[BioRuby-cvs] bioruby/lib/bio/shell/plugin codon.rb, 1.7,
1.8 flatfile.rb, 1.9, 1.10 keggapi.rb, 1.5, 1.6 obda.rb, 1.6,
1.7 seq.rb, 1.14, 1.15
Katayama Toshiaki
k at pub.open-bio.org
Mon Nov 28 07:07:44 EST 2005
Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv11293/plugin
Modified Files:
codon.rb flatfile.rb keggapi.rb obda.rb seq.rb
Log Message:
* display is removed or changed to puts
* removed require
Index: obda.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/obda.rb,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** obda.rb 28 Nov 2005 07:15:30 -0000 1.6
--- obda.rb 28 Nov 2005 12:07:42 -0000 1.7
***************
*** 27,32 ****
#
- require 'bio/io/registry'
-
module Bio::Shell
--- 27,30 ----
***************
*** 56,60 ****
def obdadbs
result = obda.databases.map {|db| db.database}
- display result
return result
end
--- 54,57 ----
***************
*** 63,67 ****
serv = Bio::Fetch.new("http://www.ebi.ac.uk/cgi-bin/dbfetch")
result = serv.fetch(db, id, style, format)
- display result
return result
end
--- 60,63 ----
Index: flatfile.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/flatfile.rb,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** flatfile.rb 28 Nov 2005 07:14:37 -0000 1.9
--- flatfile.rb 28 Nov 2005 12:07:42 -0000 1.10
***************
*** 27,32 ****
#
- require 'bio/io/flatfile'
-
module Bio::Shell
--- 27,30 ----
***************
*** 106,118 ****
return
end
Bio::FlatFileIndex.open(dir) do |db|
if results = db.include?(keyword)
results.each do |entry_id|
! display db.search_primary(entry_id)
end
else
! display "No hits found"
end
end
end
--- 104,118 ----
return
end
+ entry = ''
Bio::FlatFileIndex.open(dir) do |db|
if results = db.include?(keyword)
results.each do |entry_id|
! entry << db.search_primary(entry_id)
end
else
! warn "Error: No hits found in #{dbname} (#{keyword})"
end
end
+ return entry
end
Index: codon.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/codon.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** codon.rb 28 Nov 2005 07:12:03 -0000 1.7
--- codon.rb 28 Nov 2005 12:07:42 -0000 1.8
***************
*** 27,34 ****
#
- require 'bio/data/codontable'
- require 'bio/data/aa'
- require 'bio/data/na'
-
module Bio::Shell
--- 27,30 ----
***************
*** 188,193 ****
def codontable(num = 1, codon_usage = nil)
cct = ColoredCodonTable.new(num, codon_usage)
! display cct.output unless codon_usage
! return cct
end
--- 184,193 ----
def codontable(num = 1, codon_usage = nil)
cct = ColoredCodonTable.new(num, codon_usage)
! if codon_usage
! return cct
! else
! puts cct.output
! return cct.table
! end
end
Index: keggapi.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/keggapi.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** keggapi.rb 28 Nov 2005 07:18:14 -0000 1.5
--- keggapi.rb 28 Nov 2005 12:07:42 -0000 1.6
***************
*** 27,36 ****
#
- require 'bio/io/keggapi'
-
module Bio::Shell
module Private
! def keeggapi_definition2tab(list)
ary = []
list.each do |entry|
--- 27,34 ----
#
module Bio::Shell
module Private
! def keggapi_definition2tab(list)
ary = []
list.each do |entry|
***************
*** 54,58 ****
def binfo(db = "all")
result = keggapi.binfo(db)
! display result
return result
end
--- 52,56 ----
def binfo(db = "all")
result = keggapi.binfo(db)
! puts result
return result
end
***************
*** 60,64 ****
def bfind(str)
result = keggapi.bfind(str)
- display result
return result
end
--- 58,61 ----
***************
*** 75,79 ****
def btit(str)
result = keggapi.btit(str)
- display result
return result
end
--- 72,75 ----
***************
*** 81,85 ****
def bconv(str)
result = keggapi.bconv(str)
- display result
return result
end
--- 77,80 ----
***************
*** 90,95 ****
list = keggapi.list_databases
result = Bio::Shell.keggapi_definition2tab(list).join("\n")
! display result
! return result
end
--- 85,90 ----
list = keggapi.list_databases
result = Bio::Shell.keggapi_definition2tab(list).join("\n")
! puts result
! return list.map {|x| x.entry_id}
end
***************
*** 97,102 ****
list = keggapi.list_organisms
result = Bio::Shell.keggapi_definition2tab(list).sort.join("\n")
! display result
! return result
end
--- 92,97 ----
list = keggapi.list_organisms
result = Bio::Shell.keggapi_definition2tab(list).sort.join("\n")
! puts result
! return list.map {|x| x.entry_id}
end
***************
*** 104,113 ****
list = keggapi.list_pathways(org)
result = Bio::Shell.keggapi_definition2tab(list).join("\n")
! display result
! return result
end
! =begin
! def kegggenome(org) # *TODO* use das instead?
result = ""
require 'net/ftp'
--- 99,107 ----
list = keggapi.list_pathways(org)
result = Bio::Shell.keggapi_definition2tab(list).join("\n")
! puts result
! return list.map {|x| x.entry_id}
end
! def kegggenomeseq(org)
result = ""
require 'net/ftp'
***************
*** 117,128 ****
file = list.grep(/.*genome$/).shift
if file
! base = File.basename(file)
! ftp.getbinaryfile(file, base)
! result = File.read(base)
end
end
return result
end
- =end
end
--- 111,121 ----
file = list.grep(/.*genome$/).shift
if file
! open("ftp://ftp.genome.jp/#{file}") do |file|
! result = file.read
! end
end
end
return result
end
end
Index: seq.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/seq.rb,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** seq.rb 28 Nov 2005 07:13:55 -0000 1.14
--- seq.rb 28 Nov 2005 12:07:42 -0000 1.15
***************
*** 27,33 ****
#
- require 'bio/sequence'
- require 'bio/util/color_scheme'
-
module Bio::Shell
--- 27,30 ----
***************
*** 138,142 ****
end
rep << "//\n"
! display rep
end
--- 135,140 ----
end
rep << "//\n"
! puts rep
! return rep
end
***************
*** 146,157 ****
seq = seq(str)
if str.length < 16
! display "Sequence must be longer than 16 bases."
return
end
if ! seq.respond_to?(:complement)
! display "Sequence must be a DNA sequence."
return
end
- helix = ''
pairs = [ [5, 0], [4, 2], [3, 3], [2, 4],
[1, 4], [0, 3], [0, 2], [1, 0] ]
--- 144,154 ----
seq = seq(str)
if str.length < 16
! warn "Error: Sequence must be longer than 16 bases."
return
end
if ! seq.respond_to?(:complement)
! warn "Error: Sequence must be a DNA sequence."
return
end
pairs = [ [5, 0], [4, 2], [3, 3], [2, 4],
[1, 4], [0, 3], [0, 2], [1, 0] ]
***************
*** 159,170 ****
pairs.each_with_index do |ij, x|
base = subseq[x, 1]
! helix << ' ' * ij[0] + base + '-' * ij[1] + base.complement + "\n"
end
pairs.reverse.each_with_index do |ij, x|
base = subseq[x + 8, 1]
! helix << ' ' * ij[0] + base.complement + '-' * ij[1] + base + "\n"
end
end
- display helix
end
--- 156,166 ----
pairs.each_with_index do |ij, x|
base = subseq[x, 1]
! puts ' ' * ij[0] + base + '-' * ij[1] + base.complement + "\n"
end
pairs.reverse.each_with_index do |ij, x|
base = subseq[x + 8, 1]
! puts ' ' * ij[0] + base.complement + '-' * ij[1] + base + "\n"
end
end
end
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