[BioRuby-cvs]
bioruby/lib/bio/appl blast.rb, 1.21, 1.22 clustalw.rb,
1.5, 1.6 emboss.rb, 1.1, 1.2 fasta.rb, 1.17, 1.18 mafft.rb,
1.4, 1.5 psort.rb, 1.4, 1.5
Katayama Toshiaki
k at pub.open-bio.org
Wed Sep 7 21:22:10 EDT 2005
- Previous message: [BioRuby-cvs] bioruby/lib/bio alignment.rb, 1.7, 1.8 db.rb, 0.27,
0.28 feature.rb, 1.5, 1.6 location.rb, 0.18, 0.19 pathway.rb,
1.29, 1.30 reference.rb, 1.16, 1.17 sequence.rb, 0.40, 0.41
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Update of /home/repository/bioruby/bioruby/lib/bio/appl
In directory pub.open-bio.org:/tmp/cvs-serv9021/lib/bio/appl
Modified Files:
blast.rb clustalw.rb emboss.rb fasta.rb mafft.rb psort.rb
Log Message:
* expanded tab at the line head
Index: emboss.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/emboss.rb,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** emboss.rb 19 Aug 2002 02:49:29 -0000 1.1
--- emboss.rb 8 Sep 2005 01:22:08 -0000 1.2
***************
*** 31,39 ****
def exec
begin
! @io = IO.popen(@cmd_line, "w+")
! @result = @io.read
! return @result
ensure
! @io.close
end
end
--- 31,39 ----
def exec
begin
! @io = IO.popen(@cmd_line, "w+")
! @result = @io.read
! return @result
ensure
! @io.close
end
end
Index: blast.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/blast.rb,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** blast.rb 16 Aug 2005 09:38:34 -0000 1.21
--- blast.rb 8 Sep 2005 01:22:08 -0000 1.22
***************
*** 36,42 ****
def initialize(program, db, opt = [], server = 'local')
if defined?(XMLParser) or defined?(REXML)
! @format = 7
else
! @format = 8
end
--- 36,42 ----
def initialize(program, db, opt = [], server = 'local')
if defined?(XMLParser) or defined?(REXML)
! @format = 7
else
! @format = 8
end
***************
*** 118,130 ****
form = {
! 'style' => 'raw',
! 'prog' => @program,
! 'dbname' => @db,
! 'sequence' => CGI.escape(query),
! 'other_param' => CGI.escape(make_command_line_unix(@options)),
! 'matrix' => matrix,
! 'filter' => filter,
! 'V_value' => 500, # default value for GenomeNet
! 'B_value' => 250, # default value for GenomeNet
'alignment_view' => 0,
}
--- 118,130 ----
form = {
! 'style' => 'raw',
! 'prog' => @program,
! 'dbname' => @db,
! 'sequence' => CGI.escape(query),
! 'other_param' => CGI.escape(make_command_line_unix(@options)),
! 'matrix' => matrix,
! 'filter' => filter,
! 'V_value' => 500, # default value for GenomeNet
! 'B_value' => 250, # default value for GenomeNet
'alignment_view' => 0,
}
***************
*** 133,137 ****
form.each do |k, v|
! data.push("#{k}=#{v}") if v
end
--- 133,137 ----
form.each do |k, v|
! data.push("#{k}=#{v}") if v
end
***************
*** 142,146 ****
http.open_timeout = 300
http.read_timeout = 600
! result, = http.post(path, data.join('&'))
@output = result.body
# workaround 2005.08.12
--- 142,146 ----
http.open_timeout = 300
http.read_timeout = 600
! result, = http.post(path, data.join('&'))
@output = result.body
# workaround 2005.08.12
Index: clustalw.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/clustalw.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** clustalw.rb 4 Mar 2005 04:48:41 -0000 1.5
--- clustalw.rb 8 Sep 2005 01:22:08 -0000 1.6
***************
*** 45,51 ****
def query(seqs)
if seqs then
! query_align(seqs)
else
! exec_local(@option)
end
end
--- 45,51 ----
def query(seqs)
if seqs then
! query_align(seqs)
else
! exec_local(@option)
end
end
***************
*** 55,67 ****
seqtype = nil
unless seqs.is_a?(Bio::Alignment)
! seqs = Bio::Alignment.new(seqs)
end
seqs.each do |s|
! if s.is_a?(Bio::Sequence::AA) then
! seqtype = 'PROTEIN'
! elsif s.is_a?(Bio::Sequence::NA) then
! seqtype = 'DNA'
! end
! break if seqtype
end
query_string(seqs.to_fasta(70, :avoid_same_name => true), seqtype)
--- 55,67 ----
seqtype = nil
unless seqs.is_a?(Bio::Alignment)
! seqs = Bio::Alignment.new(seqs)
end
seqs.each do |s|
! if s.is_a?(Bio::Sequence::AA) then
! seqtype = 'PROTEIN'
! elsif s.is_a?(Bio::Sequence::NA) then
! seqtype = 'DNA'
! end
! break if seqtype
end
query_string(seqs.to_fasta(70, :avoid_same_name => true), seqtype)
***************
*** 70,77 ****
def query_string(str, *arg)
begin
! tf_in = Tempfile.open('align')
! tf_in.print str
ensure
! tf_in.close(false)
end
r = query_by_filename(tf_in.path, *arg)
--- 70,77 ----
def query_string(str, *arg)
begin
! tf_in = Tempfile.open('align')
! tf_in.print str
ensure
! tf_in.close(false)
end
r = query_by_filename(tf_in.path, *arg)
***************
*** 89,96 ****
opt = [ "-align",
! "-infile=#{path}",
! "-outfile=#{tf_out.path}",
! "-newtree=#{tf_dnd.path}",
! "-outorder=input"
]
opt << "-type=#{seqtype}" if seqtype
--- 89,96 ----
opt = [ "-align",
! "-infile=#{path}",
! "-outfile=#{tf_out.path}",
! "-newtree=#{tf_dnd.path}",
! "-outorder=input"
]
opt << "-type=#{seqtype}" if seqtype
***************
*** 117,125 ****
Open3.popen3(*@command) do |din, dout, derr|
din.close
! t = Thread.start do
! @errorlog = derr.read
! end
! @log = dout.read
! t.join
end
# @command_string = @command.join(" ")
--- 117,125 ----
Open3.popen3(*@command) do |din, dout, derr|
din.close
! t = Thread.start do
! @errorlog = derr.read
! end
! @log = dout.read
! t.join
end
# @command_string = @command.join(" ")
Index: psort.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/psort.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** psort.rb 21 Jul 2004 03:12:02 -0000 1.4
--- psort.rb 8 Sep 2005 01:22:08 -0000 1.5
***************
*** 40,47 ****
'Okazaki' => {'host' => 'psort.nibb.ac.jp',
'PSORT1' => '/cgi-bin/okumura.pl',
! 'PSORT2' => '/cgi-bin/runpsort.pl'},
'Peking' => {'host' => 'srs.pku.edu.en:8088',
'PSORT1' => '/cgi-bin/okumura.pl',
! 'PSORT2' => '/cgi-bin/runpsort.pl'}
}
--- 40,47 ----
'Okazaki' => {'host' => 'psort.nibb.ac.jp',
'PSORT1' => '/cgi-bin/okumura.pl',
! 'PSORT2' => '/cgi-bin/runpsort.pl'},
'Peking' => {'host' => 'srs.pku.edu.en:8088',
'PSORT1' => '/cgi-bin/okumura.pl',
! 'PSORT2' => '/cgi-bin/runpsort.pl'}
}
***************
*** 53,60 ****
class CGIDriver
def initialize(host = '', path = '')
! @host = host
! @path = path
! @args = {}
! @report
end
attr_accessor :args
--- 53,60 ----
class CGIDriver
def initialize(host = '', path = '')
! @host = host
! @path = path
! @args = {}
! @report
end
attr_accessor :args
***************
*** 64,76 ****
# CGIDriver#exec(query) -> aReport
def exec(query)
! data = make_args(query)
! begin
! result, = Net::HTTP.new(@host).post(@path, data)
! @report = result.body
! output = parse_report(@report)
! end
! return output
end
--- 64,76 ----
# CGIDriver#exec(query) -> aReport
def exec(query)
! data = make_args(query)
! begin
! result, = Net::HTTP.new(@host).post(@path, data)
! @report = result.body
! output = parse_report(@report)
! end
! return output
end
***************
*** 79,87 ****
def make_args(args_hash)
! # The routin should be provided in the inherited class
end
def parse_report(result_body)
! # The routin should be provided in the inherited class
end
--- 79,87 ----
def make_args(args_hash)
! # The routin should be provided in the inherited class
end
def parse_report(result_body)
! # The routin should be provided in the inherited class
end
***************
*** 89,101 ****
def erase_html_tags(str)
! return str.gsub(/<\S.*?>/,'')
end
def args_join(hash, delim = '&')
! tmp = []
! hash.each do |key, val|
! tmp << CGI.escape(key.to_s) + '=' + CGI.escape(val.to_s)
! end
! return tmp.join(delim) # not ';' but '&' in psort's cgi
end
--- 89,101 ----
def erase_html_tags(str)
! return str.gsub(/<\S.*?>/,'')
end
def args_join(hash, delim = '&')
! tmp = []
! hash.each do |key, val|
! tmp << CGI.escape(key.to_s) + '=' + CGI.escape(val.to_s)
! end
! return tmp.join(delim) # not ';' but '&' in psort's cgi
end
***************
*** 108,132 ****
def self.imsut
! self.new(Remote.new(WWWServer['IMSUT']['host'],
! WWWServer['IMSUT']['PSORT1']))
end
def self.okazaki
! self.new(Remote.new(WWWServer['Okazaki']['host'],
! WWWServer['Okazaki']['PSORT1']))
end
def self.peking
! self.new(Remote.new(WWWServer['Peking']['host'],
! WWWServer['Peking']['PSORT1']))
end
#
def initialize(serv)
! @serv = serv
! @origin = 'yeast' # Gram-positive bacterium, Gram-negative bacterium,
! # yeast, aminal, plant
! @title = 'MYSEQ'
! @sequence = ''
end
attr_accessor :origin, :sequence, :title
--- 108,132 ----
def self.imsut
! self.new(Remote.new(WWWServer['IMSUT']['host'],
! WWWServer['IMSUT']['PSORT1']))
end
def self.okazaki
! self.new(Remote.new(WWWServer['Okazaki']['host'],
! WWWServer['Okazaki']['PSORT1']))
end
def self.peking
! self.new(Remote.new(WWWServer['Peking']['host'],
! WWWServer['Peking']['PSORT1']))
end
#
def initialize(serv)
! @serv = serv
! @origin = 'yeast' # Gram-positive bacterium, Gram-negative bacterium,
! # yeast, aminal, plant
! @title = 'MYSEQ'
! @sequence = ''
end
attr_accessor :origin, :sequence, :title
***************
*** 134,146 ****
#
def exec(faa, parsing = true)
! if faa.class == Bio::FastaFormat
! @title = faa.entry_id if @title == 'MYSEQ'
! @sequence = faa.seq
! @serv.args = {'title' => @title, 'origin' => @origin}
! @serv.parsing = parsing
! return @serv.exec(sequence)
! else
! self.exec(Bio::FastaFormat.new(faa), parsing)
! end
end
--- 134,146 ----
#
def exec(faa, parsing = true)
! if faa.class == Bio::FastaFormat
! @title = faa.entry_id if @title == 'MYSEQ'
! @sequence = faa.seq
! @serv.args = {'title' => @title, 'origin' => @origin}
! @serv.parsing = parsing
! return @serv.exec(sequence)
! else
! self.exec(Bio::FastaFormat.new(faa), parsing)
! end
end
***************
*** 149,175 ****
class Remote < CGIDriver
! def initialize(host, path)
! @origin = 'yeast' # Gram-positive bacterium,
# Gram-negative bacterium,
! # yeast, aminal, plant
! @title = 'MYSEQ'
! @parsing = true
! super(host, path)
! end
! attr_accessor :origin, :title, :parsing
! private
! def make_args(query)
! @args.update({'sequence' => query})
! return args_join(@args)
! end
! def parse_report(str)
! str = erase_html_tags(str)
! str = Bio::PSORT::PSORT1::Report.parser(str) if @parsing
! return str
! end
end # Class Remote
--- 149,175 ----
class Remote < CGIDriver
! def initialize(host, path)
! @origin = 'yeast' # Gram-positive bacterium,
# Gram-negative bacterium,
! # yeast, aminal, plant
! @title = 'MYSEQ'
! @parsing = true
! super(host, path)
! end
! attr_accessor :origin, :title, :parsing
! private
! def make_args(query)
! @args.update({'sequence' => query})
! return args_join(@args)
! end
! def parse_report(str)
! str = erase_html_tags(str)
! str = Bio::PSORT::PSORT1::Report.parser(str) if @parsing
! return str
! end
end # Class Remote
***************
*** 184,223 ****
# remote
def self.remote(host, path)
! self.new(Remote.new(host, path))
end
def self.imsut
! self.remote(WWWServer['IMSUT']['host'],
! WWWServer['IMSUT']['PSORT2'])
end
def self.okazaki
! self.remote(WWWServer['Okazaki']['host'],
! WWWServer['Okazaki']['PSORT2'])
end
def self.peking
! self.remote(WWWServer['Peking']['host'],
! WWWServer['Peking']['PSORT2'])
end
# wrapper for ``psort'' command
def initialize(serv, origin = 'yeast')
! @serv = serv
! @origin = origin
! @title = nil
end
attr_accessor :origin, :title
def exec(faa, parsing = true)
! if faa.class == Bio::FastaFormat
! @title = faa.entry_id if @title == nil
! @sequence = faa.seq
! @serv.args = {'origin' => @origin, 'title' => @title}
! @serv.parsing = parsing
! return @serv.exec(@sequence)
! else
! self.exec(Bio::FastaFormat.new(faa), parsing)
! end
end
--- 184,223 ----
# remote
def self.remote(host, path)
! self.new(Remote.new(host, path))
end
def self.imsut
! self.remote(WWWServer['IMSUT']['host'],
! WWWServer['IMSUT']['PSORT2'])
end
def self.okazaki
! self.remote(WWWServer['Okazaki']['host'],
! WWWServer['Okazaki']['PSORT2'])
end
def self.peking
! self.remote(WWWServer['Peking']['host'],
! WWWServer['Peking']['PSORT2'])
end
# wrapper for ``psort'' command
def initialize(serv, origin = 'yeast')
! @serv = serv
! @origin = origin
! @title = nil
end
attr_accessor :origin, :title
def exec(faa, parsing = true)
! if faa.class == Bio::FastaFormat
! @title = faa.entry_id if @title == nil
! @sequence = faa.seq
! @serv.args = {'origin' => @origin, 'title' => @title}
! @serv.parsing = parsing
! return @serv.exec(@sequence)
! else
! self.exec(Bio::FastaFormat.new(faa), parsing)
! end
end
***************
*** 225,249 ****
# PSORT2 specific CGIDriver
class Remote < CGIDriver
! def initialize(host, path)
! @origin = 'yeast'
! super(host, path)
! @parsing = true
! end
! attr_accessor :origin, :parsing
!
! private
!
! def make_args(query)
! @args.update({'sequence' => query})
! return args_join(@args)
! end
! def parse_report(str)
! str = str.gsub(/\n<hr>/i, Report::BOUNDARY)
! str = erase_html_tags(str)
! str = Bio::PSORT::PSORT2::Report.parser(str, self.args['title']) if @parsing
! return str
! end
end # class Remote
--- 225,249 ----
# PSORT2 specific CGIDriver
class Remote < CGIDriver
! def initialize(host, path)
! @origin = 'yeast'
! super(host, path)
! @parsing = true
! end
! attr_accessor :origin, :parsing
!
! private
!
! def make_args(query)
! @args.update({'sequence' => query})
! return args_join(@args)
! end
! def parse_report(str)
! str = str.gsub(/\n<hr>/i, Report::BOUNDARY)
! str = erase_html_tags(str)
! str = Bio::PSORT::PSORT2::Report.parser(str, self.args['title']) if @parsing
! return str
! end
end # class Remote
Index: fasta.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/fasta.rb,v
retrieving revision 1.17
retrieving revision 1.18
diff -C2 -d -r1.17 -r1.18
*** fasta.rb 16 Aug 2005 09:38:34 -0000 1.17
--- fasta.rb 8 Sep 2005 01:22:08 -0000 1.18
***************
*** 98,104 ****
case @format
when 6
! require 'bio/appl/fasta/format6'
when 10
! require 'bio/appl/fasta/format10'
end
Report.new(data)
--- 98,104 ----
case @format
when 6
! require 'bio/appl/fasta/format6'
when 10
! require 'bio/appl/fasta/format10'
end
Report.new(data)
***************
*** 125,135 ****
form = {
! 'style' => 'raw',
! 'prog' => @program,
! 'dbname' => @db,
! 'sequence' => CGI.escape(query),
! 'other_param' => CGI.escape(make_command_line_unix(@options)),
! 'ktup_value' => @ktup,
! 'matrix' => @matrix,
}
--- 125,135 ----
form = {
! 'style' => 'raw',
! 'prog' => @program,
! 'dbname' => @db,
! 'sequence' => CGI.escape(query),
! 'other_param' => CGI.escape(make_command_line_unix(@options)),
! 'ktup_value' => @ktup,
! 'matrix' => @matrix,
}
***************
*** 137,141 ****
form.each do |k, v|
! data.push("#{k}=#{v}") if v
end
--- 137,141 ----
form.each do |k, v|
! data.push("#{k}=#{v}") if v
end
***************
*** 146,150 ****
http.open_timeout = 300
http.read_timeout = 600
! result, = http.post(path, data.join('&'))
@output = result.body
# workaround 2005.08.12
--- 146,150 ----
http.open_timeout = 300
http.read_timeout = 600
! result, = http.post(path, data.join('&'))
@output = result.body
# workaround 2005.08.12
Index: mafft.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/appl/mafft.rb,v
retrieving revision 1.4
retrieving revision 1.5
diff -C2 -d -r1.4 -r1.5
*** mafft.rb 4 Mar 2005 04:48:41 -0000 1.4
--- mafft.rb 8 Sep 2005 01:22:08 -0000 1.5
***************
*** 35,42 ****
opt = []
if n.to_s == 'i' then
! self.new2(nil, 'fftnsi', *opt)
else
! opt << n.to_s if n
! self.new2(nil, 'fftns', *opt)
end
end
--- 35,42 ----
opt = []
if n.to_s == 'i' then
! self.new2(nil, 'fftnsi', *opt)
else
! opt << n.to_s if n
! self.new2(nil, 'fftns', *opt)
end
end
***************
*** 50,57 ****
opt << '--all-positive' if ap
if n.to_s == 'i' then
! self.new2(nil, 'nwnsi', *opt)
else
! opt << n.to_s if n
! self.new2(nil, 'nwns', *opt)
end
end
--- 50,57 ----
opt << '--all-positive' if ap
if n.to_s == 'i' then
! self.new2(nil, 'nwnsi', *opt)
else
! opt << n.to_s if n
! self.new2(nil, 'nwns', *opt)
end
end
***************
*** 69,73 ****
def self.new2(dir, prog, *opt)
if dir then
! prog = File.join(dir, prog)
end
self.new(prog, opt)
--- 69,73 ----
def self.new2(dir, prog, *opt)
if dir then
! prog = File.join(dir, prog)
end
self.new(prog, opt)
***************
*** 88,94 ****
def query(seqs)
if seqs then
! query_align(seqs)
else
! exec_local(@option)
end
end
--- 88,94 ----
def query(seqs)
if seqs then
! query_align(seqs)
else
! exec_local(@option)
end
end
***************
*** 97,101 ****
# seqs should be Bio::Alignment or Array of sequences or nil
unless seqs.is_a?(Bio::Alignment)
! seqs = Bio::Alignment.new(seqs, *arg)
end
query_string(seqs.to_fasta(70))
--- 97,101 ----
# seqs should be Bio::Alignment or Array of sequences or nil
unless seqs.is_a?(Bio::Alignment)
! seqs = Bio::Alignment.new(seqs, *arg)
end
query_string(seqs.to_fasta(70))
***************
*** 104,111 ****
def query_string(str, *arg)
begin
! tf_in = Tempfile.open('align')
! tf_in.print str
ensure
! tf_in.close(false)
end
r = query_by_filename(tf_in.path, *arg)
--- 104,111 ----
def query_string(str, *arg)
begin
! tf_in = Tempfile.open('align')
! tf_in.print str
ensure
! tf_in.close(false)
end
r = query_by_filename(tf_in.path, *arg)
***************
*** 128,139 ****
@log = nil
Open3.popen3(*@command) do |din, dout, derr|
! din.close
! derr.sync = true
! t = Thread.start do
! @log = derr.read
! end
! ff = Bio::FlatFile.new(Bio::FastaFormat, dout)
! @output = ff.to_a
! t.join
end
@log
--- 128,139 ----
@log = nil
Open3.popen3(*@command) do |din, dout, derr|
! din.close
! derr.sync = true
! t = Thread.start do
! @log = derr.read
! end
! ff = Bio::FlatFile.new(Bio::FastaFormat, dout)
! @output = ff.to_a
! t.join
end
@log
- Previous message: [BioRuby-cvs] bioruby/lib/bio alignment.rb, 1.7, 1.8 db.rb, 0.27,
0.28 feature.rb, 1.5, 1.6 location.rb, 0.18, 0.19 pathway.rb,
1.29, 1.30 reference.rb, 1.16, 1.17 sequence.rb, 0.40, 0.41
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