
end
! # = GFF::Record
! class Record
!
! # Returns
! attr_accessor :seqname
!
! # Returns
! attr_accessor :source
!
! # Returns
! attr_accessor :feature
!
! # Returns
! attr_accessor :start
!
! # Returns
! attr_accessor :end
!
! # Returns
! attr_accessor :score
!
! # Returns
! attr_accessor :strand
!
! # Returns
! attr_accessor :frame
!
! # Returns
! attr_accessor :attributes
! # Returns
! attr_accessor :comments
! #
! def initialize(str)
! @comments = str.chomp[/#.*/]
! return if /^#/.match(str)
! @seqname, @source, @feature, @start, @end, @score, @strand, @frame,
! attributes, = str.chomp.split("\t")
! @attributes = parse_attributes(attributes) if attributes
! end
! private
! def parse_attributes(attributes)
! hash = Hash.new
! attributes.split(/[^\\];/).each do |atr|
! key, value = atr.split(' ', 2)
! hash[key] = value
! end
! return hash
end
end
end
- # = GFF2
class GFF2 < GFF
-
- #
VERSION = 2
end
- # = GFF3
class GFF3 < GFF
-
- #
VERSION = 3
end
! end
--- 39,97 ----
module Bio
! class GFF
! attr_accessor :records
! def initialize(str = '')
! @records = Array.new
! str.each_line do |line|
! @records << Record.new(line)
end
+ end
! class Record
! attr_accessor :seqname
! attr_accessor :source
! attr_accessor :feature
! attr_accessor :start
! attr_accessor :end
! attr_accessor :score
! attr_accessor :strand
! attr_accessor :frame
! attr_accessor :attributes
! attr_accessor :comments
! def initialize(str)
! @comments = str.chomp[/#.*/]
! return if /^#/.match(str)
! @seqname, @source, @feature, @start, @end, @score, @strand, @frame,
! attributes, = str.chomp.split("\t")
! @attributes = parse_attributes(attributes) if attributes
! end
! private
! def parse_attributes(attributes)
! hash = Hash.new
! attributes.split(/[^\\];/).each do |atr|
! key, value = atr.split(' ', 2)
! hash[key] = value
end
+ return hash
end
end
class GFF2 < GFF
VERSION = 2
end
class GFF3 < GFF
VERSION = 3
end
! end # class GFF
!
! end # module Bio
From nakao at pub.open-bio.org Sun Dec 18 11:56:08 2005
From: nakao at pub.open-bio.org (Mitsuteru C. Nakao)
Date: Sun Dec 18 11:48:56 2005
Subject: [BioRuby-cvs] bioruby/test/data/genscan - New directory
Message-ID: <200512181656.jBIGu8VL029439@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/data/genscan
In directory pub.open-bio.org:/tmp/cvs-serv29429/test/data/genscan
Log Message:
Directory /home/repository/bioruby/bioruby/test/data/genscan added to the repository
From nakao at pub.open-bio.org Sun Dec 18 11:56:38 2005
From: nakao at pub.open-bio.org (Mitsuteru C. Nakao)
Date: Sun Dec 18 11:49:28 2005
Subject: [BioRuby-cvs] bioruby/test/data/genscan sample.report,NONE,1.1
Message-ID: <200512181656.jBIGucVL029476@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/data/genscan
In directory pub.open-bio.org:/tmp/cvs-serv29466/test/data/genscan
Added Files:
sample.report
Log Message:
* Newly added.
--- NEW FILE: sample.report ---
GENSCAN 1.0 Date run: 30-May-103 Time: 14:06:28
Sequence HUMRASH : 12942 bp : 68.17% C+G : Isochore 4 (57 - 100 C+G%)
Parameter matrix: HumanIso.smat
Predicted genes/exons:
Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------
1.01 Init + 1664 1774 111 1 0 94 83 212 0.997 21.33
1.02 Intr + 2042 2220 179 1 2 104 66 408 0.997 40.12
1.03 Intr + 2374 2533 160 1 1 89 94 302 0.999 32.08
1.04 Term + 3231 3350 120 2 0 115 48 202 0.980 18.31
1.05 PlyA + 3722 3727 6 -5.80
2.00 Prom + 6469 6508 40 -7.92
2.01 Init + 8153 8263 111 1 0 94 83 212 0.998 21.33
2.02 Intr + 8531 8709 179 1 2 104 66 408 0.997 40.12
2.03 Intr + 8863 9022 160 1 1 89 94 302 0.999 32.08
2.04 Term + 9720 9839 120 2 0 115 48 202 0.961 18.31
Predicted peptide sequence(s):
Predicted coding sequence(s):
>HUMRASH|GENSCAN_predicted_peptide_1|189_aa
MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
CMSCKCVLS
>HUMRASH|GENSCAN_predicted_CDS_1|570_bp
atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgacc
atccagctgatccagaaccattttgtggacgaatacgaccccactatagaggattcctac
cggaagcaggtggtcattgatggggagacgtgcctgttggacatcctggataccgccggc
caggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgt
gtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatc
aaacgggtgaaggactcggatgacgtgcccatggtgctggtggggaacaagtgtgacctg
gctgcacgcactgtggaatctcggcaggctcaggacctcgcccgaagctacggcatcccc
tacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtg
cgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggc
tgcatgagctgcaagtgtgtgctctcctga
>HUMRASH|GENSCAN_predicted_peptide_2|189_aa
MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
QEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDL
AARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPG
CMSCKCVLS
>HUMRASH|GENSCAN_predicted_CDS_2|570_bp
atgacggaatataagctggtggtggtgggcgccggcggtgtgggcaagagtgcgctgacc
atccagctgatccagaaccattttgtggacgaatacgaccccactatagaggattcctac
cggaagcaggtggtcattgatggggagacgtgcctgttggacatcctggataccgccggc
caggaggagtacagcgccatgcgggaccagtacatgcgcaccggggagggcttcctgtgt
gtgtttgccatcaacaacaccaagtcttttgaggacatccaccagtacagggagcagatc
aaacgggtgaaggactcggatgacgtgcccatggtgctggtggggaacaagtgtgacctg
gctgcacgcactgtggaatctcggcaggctcaggacctcgcccgaagctacggcatcccc
tacatcgagacctcggccaagacccggcagggagtggaggatgccttctacacgttggtg
cgtgagatccggcagcacaagctgcggaagctgaaccctcctgatgagagtggccccggc
tgcatgagctgcaagtgtgtgctctcctga
From k at pub.open-bio.org Sun Dec 18 11:57:18 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 11:50:06 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio test_shell.rb,1.2,1.3
Message-ID: <200512181657.jBIGvIVL029504@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory pub.open-bio.org:/tmp/cvs-serv29415/test/unit/bio
Modified Files:
test_shell.rb
Log Message:
* removed some test methods as the test targets (global variables) are already removed
Index: test_shell.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_shell.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_shell.rb 23 Nov 2005 11:49:50 -0000 1.2
--- test_shell.rb 18 Dec 2005 16:57:15 -0000 1.3
***************
*** 31,42 ****
class TestShell < Test::Unit::TestCase
- def test_const_bioruby_config
- assert_equal({}, $bioruby_config)
- end
-
- def test_const_bioruby_cache
- assert_equal({}, $bioruby_cache)
- end
-
end
end
--- 31,34 ----
From nakao at pub.open-bio.org Sun Dec 18 11:59:00 2005
From: nakao at pub.open-bio.org (Mitsuteru C. Nakao)
Date: Sun Dec 18 11:51:47 2005
Subject: [BioRuby-cvs] bioruby/lib/bio reference.rb,1.17,1.18
Message-ID: <200512181659.jBIGx0VL029575@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv29565/lib/bio
Modified Files:
reference.rb
Log Message:
* Removed TAB.
Index: reference.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/reference.rb,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** reference.rb 8 Sep 2005 01:22:08 -0000 1.17
--- reference.rb 18 Dec 2005 16:58:58 -0000 1.18
***************
*** 27,45 ****
def initialize(hash)
hash.default = ''
! @authors = hash['authors'] # [ "Hoge, J.P.", "Fuga, F.B." ]
! @title = hash['title'] # "Title of the study."
! @journal = hash['journal'] # "Theor. J. Hoge"
! @volume = hash['volume'] # 12
! @issue = hash['issue'] # 3
! @pages = hash['pages'] # 123-145
! @year = hash['year'] # 2001
! @pubmed = hash['pubmed'] # 12345678
! @medline = hash['medline'] # 98765432
! @abstract = hash['abstract']
! @url = hash['url']
! @mesh = hash['mesh']
@affiliations = hash['affiliations']
! @authors = [] if @authors.empty?
! @mesh = [] if @mesh.empty?
@affiliations = [] if @affiliations.empty?
end
--- 27,45 ----
def initialize(hash)
hash.default = ''
! @authors = hash['authors'] # [ "Hoge, J.P.", "Fuga, F.B." ]
! @title = hash['title'] # "Title of the study."
! @journal = hash['journal'] # "Theor. J. Hoge"
! @volume = hash['volume'] # 12
! @issue = hash['issue'] # 3
! @pages = hash['pages'] # 123-145
! @year = hash['year'] # 2001
! @pubmed = hash['pubmed'] # 12345678
! @medline = hash['medline'] # 98765432
! @abstract = hash['abstract']
! @url = hash['url']
! @mesh = hash['mesh']
@affiliations = hash['affiliations']
! @authors = [] if @authors.empty?
! @mesh = [] if @mesh.empty?
@affiliations = [] if @affiliations.empty?
end
From k at pub.open-bio.org Sun Dec 18 12:00:12 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 11:53:01 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio test_shell.rb,1.3,1.4
Message-ID: <200512181700.jBIH0CVL029640@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio
In directory pub.open-bio.org:/tmp/cvs-serv29620/test/unit/bio
Modified Files:
test_shell.rb
Log Message:
* removed class to avoid test failure with 'No tests were specified.'
Index: test_shell.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/test_shell.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** test_shell.rb 18 Dec 2005 16:57:15 -0000 1.3
--- test_shell.rb 18 Dec 2005 17:00:10 -0000 1.4
***************
*** 26,34 ****
require 'test/unit'
! require 'bio/shell'
module Bio
- class TestShell < Test::Unit::TestCase
-
- end
end
--- 26,31 ----
require 'test/unit'
! require 'bioruby'
module Bio
end
From nakao at pub.open-bio.org Sun Dec 18 12:06:58 2005
From: nakao at pub.open-bio.org (Mitsuteru C. Nakao)
Date: Sun Dec 18 11:59:47 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio/appl/blast test_xmlparser.rb,
1.2, 1.3
Message-ID: <200512181706.jBIH6wVL029705@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio/appl/blast
In directory pub.open-bio.org:/tmp/cvs-serv29695/test/unit/bio/appl/blast
Modified Files:
test_xmlparser.rb
Log Message:
* Fix a test data class.
Index: test_xmlparser.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/appl/blast/test_xmlparser.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_xmlparser.rb 22 Nov 2005 08:31:47 -0000 1.2
--- test_xmlparser.rb 18 Dec 2005 17:06:56 -0000 1.3
***************
*** 175,179 ****
class TestBlastReportIteration < Test::Unit::TestCase
def setup
! data = Bio::TestBlastData.data
report = Bio::Blast::Report.new(data)
@itr = report.iterations.first
--- 175,179 ----
class TestBlastReportIteration < Test::Unit::TestCase
def setup
! data = TestBlastFormat7XMLParserData.output
report = Bio::Blast::Report.new(data)
@itr = report.iterations.first
From nakao at pub.open-bio.org Sun Dec 18 12:08:31 2005
From: nakao at pub.open-bio.org (Mitsuteru C. Nakao)
Date: Sun Dec 18 12:01:23 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/db prosite.rb,0.11,0.12
Message-ID: <200512181708.jBIH8VVL029754@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv29744/lib/bio/db
Modified Files:
prosite.rb
Log Message:
* Added some RDoc documents.
Index: prosite.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/prosite.rb,v
retrieving revision 0.11
retrieving revision 0.12
diff -C2 -d -r0.11 -r0.12
*** prosite.rb 26 Sep 2005 13:00:06 -0000 0.11
--- prosite.rb 18 Dec 2005 17:08:29 -0000 0.12
***************
*** 1,6 ****
#
! # bio/db/prosite.rb - PROSITE database class
#
! # Copyright (C) 2001 KATAYAMA Toshiaki
#
# This library is free software; you can redistribute it and/or
--- 1,16 ----
#
! # = bio/db/prosite.rb - PROSITE database class
! #
! # Copyright:: Copyright (C) 2001 KATAYAMA Toshiaki
! # Licence:: LGPL
! #
! # $Id$
! #
! # == Description
#
! #
! # == Example
! # == References
! #--
#
# This library is free software; you can redistribute it and/or
***************
*** 18,22 ****
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! # $Id$
#
--- 28,32 ----
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! #++
#
***************
*** 27,32 ****
class PROSITE < EMBLDB
! DELIMITER = RS = "\n//\n"
! TAGSIZE = 5
def initialize(entry)
--- 37,49 ----
class PROSITE < EMBLDB
! # Delimiter
! DELIMITER = "\n//\n"
!
! # Delimiter
! RS = DELIMITER
!
! # Bio::DB API
! TAGSIZE = 5
!
def initialize(entry)
***************
*** 39,42 ****
--- 56,60 ----
# ID ENTRY_NAME; ENTRY_TYPE. (ENTRY_TYPE : PATTERN, MATRIX, RULE)
#
+ # Returns
def name
unless @data['ID']
***************
*** 45,48 ****
--- 63,68 ----
@data['ID']
end
+
+ # Returns
def division
unless @data['TYPE']
***************
*** 57,60 ****
--- 77,81 ----
# AC PSnnnnn;
#
+ # Returns
def ac
unless @data['AC']
***************
*** 63,66 ****
--- 84,88 ----
@data['AC']
end
+
alias entry_id ac
***************
*** 70,76 ****
--- 92,100 ----
# DT MMM-YYYY (CREATED); MMM-YYYY (DATA UPDATE); MMM-YYYY (INFO UPDATE).
#
+ # Returns
def dt
field_fetch('DT')
end
+
alias date dt
***************
*** 80,86 ****
--- 104,112 ----
# DE Description.
#
+ # Returns
def de
field_fetch('DE')
end
+
alias definition de
***************
*** 90,93 ****
--- 116,120 ----
# see - pa2re method
#
+ # Returns
def pa
field_fetch('PA')
***************
*** 96,99 ****
--- 123,127 ----
@data['PA']
end
+
alias pattern pa
***************
*** 103,109 ****
--- 131,139 ----
# see - ma2re method
#
+ # Returns
def ma
field_fetch('MA')
end
+
alias profile ma
***************
*** 115,121 ****
--- 145,153 ----
# The rule is described in ordinary English and is free-format.
#
+ # Returns
def ru
field_fetch('RU')
end
+
alias rule ru
***************
*** 138,141 ****
--- 170,174 ----
# profile because they are partial (fragment) sequences.
#
+ # Returns
def nr
unless @data['NR']
***************
*** 159,224 ****
--- 192,274 ----
@data['NR']
end
+
alias statistics nr
+ # Returns
def release
statistics['RELEASE']
end
+ # Returns
def swissprot_release_number
release.first
end
+ # Returns
def swissprot_release_sequences
release.last
end
+ # Returns
def total
statistics['TOTAL']
end
+ # Returns
def total_hits
total.first
end
+ # Returns
def total_sequences
total.last
end
+ # Returns
def positive
statistics['POSITIVE']
end
+ # Returns
def positive_hits
positive.first
end
+ # Returns
def positive_sequences
positive.last
end
+ # Returns
def unknown
statistics['UNKNOWN']
end
+ # Returns
def unknown_hits
unknown.first
end
+ # Returns
def unknown_sequences
unknown.last
end
+ # Returns
def false_pos
statistics['FALSE_POS']
end
+ # Returns
def false_positive_hits
false_pos.first
end
+ # Returns
def false_positive_sequences
false_pos.last
end
+ # Returns
def false_neg
statistics['FALSE_NEG']
***************
*** 226,229 ****
--- 276,280 ----
alias false_negative_hits false_neg
+ # Returns
def partial
statistics['PARTIAL']
***************
*** 242,245 ****
--- 293,297 ----
# by a program (because it is too unspecific).
#
+ # Returns
def cc
unless @data['CC']
***************
*** 252,257 ****
--- 304,311 ----
@data['CC']
end
+
alias comment cc
+ # Returns
def taxon_range(expand = nil)
range = comment['TAXO-RANGE']
***************
*** 272,279 ****
--- 326,335 ----
end
+ # Returns
def max_repeat
comment['MAX-REPEAT'].to_i
end
+ # Returns
def site
if comment['SITE']
***************
*** 283,286 ****
--- 339,343 ----
end
+ # Returns
def skip_flag
if comment['SKIP-FLAG'] == 'TRUE'
***************
*** 312,315 ****
--- 369,373 ----
# consideration.
#
+ # Returns
def dr
unless @data['DR']
***************
*** 324,329 ****
--- 382,389 ----
@data['DR']
end
+
alias sp_xref dr
+ # Returns
def list_xref(flag, by_name = nil)
ary = []
***************
*** 341,360 ****
--- 401,425 ----
end
+ # Returns
def list_truepositive(by_name = nil)
list_xref('T', by_name)
end
+ # Returns
def list_falsenegative(by_name = nil)
list_xref('F', by_name)
end
+ # Returns
def list_falsepositive(by_name = nil)
list_xref('P', by_name)
end
+ # Returns
def list_potentialhit(by_name = nil)
list_xref('P', by_name)
end
+ # Returns
def list_unknown(by_name = nil)
list_xref('?', by_name)
***************
*** 366,369 ****
--- 431,435 ----
# 3D name; [name2;...]
#
+ # Returns
def pdb_xref
unless @data['3D']
***************
*** 378,381 ****
--- 444,448 ----
# DO PDOCnnnnn;
#
+ # Returns
def pdoc_xref
@data['DO'] = fetch('DO').chomp(';')
***************
*** 421,424 ****
--- 488,492 ----
# translated as: Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val
#
+ # Returns
def pa2re(pattern)
pattern.gsub!(/\s/, '') # remove white spaces
***************
*** 442,445 ****
--- 510,514 ----
# prosite/profile.txt:
#
+ # Returns
def ma2re(matrix)
raise NotImplementedError
From nakao at pub.open-bio.org Sun Dec 18 12:09:55 2005
From: nakao at pub.open-bio.org (Mitsuteru C. Nakao)
Date: Sun Dec 18 12:03:08 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio/io test_soapwsdl.rb,NONE,1.1
Message-ID: <200512181709.jBIH9tVL029782@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio/io
In directory pub.open-bio.org:/tmp/cvs-serv29772/test/unit/bio/io
Added Files:
test_soapwsdl.rb
Log Message:
* Newly added.
--- NEW FILE: test_soapwsdl.rb ---
#
# test/unit/bio/io/test_soapwsdl.rb - Unit test for SOAP/WSDL
#
# Copyright (C) 2005 Mitsuteru Nakao
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: test_soapwsdl.rb,v 1.1 2005/12/18 17:09:53 nakao Exp $
#
require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)
require 'test/unit'
require 'bio/io/soapwsdl'
module Bio
class TestSOAPWSDL < Test::Unit::TestCase
def setup
@obj = Bio::SOAPWSDL
end
def test_methods
methods = ['wsdl', 'wsdl=', 'log', 'log=']
assert_equal(methods.sort, (@obj.instance_methods - Object.methods).sort)
end
end
end
From nakao at pub.open-bio.org Sun Dec 18 12:11:27 2005
From: nakao at pub.open-bio.org (Mitsuteru C. Nakao)
Date: Sun Dec 18 12:04:18 2005
Subject: [BioRuby-cvs]
bioruby/test/functional/bio/io test_soapwsdl.rb, NONE, 1.1
Message-ID: <200512181711.jBIHBRVL029836@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/functional/bio/io
In directory pub.open-bio.org:/tmp/cvs-serv29816/test/functional/bio/io
Added Files:
test_soapwsdl.rb
Log Message:
* Newly added.
--- NEW FILE: test_soapwsdl.rb ---
#
# test/functional/bio/io/test_soapwsdl.rb - Unit test for SOAP/WSDL
#
# Copyright (C) 2005 Mitsuteru Nakao
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this library; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
# $Id: test_soapwsdl.rb,v 1.1 2005/12/18 17:11:25 nakao Exp $
#
require 'pathname'
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
$:.unshift(libpath) unless $:.include?(libpath)
require 'test/unit'
require 'bio/io/soapwsdl'
module Bio
class TestSOAPWSDL < Test::Unit::TestCase
def setup
@wsdl = 'http://www.ebi.ac.uk/xembl/XEMBL.wsdl'
@obj = Bio::SOAPWSDL.new(@wsdl)
end
def test_wsdl
assert_equal(@wsdl, @obj.wsdl)
end
def test_set_wsdl
@obj.wsdl = 'http://soap.genome.jp/KEGG.wsdl'
assert_equal('http://soap.genome.jp/KEGG.wsdl', @obj.wsdl)
end
def test_log
assert_equal(nil, @obj.log)
end
def test_set_log
require 'stringio'
io = StringIO.new
@obj.log = io
assert_equal(StringIO, @obj.log.class)
end
end
end
From nakao at pub.open-bio.org Sun Dec 18 12:28:58 2005
From: nakao at pub.open-bio.org (Mitsuteru C. Nakao)
Date: Sun Dec 18 12:21:46 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/appl blast.rb,1.26,1.27
Message-ID: <200512181728.jBIHSwVL029938@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory pub.open-bio.org:/tmp/cvs-serv29928/lib/bio/appl
Modified Files:
blast.rb
Log Message:
* Removed TAB.
Index: blast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast.rb,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** blast.rb 26 Sep 2005 13:00:04 -0000 1.26
--- blast.rb 18 Dec 2005 17:28:55 -0000 1.27
***************
*** 40,53 ****
def initialize(program, db, opt = [], server = 'local')
! @program = program
! @db = db
! @server = server
@blastall = 'blastall'
! @matrix = nil
! @filter = nil
! @output = ''
! @parser = nil
begin
--- 40,53 ----
def initialize(program, db, opt = [], server = 'local')
! @program = program
! @db = db
! @server = server
@blastall = 'blastall'
! @matrix = nil
! @filter = nil
! @output = ''
! @parser = nil
begin
***************
*** 64,72 ****
end
end
! @options = [ *a ]
end
attr_accessor :program, :db, :options, :server, :blastall, :matrix, :filter
attr_reader :output, :format
! attr_writer :parser # to change :xmlparser, :rexml, :tab
def self.local(program, db, option = '')
--- 64,72 ----
end
end
! @options = [ *a ]
end
attr_accessor :program, :db, :options, :server, :blastall, :matrix, :filter
attr_reader :output, :format
! attr_writer :parser # to change :xmlparser, :rexml, :tab
def self.local(program, db, option = '')
***************
*** 97,102 ****
ary = []
input.each("\n") do |xml|
! xml.sub!(/[^<]*()/, '\1') # skip before tag
! next if xml.empty? # skip trailing no hits
if block_given?
yield Report.new(xml, parser)
--- 97,102 ----
ary = []
input.each("\n") do |xml|
! xml.sub!(/[^<]*()/, '\1') # skip before tag
! next if xml.empty? # skip trailing no hits
if block_given?
yield Report.new(xml, parser)
***************
*** 146,158 ****
form = {
! 'style' => 'raw',
! 'prog' => @program,
! 'dbname' => @db,
! 'sequence' => CGI.escape(query),
! 'other_param' => CGI.escape(make_command_line_unix(opt)),
! 'matrix' => matrix,
! 'filter' => filter,
! 'V_value' => 500, # default value for GenomeNet
! 'B_value' => 250, # default value for GenomeNet
'alignment_view' => 0,
}
--- 146,158 ----
form = {
! 'style' => 'raw',
! 'prog' => @program,
! 'dbname' => @db,
! 'sequence' => CGI.escape(query),
! 'other_param' => CGI.escape(make_command_line_unix(opt)),
! 'matrix' => matrix,
! 'filter' => filter,
! 'V_value' => 500, # default value for GenomeNet
! 'B_value' => 250, # default value for GenomeNet
'alignment_view' => 0,
}
From ngoto at pub.open-bio.org Sun Dec 18 12:33:34 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Sun Dec 18 12:26:22 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb atom.rb,1.4,1.5
Message-ID: <200512181733.jBIHXYVL029982@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory pub.open-bio.org:/tmp/cvs-serv29972
Modified Files:
atom.rb
Log Message:
removed Bio::PDB::Atom (and Bio::PDB::HetAtm)
Index: atom.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/atom.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** atom.rb 18 Dec 2005 15:09:46 -0000 1.4
--- atom.rb 18 Dec 2005 17:33:32 -0000 1.5
***************
*** 56,113 ****
end #class Coordinate
- # Bio::PDB::Atom is a class for atom data.
- # Each ATOM line is parsed into an Atom object.
- Atom = Struct.new(:serial, :element, :alt_loc, :x, :y, :z,
- :occ, :bfac, :residue)
- class Atom
- include Utils
- include Comparable
-
- #Returns a Coordinate class instance of the xyz positions
- def xyz
- Coordinate[ x, y, z ]
- end
-
- #Returns an array of the xyz positions
- def to_a
- [ x, y, z ]
- end
-
- #Sorts based on serial numbers
- def <=>(other)
- return serial <=> other.serial
- end
-
- #Stringifies to PDB format
- def to_s
- if element.length < 4
- elementOutput = sprintf(" %-3s", element)
- else
- elementOutput = element
- end
- sprintf("%-6s%5s %s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f",
- record_type,
- serial, elementOutput, alt_loc, residue.resName,
- residue.chain.id, residue.resSeq, residue.iCode,
- x, y, z, occ, bfac)
- end
-
- def record_name
- 'ATOM'
- end
- def record_type
- record_name
- end
- end #class Atom
-
- # Bio::PDB::HetAtm is a class for HETATM data.
- # Each HETATM line is parsed into an HetAtm object.
- # Since HetAtm inherits Atom class, please refer Atom class for usage.
- class HetAtm < Atom
- def record_name
- 'HETATM'
- end
- end #class HetAtm
-
end #class PDB
end #class Bio
--- 56,60 ----
end #class Coordinate
end #class PDB
end #class Bio
+
From ngoto at pub.open-bio.org Sun Dec 18 12:34:49 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Sun Dec 18 12:27:36 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb residue.rb,1.3,1.4
Message-ID: <200512181734.jBIHYnVL029999@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory pub.open-bio.org:/tmp/cvs-serv29989
Modified Files:
residue.rb
Log Message:
changed the ID generation codes
Index: residue.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/residue.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** residue.rb 18 Dec 2005 15:09:46 -0000 1.3
--- residue.rb 18 Dec 2005 17:34:47 -0000 1.4
***************
*** 52,58 ****
@id = nil
else
! @id = @resSeq.to_s << @iCode
if @hetatm
! @id = 'LIGAND' << @id
end
end
--- 52,58 ----
@id = nil
else
! @id = "#{@resSeq}#{@iCode.strip}"
if @hetatm
! @id = 'LIGAND' + @id
end
end
***************
*** 72,78 ****
def resSeq=(resSeq)
@resSeq = resSeq.to_i
! @id = resSeq.to_s << @iCode
if @hetatm
! @id = 'LIGAND' << @id
end
end
--- 72,78 ----
def resSeq=(resSeq)
@resSeq = resSeq.to_i
! @id = "#{@resSeq}#{@iCode.strip}"
if @hetatm
! @id = 'LIGAND' + @id
end
end
***************
*** 80,86 ****
def iCode=(iCode)
@iCode = iCode
! @id = @resSeq.to_s << iCode
if @hetatm
! @id = 'LIGAND' << @id
end
end
--- 80,86 ----
def iCode=(iCode)
@iCode = iCode
! @id = "#{@resSeq}#{@iCode.strip}"
if @hetatm
! @id = 'LIGAND' + @id
end
end
From ngoto at pub.open-bio.org Sun Dec 18 12:37:16 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Sun Dec 18 12:30:06 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/db/pdb pdb.rb,1.5,1.6
Message-ID: <200512181737.jBIHbGVL030018@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/db/pdb
In directory pub.open-bio.org:/tmp/cvs-serv30006
Modified Files:
pdb.rb
Log Message:
changed logics
It might work correctly, but would stil have many bugs.
Index: pdb.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/pdb/pdb.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** pdb.rb 18 Dec 2005 15:09:46 -0000 1.5
--- pdb.rb 18 Dec 2005 17:37:14 -0000 1.6
***************
*** 1196,1205 ****
}
- #Aha! Our entry into the world of PDB parsing, we initialise a PDB
- #object with the whole PDB file as a string
- #each PDB has an array of the lines of the original file
- #a bit memory-tastic! A hash of records and an array of models
- #also has an id
def initialize(str)
@data = str.split(/[\r\n]+/)
--- 1196,1205 ----
}
def initialize(str)
+ #Aha! Our entry into the world of PDB parsing, we initialise a PDB
+ #object with the whole PDB file as a string
+ #each PDB has an array of the lines of the original file
+ #a bit memory-tastic! A hash of records and an array of models
+ #also has an id
@data = str.split(/[\r\n]+/)
***************
*** 1236,1252 ****
end
! #The meat of the atom parsing - could be speeded up I think
case key
! when 'ATOM', 'HETATM'
#Each model has a special solvent chain
#any chain id with the solvent is lost
#I can fix this if really needed
! if key == 'HETATM' and f.resName == 'HOH'
solvent = Residue.new(f.resName, f.resSeq, f.iCode,
cModel.solvent, true)
! solvent_atom = f
f.residue = solvent
! solvent.addAtom(solvent_atom)
cModel.addSolvent(solvent)
--- 1236,1278 ----
end
! # Do something for ATOM and HETATM
case key
! when 'ATOM'
! residueID = "#{f.resSeq}#{f.iCode.strip}".strip
! #p f
!
! if f.chainID == cChain.id
! chain = cChain
! elsif !(chain = cModel[f.chainID])
! #If we don't have chain, add a new chain
! newChain = Chain.new(f.chainID, cModel)
! cModel.addChain(newChain)
! cChain = newChain
! chain = newChain
! end
!
! if !newChain and residueID == cResidue.id
! residue = cResidue
! elsif newChain or !(residue = chain[residueID])
! newResidue = Residue.new(f.resName, f.resSeq, f.iCode, chain)
! chain.addResidue(newResidue)
! cResidue = newResidue
! residue = newResidue
! end
!
! f.residue = residue
! residue.addAtom(f)
!
! when 'HETATM'
#Each model has a special solvent chain
#any chain id with the solvent is lost
#I can fix this if really needed
! if f.resName == 'HOH'
solvent = Residue.new(f.resName, f.resSeq, f.iCode,
cModel.solvent, true)
! #p solvent
f.residue = solvent
! solvent.addAtom(f)
cModel.addSolvent(solvent)
***************
*** 1257,1317 ****
#numbers for HETATMS
residueID = "#{f.resSeq}#{f.iCode.strip}".strip
! if key == 'HETATM'
! residueID = "LIGAND" + residueID
! end
!
! #If this atom is part of the current residue then add it to
! #the current residue straight away
! if f.chainID == cChain.id and residueID == cResidue.id
!
! #If we have this chain and residue just add the atom
! atom = f
! f.residue = cResidue
! cResidue.addAtom(atom)
! elsif !cModel[f.chainID]
!
! #If we don't have anyhting, add a new chain, residue and atom
! newChain = Chain.new(f.chainID, cModel)
cModel.addChain(newChain)
!
! if key == 'ATOM'
! newResidue = Residue.new(f.resName, f.resSeq, f.iCode,
! newChain)
! newChain.addResidue(newResidue)
! else
! newResidue = Residue.new(f.resName, f.resSeq, f.iCode,
! newChain, true)
! newChain.addLigand(newResidue)
! end
! atom = f
! f.residue = newResidue
! newResidue.addAtom(atom)
!
! cChain = newChain
! cResidue = newResidue
!
! elsif !cModel[f.chainID][residueID]
! #If we have the chain (but not the residue)
! #make a new residue, add it and add the atom
! chain = cModel[f.chainID]
!
! if key == 'ATOM'
! newResidue = Residue.new(f.resName, f.resSeq, f.iCode,
! chain)
! chain.addResidue(newResidue)
! else
! newResidue = Residue.new(f.resName, f.resSeq, f.iCode,
! chain, true)
! chain.addLigand(newResidue)
! end
!
! atom = f
! f.residue = newResidue
! newResidue.addAtom(atom)
cResidue = newResidue
!
end
end
--- 1283,1313 ----
#numbers for HETATMS
residueID = "#{f.resSeq}#{f.iCode.strip}".strip
! residueID = "LIGAND" + residueID
! #p f
! #p residueID
! if f.chainID == cChain.id
! chain = cChain
! elsif !(chain = cModel[f.chainID])
! #If we don't have chain, add a new chain
! newChain = Chain.new(f.chainID, cModel)
cModel.addChain(newChain)
! cChain = newChain
! chain = newChain
! end
! if !newChain and residueID == cResidue.id
! residue = cResidue
! elsif newChain or !(residue = chain[residueID])
! newResidue = Residue.new(f.resName, f.resSeq, f.iCode,
! chain, true)
! chain.addLigand(newResidue)
cResidue = newResidue
! residue = newResidue
end
+
+ f.residue = residue
+ residue.addAtom(f)
+
end
From nakao at pub.open-bio.org Sun Dec 18 12:43:53 2005
From: nakao at pub.open-bio.org (Mitsuteru C. Nakao)
Date: Sun Dec 18 12:36:42 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio/db/embl test_uniprot.rb, 1.2,
1.3
Message-ID: <200512181743.jBIHhrVL030050@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio/db/embl
In directory pub.open-bio.org:/tmp/cvs-serv30040/test/unit/bio/db/embl
Modified Files:
test_uniprot.rb
Log Message:
* Removed redundunt test codes.
Index: test_uniprot.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/embl/test_uniprot.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_uniprot.rb 23 Nov 2005 10:12:09 -0000 1.2
--- test_uniprot.rb 18 Dec 2005 17:43:51 -0000 1.3
***************
*** 37,170 ****
end
- def test_id_line
- assert(@obj.id_line)
- end
- def test_id_line_entry_name
- assert_equal('P53_HUMAN', @obj.id_line('ENTRY_NAME'))
- end
- def test_id_line_data_class
- assert_equal('STANDARD', @obj.id_line('DATA_CLASS'))
- end
- def test_id_line_molecule_type
- assert_equal('PRT', @obj.id_line('MOLECULE_TYPE'))
- end
- def test_id_line_sequence_length
- assert_equal(393, @obj.id_line('SEQUENCE_LENGTH'))
- end
-
-
- def test_ac
- assert_equal([], @obj.ac)
- assert_equal([], @obj.acccessions)
- end
- def test_accession
- assert_equal('', @obj.accession)
- end
-
- def test_de
- assert(@obj.de)
- end
-
- def test_protein_name
- assert_equal("Cellular tumor antigen p53", @obj.protein_name)
- end
-
- def test_synonyms
- assert_equal(["Tumor suppressor p53", "Phosphoprotein p53", "Antigen NY-CO-13"], @obj.synonyms)
- end
-
- def test_gn
- assert_equal([{:orfs=>[], :synonyms=>["P53"], :name=>"TP53", :loci=>[]}], @obj.gn)
- end
- def test_gn_uniprot_parser
- gn_uniprot_data = ''
- assert_equal('', @obj.instance_eval(gn_uniprot_parser(gn_uniprot_data)))
- end
- # def test_gn_old_parser
- # gn_old_data = ''
- # assert_equal('', @obj.instance_eval(gn_old_parser(gn_old_data)))
- # end
-
- def test_gene_names
- assert_equal(["TP53"], @obj.gene_names)
- end
-
def test_gene_name
assert_equal('TP53', @obj.gene_name)
end
- def test_os
- assert(@obj.os)
- end
-
- def test_os_access
- assert_equal({'name' => '', 'os' => ''}, @obj.os(1))
- end
-
- def test_os_access2
- assert_equal({}, @obj.os[1])
- end
-
-
- def test_cc
- data = ''
- assert_equal('', @obj.instance_eval(cc_scan_alternative_products(data)))
- data = ''
- assert_equal('', @obj.instance_eval(cc_scan_database(data)))
- data = ''
- assert_equal('', @obj.instance_eval(cc_scan_mass_spectorometry(data)))
-
- assert_equal([], @obj.cc)
- end
- def test_cc_database
- assert_equal([], @obj.cc('DATABASE'))
- end
- def test_cc_alternative_products
- assert_equal({}, @obj.cc('ALTERNATIVE PRODUCTS'))
- end
- def test_cc_mass_spectrometry
- assert_equal([], @obj.cc('MASS SPECTROMETRY'))
- end
-
- def test_cc_interaction
- data =<
Update of /home/repository/bioruby/bioruby/test/unit/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv30126/test/unit/bio/db
Modified Files:
test_fasta.rb
Log Message:
* fixed to pass all test, replaced the data with suitable one
Index: test_fasta.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_fasta.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_fasta.rb 23 Nov 2005 11:21:15 -0000 1.2
--- test_fasta.rb 18 Dec 2005 17:55:13 -0000 1.3
***************
*** 39,44 ****
! class TestFastaFormat < Test::Unit::TestCase
def setup
text =<gi|1171674|sp|P42267|NDD_BPR69 NUCLEAR DISRUPTION PROTEIN
! MKYMTVTDLNNAGATVIGTIKGGEWFLGTPHKDILSKPGFYFLVSKLDGRPFSNPCVSARFYVGNQRSKQGFSAVLSHIR
! QRRSQLARTIANNNMVYTVFYLPASKMKPLTTGFGKGQLALAFTRNHHSEYQTLEEMNRMLADNFKFVLQAY
! END
! @obj = Bio::FastaFormat.new(text)
! end
!
! def test_locus
! assert_equal(nil, @obj.locus)
! end
! end
!
! class TestFastaFormatKeggGenesNT < Test::Unit::TestCase
! def setup
! text =<eco:b0001 thrL; thr operon leader peptide (N)
! atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcg
! ggctga
! END
! @obj = Bio::FastaFormat.new(text)
! end
!
! def test_naseq_class
! assert_equal(Bio::Sequence::NA, @obj.naseq.class)
! end
!
! def test_naseq
! seq = 'atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcgggctga'
! assert_equal(seq, @obj.naseq)
! end
+ def test_nalen
+ assert_equal(66, @obj.nalen)
+ end
+ end
+
+ class TestFastaFormatKeggGenesAA < Test::Unit::TestCase
def setup
text =<gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]
! MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT
! IALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF
! TLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI
! LFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL
! >gi|55416190|gb|AAV50057.1| NADH dehydrogenase subunit 2 [Dasyurus hallucatus]
! MSPYVLMILTLSLFIGTCLTIFSNHWFTAWMGLEINTLAIIPLMTAPNNPRSTEAATKYFLTQATASMLMMFAIIYNAWS
! TNQWALPQLSDDWISLLMTVALAIKLGLAPFHFWVPEVTQGIPLLTGMILLTWQKIAPTAILFQIAPYLNMKFLVILAIL
! STLVGGWGGLNQTHLRKILAYSSIAHMGWMIIIVQINPTLSIFTLTIYVMATLTTFLTLNLSNSTKIKSLGNLWNKSATA
! TIIIFLTLLSLGGLPPLTGFMPKWLILQELINNGNIITATMMALSALLNLFFYMRLIYASSLTMFPSINNSKMQWYNNSM
! KTTTLIPTATVISSLLLPLTPLFVTLY
! END
! @obj = Bio::FastaFormat.new(text)
end
! def test_entry
! data = ">gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]\nMFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT\nIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF\nTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI\nLFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL\n"
! assert_equal(data, @obj.entry)
end
! def test_entry_id
! assert_equal('gi|55416189', @obj.entry_id)
end
! def test_definition
! data = "gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]"
! assert_equal(data, @obj.definition)
! end
!
! def test_data
! data = "\nMFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT\nIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF\nTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI\nLFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL\n"
! assert_equal(data, @obj.data)
! end
!
! def test_seq
! seq = 'MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALTIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSFTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTILFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL'
! assert_equal(seq, @obj.seq)
! end
!
! def test_length
! assert_equal(318, @obj.length)
end
def test_aaseq
! seq = "MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALTIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSFTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTILFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL"
assert_equal(seq, @obj.aaseq)
end
def test_aalen
! assert_equal(318, @obj.aalen)
end
def test_identifiers
! assert_equal(Bio::FastaDefline, @obj.identifiers.class)
end
def test_gi
! assert_equal('55416189', @obj.gi)
end
def test_accession
! assert_equal('AAV50056', @obj.accession)
end
def test_accessions
! assert_equal(['AAV50056'], @obj.accessions)
end
def test_acc_version
! assert_equal('AAV50056.1', @obj.acc_version)
end
From k at pub.open-bio.org Sun Dec 18 13:04:33 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 12:57:21 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio/db test_gff.rb,1.2,1.3
Message-ID: <200512181804.jBII4XVL030197@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv30193/test/unit/bio/db
Modified Files:
test_gff.rb
Log Message:
* fixed Errors and Failures
Index: test_gff.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_gff.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_gff.rb 23 Nov 2005 11:29:16 -0000 1.2
--- test_gff.rb 18 Dec 2005 18:04:31 -0000 1.3
***************
*** 55,59 ****
class TestGFF2 < Test::Unit::TestCase
def test_version
! assert_equal(2, Bio::GFF2::VERSION)
end
end
--- 55,59 ----
class TestGFF2 < Test::Unit::TestCase
def test_version
! assert_equal(2, Bio::GFF::GFF2::VERSION)
end
end
***************
*** 62,66 ****
class TestGFF3 < Test::Unit::TestCase
def test_version
! assert_equal(3, Bio::GFF3::VERSION)
end
end
--- 62,66 ----
class TestGFF3 < Test::Unit::TestCase
def test_version
! assert_equal(3, Bio::GFF::GFF3::VERSION)
end
end
***************
*** 109,118 ****
def test_attributes
! at = {"Note"=>"Chromosome I Centromere", "Gene"=>"CEN1"}
assert_equal(at, @obj.attributes)
end
def test_comments
! assert_equal('', @obj.comments)
end
--- 109,118 ----
def test_attributes
! at = {"Note"=>'"Chromosome I Centromere"', "Gene"=>'"CEN1"'}
assert_equal(at, @obj.attributes)
end
def test_comments
! assert_equal(nil, @obj.comments)
end
***************
*** 128,132 ****
def test_add_seqname
name = "test"
! record = Bio::GFF::Record.new
record.seqname = name
@obj.records << record
--- 128,132 ----
def test_add_seqname
name = "test"
! record = Bio::GFF::Record.new("")
record.seqname = name
@obj.records << record
From ngoto at pub.open-bio.org Sun Dec 18 13:20:36 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Sun Dec 18 13:13:27 2005
Subject: [BioRuby-cvs] bioruby ChangeLog,1.43,1.44
Message-ID: <200512181820.jBIIKaVL030314@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby
In directory pub.open-bio.org:/tmp/cvs-serv30301
Modified Files:
ChangeLog
Log Message:
added changelog for PDB classes
Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.43
retrieving revision 1.44
diff -C2 -d -r1.43 -r1.44
*** ChangeLog 5 Nov 2005 10:20:54 -0000 1.43
--- ChangeLog 18 Dec 2005 18:20:34 -0000 1.44
***************
*** 1,2 ****
--- 1,24 ----
+ 2005-12-19 Naohisa Goto
+
+ * lib/bio/db/pdb.rb, lib/bio/db/pdb/pdb.rb, lib/bio/db/pdb/*.rb
+ * Many changes have been made.
+ * Bio::PDB::FieldDef is removed and Bio::PDB::Record is completely
+ changed. Now, Record is changed from hash to Struct, and
+ method_missing is no longer used.
+ * In the "MODEL" record, model_serial is changed to serial.
+ * In any records, record_type is changed to record_name.
+ * In most records contains real numbers, changed to return
+ float values instead of strings.
+ * Pdb_AChar, Pdb_Atom, Pdb_Character, Pdb_Continuation,
+ Pdb_Date, Pdb_IDcode, Pdb_Integer, Pdb_LString, Pdb_List,
+ Pdb_Real, Pdb_Residue_name, Pdb_SList, Pdb_Specification_list,
+ Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
+ Bio::PDB::DataType.
+
+ * lib/bio/db/pdb/atom.rb
+ * Bio::PDB::Atom is removed.
+ Instead, please use Bio::PDB::Record::ATOM and
+ Bio::PDB::Record::HETATM.
+
2005-11-05 Toshiaki Katayama
From ngoto at pub.open-bio.org Sun Dec 18 13:20:36 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Sun Dec 18 13:13:49 2005
Subject: [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.9,1.10
Message-ID: <200512181820.jBIIKaVL030318@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/doc
In directory pub.open-bio.org:/tmp/cvs-serv30301/doc
Modified Files:
Changes-0.7.rd
Log Message:
added changelog for PDB classes
Index: Changes-0.7.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** Changes-0.7.rd 28 Nov 2005 04:57:32 -0000 1.9
--- Changes-0.7.rd 18 Dec 2005 18:20:34 -0000 1.10
***************
*** 165,168 ****
--- 165,186 ----
* Bio::GFF3 is renamed to Bio::GFF::GFF3
+ --- Bio::PDB
+
+ * Bio::PDB::Atom is removed. Instead, please use Bio::PDB::Record::ATOM and
+ Bio::PDB::Record::HETATM.
+ * Bio::PDB::FieldDef is removed and Bio::PDB::Record is completely
+ changed. Now, Record is changed from hash to Struct, and
+ method_missing is no longer used.
+ * In the "MODEL" record, model_serial is changed to serial.
+ * In records, record_type is changed to record_name.
+ * In any records, record_type is changed to record_name.
+ * In most records contains real numbers, changed to return
+ float values instead of strings.
+ * Pdb_AChar, Pdb_Atom, Pdb_Character, Pdb_Continuation,
+ Pdb_Date, Pdb_IDcode, Pdb_Integer, Pdb_LString, Pdb_List,
+ Pdb_Real, Pdb_Residue_name, Pdb_SList, Pdb_Specification_list,
+ Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
+ Bio::PDB::DataType.
+
=== Deleted files
From k at pub.open-bio.org Sun Dec 18 13:22:01 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 13:14:48 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio/db test_prosite.rb,1.2,1.3
Message-ID: <200512181822.jBIIM1VL030407@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv30403/test/unit/bio/db
Modified Files:
test_prosite.rb
Log Message:
* fixed to pass the tests
Index: test_prosite.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_prosite.rb,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** test_prosite.rb 23 Nov 2005 11:32:13 -0000 1.2
--- test_prosite.rb 18 Dec 2005 18:21:58 -0000 1.3
***************
*** 1438,1457 ****
def test_pa2re
! assert_equal('', @obj.pa2re)
! end
!
! def test_ma2re
! assert_raise(@obj.ma2re, NotImplementedError)
end
def test_self_pa2re
! assert(Bio::PROSITE.pattern2re)
! end
!
! def test_self_ma2re
! assert(Bio::PROSITE.profile2re)
end
-
end # class TestPROSITE
end
--- 1438,1450 ----
def test_pa2re
! pa = '[AC]-x-V-x(4)-{ED}.'
! assert_equal(/[AC].V.{4}[^ED]/, @obj.pa2re(pa))
end
def test_self_pa2re
! pa = '[AC]-x-V-x(4)-{ED}.'
! assert_equal(/[AC].V.{4}[^ED]/, Bio::PROSITE.pa2re(pa))
end
end # class TestPROSITE
end
From k at pub.open-bio.org Sun Dec 18 13:24:10 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 13:16:58 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/db prosite.rb,0.12,0.13
Message-ID: <200512181824.jBIIOAVL030508@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv30504/lib/bio/db
Modified Files:
prosite.rb
Log Message:
* fixed to pass the tests
* class method Bio::PROSITE.pa2re(pattern) #=> regexp is added
* pdb_xref method is fixed to remove ; from the last entry
Index: prosite.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/prosite.rb,v
retrieving revision 0.12
retrieving revision 0.13
diff -C2 -d -r0.12 -r0.13
*** prosite.rb 18 Dec 2005 17:08:29 -0000 0.12
--- prosite.rb 18 Dec 2005 18:24:08 -0000 0.13
***************
*** 434,438 ****
def pdb_xref
unless @data['3D']
! @data['3D'] = fetch('3D').split(/; /)
end
@data['3D']
--- 434,438 ----
def pdb_xref
unless @data['3D']
! @data['3D'] = fetch('3D').split(/; */)
end
@data['3D']
***************
*** 488,493 ****
# translated as: Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val
#
! # Returns
! def pa2re(pattern)
pattern.gsub!(/\s/, '') # remove white spaces
pattern.sub!(/\.$/, '') # (1) remove trailing '.'
--- 488,492 ----
# translated as: Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val
#
! def self.pa2re(pattern)
pattern.gsub!(/\s/, '') # remove white spaces
pattern.sub!(/\.$/, '') # (1) remove trailing '.'
***************
*** 503,506 ****
--- 502,509 ----
pattern.tr!('-', '') # (6) each element is separated by a '-'
Regexp.new(pattern)
+ end
+
+ def pa2re(pattern)
+ self.class.pa2re(pattern)
end
From ngoto at pub.open-bio.org Sun Dec 18 13:44:28 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Sun Dec 18 13:37:17 2005
Subject: [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.10,1.11
Message-ID: <200512181844.jBIIiSVL030701@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/doc
In directory pub.open-bio.org:/tmp/cvs-serv30685/doc
Modified Files:
Changes-0.7.rd
Log Message:
* added changelogs for Bio::Alignment
* added "to be written..." to changelogs of Bio::PDB
Index: Changes-0.7.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Changes-0.7.rd 18 Dec 2005 18:20:34 -0000 1.10
--- Changes-0.7.rd 18 Dec 2005 18:44:26 -0000 1.11
***************
*** 165,168 ****
--- 165,186 ----
* Bio::GFF3 is renamed to Bio::GFF::GFF3
+ --- Bio::Alignment
+
+ * Old Bio::Alignment class is renamed to Bio::Alignment::OriginalAlignment.
+ Now, new Bio::Alignment is a module. However, you don't mind so much
+ because most of the class methods previously existed are defined
+ to delegate to the new Bio::Alignment::OriginalAlignment class,
+ for keeping backward compatibility.
+ * New classes and modules are introduced. Please refer RDoc.
+ * each_site and some methods changed to return Bio::Alignment::Site,
+ which inherits Array (previously returned Array).
+ * consensus_iupac now returns only standard bases
+ 'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v',
+ 'h', 'd', 'b', 'n', or nil (in SiteMethods#consensus_iupac) or
+ '?' (or missing_char, in EnumerableExtension#consensus_iupac).
+ Note that consensus_iupac now does not return u and invalid letters
+ not defined in IUPAC standard even if all bases are equal.
+ * There are more and more changes to be written...
+
--- Bio::PDB
***************
*** 182,185 ****
--- 200,204 ----
Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
Bio::PDB::DataType.
+ * There are more and more changes to be written...
=== Deleted files
From ngoto at pub.open-bio.org Sun Dec 18 13:44:28 2005
From: ngoto at pub.open-bio.org (Naohisa Goto)
Date: Sun Dec 18 13:37:19 2005
Subject: [BioRuby-cvs] bioruby ChangeLog,1.44,1.45
Message-ID: <200512181844.jBIIiRVL030697@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby
In directory pub.open-bio.org:/tmp/cvs-serv30685
Modified Files:
ChangeLog
Log Message:
* added changelogs for Bio::Alignment
* added "to be written..." to changelogs of Bio::PDB
Index: ChangeLog
===================================================================
RCS file: /home/repository/bioruby/bioruby/ChangeLog,v
retrieving revision 1.44
retrieving revision 1.45
diff -C2 -d -r1.44 -r1.45
*** ChangeLog 18 Dec 2005 18:20:34 -0000 1.44
--- ChangeLog 18 Dec 2005 18:44:25 -0000 1.45
***************
*** 15,18 ****
--- 15,19 ----
Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
Bio::PDB::DataType.
+ * There are more and more changes to be written...
* lib/bio/db/pdb/atom.rb
***************
*** 20,23 ****
--- 21,46 ----
Instead, please use Bio::PDB::Record::ATOM and
Bio::PDB::Record::HETATM.
+
+ 2005-12-02 Naohisa Goto
+
+ * lib/bio/alignment.rb
+ * Old Bio::Alignment class is renamed to
+ Bio::Alignment::OriginalAlignment.
+ Now, new Bio::Alignment is a module. However,
+ you don't mind so much because most of the class methods
+ previously existed are defined to delegate to the new
+ Bio::Alignment::OriginalAlignment class,
+ for keeping backward compatibility.
+ * New classes and modules are introduced. Please refer RDoc.
+ * each_site and some methods changed to return Bio::Alignment::Site,
+ which inherits Array (previously returned Array).
+ * consensus_iupac now returns only standard bases
+ 'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v',
+ 'h', 'd', 'b', 'n', or nil (in SiteMethods#consensus_iupac) or
+ '?' (or missing_char, in EnumerableExtension#consensus_iupac).
+ Note that consensus_iupac now does not return u and invalid
+ letters not defined in IUPAC standard even if all bases
+ are equal.
+ * There are more and more changes to be written...
2005-11-05 Toshiaki Katayama
From k at pub.open-bio.org Sun Dec 18 14:10:57 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 14:03:46 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/io keggapi.rb,1.10,1.11
Message-ID: <200512181910.jBIJAvVL030900@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory pub.open-bio.org:/tmp/cvs-serv30891/lib/bio/io
Modified Files:
keggapi.rb
Log Message:
* get_neighbors_by_gene method no more available on the server side
since some while ago
Index: keggapi.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/keggapi.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** keggapi.rb 25 Nov 2005 11:28:30 -0000 1.10
--- keggapi.rb 18 Dec 2005 19:10:55 -0000 1.11
***************
*** 51,57 ****
end
! def get_all_neighbors_by_gene(genes_id, org)
! get_all(:get_neighbors_by_gene, genes_id, org)
! end
def get_all_best_best_neighbors_by_gene(genes_id)
--- 51,57 ----
end
! # def get_all_neighbors_by_gene(genes_id, org)
! # get_all(:get_neighbors_by_gene, genes_id, org)
! # end
def get_all_best_best_neighbors_by_gene(genes_id)
***************
*** 826,830 ****
--- btit(string)
--- get_linkdb_by_entry(entry_id, db, start, max_results)
! --- get_neighbors_by_gene(genes_id, org, start, max_results)
--- get_best_best_neighbors_by_gene(genes_id, start, max_results)
--- get_best_neighbors_by_gene(genes_id, start, max_results)
--- 826,830 ----
--- btit(string)
--- get_linkdb_by_entry(entry_id, db, start, max_results)
! #--- get_neighbors_by_gene(genes_id, org, start, max_results)
--- get_best_best_neighbors_by_gene(genes_id, start, max_results)
--- get_best_neighbors_by_gene(genes_id, start, max_results)
From k at pub.open-bio.org Sun Dec 18 14:13:12 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 14:05:59 2005
Subject: [BioRuby-cvs] bioruby/doc Changes-0.7.rd,1.11,1.12
Message-ID: <200512181913.jBIJDCVL030937@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/doc
In directory pub.open-bio.org:/tmp/cvs-serv30933/doc
Modified Files:
Changes-0.7.rd
Log Message:
* changes on the Pathway is delayed
Index: Changes-0.7.rd
===================================================================
RCS file: /home/repository/bioruby/bioruby/doc/Changes-0.7.rd,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** Changes-0.7.rd 18 Dec 2005 18:44:26 -0000 1.11
--- Changes-0.7.rd 18 Dec 2005 19:13:09 -0000 1.12
***************
*** 116,125 ****
can be proposed. Until then, this class is removed.
! --- Bio::Pathway
!
! * Bio::Pathway#nodes returns an Array of the node objects instead of
! the number of the node objects.
! * Bio::Pathway#edges returns an Array of the edge objects instead of
! the number of the edge objects.
--- Bio::GenBank
--- 116,129 ----
can be proposed. Until then, this class is removed.
! #
! # Following changes are suspended for a while (not yet introduced for now)
! #
! # --- Bio::Pathway
! #
! # * Bio::Pathway#nodes returns an Array of the node objects instead of
! # the number of the node objects.
! # * Bio::Pathway#edges returns an Array of the edge objects instead of
! # the number of the edge objects.
! #
--- Bio::GenBank
From k at pub.open-bio.org Sun Dec 18 20:20:08 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 20:12:56 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/shell/plugin seq.rb,1.15,1.16
Message-ID: <200512190120.jBJ1K8VL031540@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv31531/lib/bio/shell/plugin
Modified Files:
seq.rb
Log Message:
* removed comment
Index: seq.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/seq.rb,v
retrieving revision 1.15
retrieving revision 1.16
diff -C2 -d -r1.15 -r1.16
*** seq.rb 28 Nov 2005 12:07:42 -0000 1.15
--- seq.rb 19 Dec 2005 01:20:06 -0000 1.16
***************
*** 96,100 ****
hash[codon] = percent
end
! rep << codontable(1, hash).output #*TODO* how to hide?
begin
--- 96,100 ----
hash[codon] = percent
end
! rep << codontable(1, hash).output
begin
From k at pub.open-bio.org Sun Dec 18 20:21:45 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 20:14:30 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio/db test_gff.rb,1.3,1.4
Message-ID: <200512190121.jBJ1LjVL031672@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio/db
In directory pub.open-bio.org:/tmp/cvs-serv31668/test/unit/bio/db
Modified Files:
test_gff.rb
Log Message:
* separate a test method
Index: test_gff.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/db/test_gff.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** test_gff.rb 18 Dec 2005 18:04:31 -0000 1.3
--- test_gff.rb 19 Dec 2005 01:21:42 -0000 1.4
***************
*** 47,50 ****
--- 47,53 ----
def test_records
assert_equal(8, @obj.records.size)
+ end
+
+ def test_record_class
assert_equal(Bio::GFF::Record, @obj.records[0].class)
end
From k at pub.open-bio.org Sun Dec 18 21:34:27 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 21:27:14 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/shell/plugin codon.rb,1.11,1.12
Message-ID: <200512190234.jBJ2YRVL031865@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv31861/lib/bio/shell/plugin
Modified Files:
codon.rb
Log Message:
* fixed to pass the unit test (not output escape sequence in mono mode, completely)
Index: codon.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/codon.rb,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** codon.rb 7 Dec 2005 07:31:40 -0000 1.11
--- codon.rb 19 Dec 2005 02:34:24 -0000 1.12
***************
*** 178,182 ****
text = header + table
end
! text.gsub(/^\s+#/, @colors[:text])
end
--- 178,186 ----
text = header + table
end
! if Bio::Shell.config[:color]
! text.gsub(/^\s+#/, @colors[:text])
! else
! text.gsub(/^\s+#/, '')
! end
end
From k at pub.open-bio.org Sun Dec 18 21:44:06 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Sun Dec 18 21:36:54 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio/shell/plugin test_seq.rb, 1.4,
1.5
Message-ID: <200512190244.jBJ2i6VL031930@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv31926/test/unit/bio/shell/plugin
Modified Files:
test_seq.rb
Log Message:
* modified to supress puts during tests
Index: test_seq.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/shell/plugin/test_seq.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** test_seq.rb 18 Dec 2005 16:28:46 -0000 1.4
--- test_seq.rb 19 Dec 2005 02:44:03 -0000 1.5
***************
*** 100,104 ****
//
END
! assert_equal(output, seqstat(naseq))
end
--- 100,114 ----
//
END
! $str = ''
! alias puts_orig puts
! def puts(*args)
! args.each do |obj|
! $str << obj.to_s
! end
! end
! seqstat(naseq)
! undef puts
! alias puts puts_orig
! assert_equal(output, $str)
end
***************
*** 116,120 ****
//
END
! assert_equal(output, seqstat(aaseq))
end
--- 126,140 ----
//
END
! $str = ''
! alias puts_orig puts
! def puts(*args)
! args.each do |obj|
! $str << obj.to_s
! end
! end
! seqstat(aaseq)
! undef puts
! alias puts puts_orig
! assert_equal(output, $str)
end
***************
*** 139,147 ****
at
END
! $doublehelix = ''
alias puts_orig puts
def puts(*args)
args.each do |obj|
! $doublehelix << obj.to_s
end
end
--- 159,167 ----
at
END
! $str = ''
alias puts_orig puts
def puts(*args)
args.each do |obj|
! $str << obj.to_s
end
end
***************
*** 149,153 ****
undef puts
alias puts puts_orig
! assert_equal(output, $doublehelix)
end
--- 169,173 ----
undef puts
alias puts puts_orig
! assert_equal(output, $str)
end
From k at pub.open-bio.org Tue Dec 27 12:27:40 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Tue Dec 27 12:19:35 2005
Subject: [BioRuby-cvs] bioruby/lib/bio/util sirna.rb,1.6,1.7
Message-ID: <200512271727.jBRHReVL000863@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/lib/bio/util
In directory pub.open-bio.org:/tmp/cvs-serv830/lib/bio/util
Modified Files:
sirna.rb
Log Message:
* unit tests are fixed to run without errors with Ruby 1.8.4 (due to the
change of rand algorithm in 1.8.3) as reported by N. Goto.
Index: sirna.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/sirna.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** sirna.rb 14 Nov 2005 15:44:30 -0000 1.6
--- sirna.rb 27 Dec 2005 17:27:38 -0000 1.7
***************
*** 202,209 ****
class ShRNA
! # aBio::Sequence::NA
attr_accessor :top_strand
! # aBio::Sequence::NA
attr_accessor :bottom_strand
--- 202,209 ----
class ShRNA
! # Bio::Sequence::NA
attr_accessor :top_strand
! # Bio::Sequence::NA
attr_accessor :bottom_strand
From k at pub.open-bio.org Tue Dec 27 12:27:40 2005
From: k at pub.open-bio.org (Katayama Toshiaki)
Date: Tue Dec 27 12:19:41 2005
Subject: [BioRuby-cvs] bioruby/test/unit/bio/util test_sirna.rb,1.1,1.2
Message-ID: <200512271727.jBRHReVL000861@pub.open-bio.org>
Update of /home/repository/bioruby/bioruby/test/unit/bio/util
In directory pub.open-bio.org:/tmp/cvs-serv830/test/unit/bio/util
Modified Files:
test_sirna.rb
Log Message:
* unit tests are fixed to run without errors with Ruby 1.8.4 (due to the
change of rand algorithm in 1.8.3) as reported by N. Goto.
Index: test_sirna.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/test/unit/bio/util/test_sirna.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** test_sirna.rb 14 Nov 2005 14:46:06 -0000 1.1
--- test_sirna.rb 27 Dec 2005 17:27:38 -0000 1.2
***************
*** 29,36 ****
module Bio
class TestSiRNANew < Test::Unit::TestCase
def test_new
! srand(1)
! naseq = Bio::Sequence::NA.new("ACGT" * 100).randomize
assert(Bio::SiRNA.new(naseq))
assert(Bio::SiRNA.new(naseq, 21))
--- 29,38 ----
module Bio
+
+ RANDOM_SEQ = "ctttcggtgcggacgtaaggagtattcctgtactaactaaatggagttaccaaggtaggaccacggtaaaatcgcgagcagcctcgatacaagcgttgtgctgaagcctatcgctgacctgaaggggggcgtaagcaaggcagcggttcaccttcatcagttctgctagaaatcacctagcaccccttatcatccgcgtcaggtccattacccttcccattatgtcggactcaattgaggtgcttgtgaacttatacttgaatccaaaacgtctactgtattggcgactaaaaagcacttgtggggagtcggcttgatcagcctccattagggccaggcactgaggatcatccagttaacgtcagattcaaggtctggctcttagcactcggagttgcac"
+
class TestSiRNANew < Test::Unit::TestCase
def test_new
! naseq = Bio::Sequence::NA.new(RANDOM_SEQ)
assert(Bio::SiRNA.new(naseq))
assert(Bio::SiRNA.new(naseq, 21))
***************
*** 44,49 ****
class TestSiRNA < Test::Unit::TestCase
def setup
! srand(1)
! naseq = Bio::Sequence::NA.new("ACGT" * 100).randomize
@obj = Bio::SiRNA.new(naseq)
end
--- 46,50 ----
class TestSiRNA < Test::Unit::TestCase
def setup
! naseq = Bio::Sequence::NA.new(RANDOM_SEQ)
@obj = Bio::SiRNA.new(naseq)
end
***************
*** 117,122 ****
class TestSiRNAPair < Test::Unit::TestCase
def setup
! srand(1)
! naseq = Bio::Sequence::NA.new("ACGT" * 100).randomize
@obj = Bio::SiRNA.new(naseq).design.first
end
--- 118,122 ----
class TestSiRNAPair < Test::Unit::TestCase
def setup
! naseq = Bio::Sequence::NA.new(RANDOM_SEQ)
@obj = Bio::SiRNA.new(naseq).design.first
end
***************
*** 176,181 ****
class TestShRNA < Test::Unit::TestCase
def setup
! srand(1)
! naseq = Bio::Sequence::NA.new("ACGT" * 100).randomize
sirna = Bio::SiRNA.new(naseq)
pairs = sirna.design
--- 176,180 ----
class TestShRNA < Test::Unit::TestCase
def setup
! naseq = Bio::Sequence::NA.new(RANDOM_SEQ)
sirna = Bio::SiRNA.new(naseq)
pairs = sirna.design
***************
*** 247,251 ****
3'-CCUGCAUUCCUCAUAAGGACACACACGACAGGUGUCCUUAUGAGGAAUGCAGGAAAA-5'
END
! @obj.design
assert_equal(report, @obj.report)
end
--- 246,251 ----
3'-CCUGCAUUCCUCAUAAGGACACACACGACAGGUGUCCUUAUGAGGAAUGCAGGAAAA-5'
END
! #@obj.design
! @obj.block_it
assert_equal(report, @obj.report)
end