bio 1.4.3.0001 → 1.5.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.travis.yml +39 -33
- data/BSDL +22 -0
- data/COPYING +2 -2
- data/COPYING.ja +36 -36
- data/ChangeLog +2404 -1025
- data/KNOWN_ISSUES.rdoc +15 -55
- data/README.rdoc +17 -23
- data/RELEASE_NOTES.rdoc +246 -183
- data/Rakefile +3 -2
- data/bin/br_biofetch.rb +29 -5
- data/bioruby.gemspec +15 -32
- data/bioruby.gemspec.erb +10 -20
- data/doc/ChangeLog-1.4.3 +1478 -0
- data/doc/RELEASE_NOTES-1.4.3.rdoc +204 -0
- data/doc/Tutorial.rd +0 -6
- data/doc/Tutorial.rd.html +7 -12
- data/doc/Tutorial.rd.ja +960 -1064
- data/doc/Tutorial.rd.ja.html +977 -1067
- data/gemfiles/Gemfile.travis-jruby1.8 +2 -1
- data/gemfiles/Gemfile.travis-jruby1.9 +2 -4
- data/gemfiles/Gemfile.travis-rbx +13 -0
- data/gemfiles/Gemfile.travis-ruby1.8 +2 -1
- data/gemfiles/Gemfile.travis-ruby1.9 +2 -4
- data/gemfiles/Gemfile.travis-ruby2.2 +9 -0
- data/lib/bio.rb +10 -43
- data/lib/bio/alignment.rb +8 -14
- data/lib/bio/appl/blast.rb +1 -2
- data/lib/bio/appl/blast/format0.rb +18 -7
- data/lib/bio/appl/blast/remote.rb +0 -9
- data/lib/bio/appl/blast/report.rb +1 -1
- data/lib/bio/appl/clustalw/report.rb +3 -1
- data/lib/bio/appl/genscan/report.rb +1 -2
- data/lib/bio/appl/iprscan/report.rb +1 -2
- data/lib/bio/appl/meme/mast.rb +4 -4
- data/lib/bio/appl/meme/mast/report.rb +1 -1
- data/lib/bio/appl/paml/codeml.rb +2 -2
- data/lib/bio/appl/paml/codeml/report.rb +1 -0
- data/lib/bio/appl/paml/common.rb +1 -1
- data/lib/bio/appl/sosui/report.rb +1 -2
- data/lib/bio/command.rb +62 -2
- data/lib/bio/data/aa.rb +13 -31
- data/lib/bio/data/codontable.rb +1 -2
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +1 -0
- data/lib/bio/db/biosql/sequence.rb +1 -1
- data/lib/bio/db/embl/common.rb +1 -1
- data/lib/bio/db/embl/embl.rb +5 -4
- data/lib/bio/db/embl/format_embl.rb +3 -3
- data/lib/bio/db/embl/sptr.rb +9 -1444
- data/lib/bio/db/embl/swissprot.rb +12 -29
- data/lib/bio/db/embl/trembl.rb +13 -30
- data/lib/bio/db/embl/uniprot.rb +12 -29
- data/lib/bio/db/embl/uniprotkb.rb +1455 -0
- data/lib/bio/db/fasta.rb +17 -0
- data/lib/bio/db/fasta/defline.rb +1 -3
- data/lib/bio/db/fastq.rb +1 -1
- data/lib/bio/db/genbank/ddbj.rb +9 -5
- data/lib/bio/db/genbank/refseq.rb +11 -3
- data/lib/bio/db/gff.rb +3 -4
- data/lib/bio/db/go.rb +5 -6
- data/lib/bio/db/kegg/module.rb +4 -5
- data/lib/bio/db/kegg/pathway.rb +4 -5
- data/lib/bio/db/kegg/reaction.rb +1 -1
- data/lib/bio/db/nexus.rb +3 -2
- data/lib/bio/db/pdb/pdb.rb +2 -2
- data/lib/bio/db/phyloxml/phyloxml_elements.rb +82 -59
- data/lib/bio/db/phyloxml/phyloxml_parser.rb +2 -2
- data/lib/bio/db/phyloxml/phyloxml_writer.rb +1 -2
- data/lib/bio/db/sanger_chromatogram/chromatogram.rb +1 -2
- data/lib/bio/db/transfac.rb +1 -1
- data/lib/bio/io/das.rb +40 -41
- data/lib/bio/io/fastacmd.rb +0 -16
- data/lib/bio/io/fetch.rb +111 -55
- data/lib/bio/io/flatfile/buffer.rb +4 -5
- data/lib/bio/io/hinv.rb +2 -3
- data/lib/bio/io/ncbirest.rb +43 -6
- data/lib/bio/io/pubmed.rb +76 -81
- data/lib/bio/io/togows.rb +33 -10
- data/lib/bio/map.rb +1 -1
- data/lib/bio/pathway.rb +1 -1
- data/lib/bio/sequence/compat.rb +1 -1
- data/lib/bio/sequence/na.rb +63 -12
- data/lib/bio/shell.rb +0 -2
- data/lib/bio/shell/core.rb +5 -6
- data/lib/bio/shell/interface.rb +3 -4
- data/lib/bio/shell/irb.rb +1 -2
- data/lib/bio/shell/plugin/entry.rb +2 -3
- data/lib/bio/shell/plugin/seq.rb +7 -6
- data/lib/bio/shell/setup.rb +1 -2
- data/lib/bio/tree.rb +2 -2
- data/lib/bio/util/contingency_table.rb +0 -2
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +2 -2
- data/lib/bio/util/sirna.rb +76 -16
- data/lib/bio/version.rb +8 -9
- data/sample/benchmark_clustalw_report.rb +47 -0
- data/sample/biofetch.rb +248 -151
- data/setup.rb +6 -7
- data/test/data/clustalw/example1-seqnos.aln +58 -0
- data/test/network/bio/appl/blast/test_remote.rb +1 -15
- data/test/network/bio/appl/test_blast.rb +0 -12
- data/test/network/bio/io/test_pubmed.rb +49 -0
- data/test/network/bio/io/test_togows.rb +0 -1
- data/test/network/bio/test_command.rb +65 -2
- data/test/unit/bio/appl/bl2seq/test_report.rb +0 -1
- data/test/unit/bio/appl/blast/test_report.rb +110 -48
- data/test/unit/bio/appl/clustalw/test_report.rb +67 -51
- data/test/unit/bio/appl/sim4/test_report.rb +46 -17
- data/test/unit/bio/appl/test_blast.rb +2 -2
- data/test/unit/bio/db/embl/test_embl.rb +0 -1
- data/test/unit/bio/db/embl/test_embl_rel89.rb +0 -1
- data/test/unit/bio/db/embl/{test_sptr.rb → test_uniprotkb.rb} +111 -115
- data/test/unit/bio/db/embl/{test_uniprot_new_part.rb → test_uniprotkb_new_part.rb} +11 -11
- data/test/unit/bio/db/genbank/test_genbank.rb +10 -4
- data/test/unit/bio/db/pdb/test_pdb.rb +14 -8
- data/test/unit/bio/db/test_fasta.rb +41 -1
- data/test/unit/bio/db/test_fastq.rb +14 -4
- data/test/unit/bio/db/test_gff.rb +2 -2
- data/test/unit/bio/db/test_phyloxml.rb +30 -30
- data/test/unit/bio/db/test_phyloxml_writer.rb +2 -2
- data/test/unit/bio/io/flatfile/test_autodetection.rb +1 -2
- data/test/unit/bio/io/flatfile/test_buffer.rb +7 -1
- data/test/unit/bio/io/flatfile/test_splitter.rb +1 -1
- data/test/unit/bio/io/test_togows.rb +3 -2
- data/test/unit/bio/sequence/test_dblink.rb +1 -1
- data/test/unit/bio/sequence/test_na.rb +3 -1
- data/test/unit/bio/test_alignment.rb +1 -2
- data/test/unit/bio/test_command.rb +5 -4
- data/test/unit/bio/test_db.rb +4 -2
- data/test/unit/bio/test_pathway.rb +25 -10
- data/test/unit/bio/util/test_sirna.rb +22 -22
- metadata +656 -1430
- data/doc/KEGG_API.rd +0 -1843
- data/doc/KEGG_API.rd.ja +0 -1834
- data/extconf.rb +0 -2
- data/lib/bio/appl/blast/ddbj.rb +0 -131
- data/lib/bio/db/kegg/taxonomy.rb +0 -280
- data/lib/bio/io/dbget.rb +0 -194
- data/lib/bio/io/ddbjrest.rb +0 -344
- data/lib/bio/io/ddbjxml.rb +0 -458
- data/lib/bio/io/ebisoap.rb +0 -158
- data/lib/bio/io/ensembl.rb +0 -229
- data/lib/bio/io/higet.rb +0 -73
- data/lib/bio/io/keggapi.rb +0 -363
- data/lib/bio/io/ncbisoap.rb +0 -156
- data/lib/bio/io/soapwsdl.rb +0 -119
- data/lib/bio/shell/plugin/keggapi.rb +0 -181
- data/lib/bio/shell/plugin/soap.rb +0 -87
- data/sample/dbget +0 -37
- data/sample/demo_ddbjxml.rb +0 -212
- data/sample/demo_kegg_taxonomy.rb +0 -92
- data/sample/demo_keggapi.rb +0 -502
- data/sample/psortplot_html.rb +0 -214
- data/test/network/bio/io/test_ddbjrest.rb +0 -47
- data/test/network/bio/io/test_ensembl.rb +0 -230
- data/test/network/bio/io/test_soapwsdl.rb +0 -53
- data/test/unit/bio/io/test_ddbjxml.rb +0 -81
- data/test/unit/bio/io/test_ensembl.rb +0 -111
- data/test/unit/bio/io/test_soapwsdl.rb +0 -33
@@ -1,92 +0,0 @@
|
|
1
|
-
#
|
2
|
-
# = sample/demo_kegg_taxonomy.rb - demonstration of Bio::KEGG::Taxonomy
|
3
|
-
#
|
4
|
-
# Copyright:: Copyright (C) 2007 Toshiaki Katayama <k@bioruby.org>
|
5
|
-
# License:: The Ruby License
|
6
|
-
#
|
7
|
-
#
|
8
|
-
# == Description
|
9
|
-
#
|
10
|
-
# IMPORTANT NOTE: currently, this sample does not work!
|
11
|
-
#
|
12
|
-
# Demonstration of Bio::KEGG::Taxonomy.
|
13
|
-
#
|
14
|
-
# == Usage
|
15
|
-
#
|
16
|
-
# Specify a file containing KEGG Taxonomy data.
|
17
|
-
#
|
18
|
-
# $ ruby demo_kegg_taxonomy.rb file
|
19
|
-
#
|
20
|
-
# Optionally, when a file containing organisms list (1 line per 1 organism)
|
21
|
-
# is specified after the file, only the specified organisms are shown.
|
22
|
-
#
|
23
|
-
# $ ruby demo_kegg_taxonomy.rb kegg_taxonomy_file org_list_file
|
24
|
-
#
|
25
|
-
# == Example of running this script
|
26
|
-
#
|
27
|
-
# Download test data.
|
28
|
-
#
|
29
|
-
# $ wget ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
|
30
|
-
#
|
31
|
-
# The downloaded filename is "taxonomy".
|
32
|
-
#
|
33
|
-
# Run this script.
|
34
|
-
#
|
35
|
-
# $ ruby -Ilib sample/demo_kegg_taxonomy.rb taxonomy
|
36
|
-
#
|
37
|
-
# == Development information
|
38
|
-
#
|
39
|
-
# The code was moved from lib/bio/db/kegg/taxonomy.rb.
|
40
|
-
#
|
41
|
-
|
42
|
-
require 'bio'
|
43
|
-
|
44
|
-
#if __FILE__ == $0
|
45
|
-
|
46
|
-
# Usage:
|
47
|
-
# % wget ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
|
48
|
-
# % ruby taxonomy.rb taxonomy | less -S
|
49
|
-
|
50
|
-
taxonomy = ARGV.shift
|
51
|
-
org_list = ARGV.shift || nil
|
52
|
-
|
53
|
-
if org_list
|
54
|
-
orgs = File.readlines(org_list).map{|x| x.strip}
|
55
|
-
else
|
56
|
-
orgs = nil
|
57
|
-
end
|
58
|
-
|
59
|
-
tree = Bio::KEGG::Taxonomy.new(taxonomy, orgs)
|
60
|
-
|
61
|
-
puts ">>> tree - original"
|
62
|
-
puts tree
|
63
|
-
|
64
|
-
puts ">>> tree - after compact"
|
65
|
-
tree.compact
|
66
|
-
puts tree
|
67
|
-
|
68
|
-
puts ">>> tree - after reduce"
|
69
|
-
tree.reduce
|
70
|
-
puts tree
|
71
|
-
|
72
|
-
puts ">>> path - sorted"
|
73
|
-
tree.path.sort.each do |path|
|
74
|
-
puts path.join("/")
|
75
|
-
end
|
76
|
-
|
77
|
-
puts ">>> group : orgs"
|
78
|
-
tree.dfs(tree.root) do |parent, children|
|
79
|
-
if orgs = tree.organisms(parent)
|
80
|
-
puts "#{parent.ljust(30)} (#{orgs.size})\t#{orgs.join(', ')}"
|
81
|
-
end
|
82
|
-
end
|
83
|
-
|
84
|
-
puts ">>> group : subgroups"
|
85
|
-
tree.dfs_with_level(tree.root) do |parent, children, level|
|
86
|
-
subgroups = children.keys.sort
|
87
|
-
indent = " " * level
|
88
|
-
label = "#{indent} #{level} #{parent}"
|
89
|
-
puts "#{label.ljust(35)}\t#{subgroups.join(', ')}"
|
90
|
-
end
|
91
|
-
|
92
|
-
#end
|
data/sample/demo_keggapi.rb
DELETED
@@ -1,502 +0,0 @@
|
|
1
|
-
#
|
2
|
-
# = sample/demo_keggapi.rb - demonstration of Bio::KEGG::API web service client
|
3
|
-
#
|
4
|
-
# Copyright:: Copyright (C) 2003, 2004 Toshiaki Katayama <k@bioruby.org>
|
5
|
-
# License:: The Ruby License
|
6
|
-
#
|
7
|
-
#
|
8
|
-
# == Description
|
9
|
-
#
|
10
|
-
# Demonstration of Bio::KEGG::API, the KEGG API web service client via
|
11
|
-
# SOAP/WSDL.
|
12
|
-
#
|
13
|
-
# == Requirements
|
14
|
-
#
|
15
|
-
# Internet connection is needed.
|
16
|
-
#
|
17
|
-
# == Usage
|
18
|
-
#
|
19
|
-
# Simply run this script.
|
20
|
-
#
|
21
|
-
# $ ruby demo_keggapi.rb
|
22
|
-
#
|
23
|
-
# == Notes
|
24
|
-
#
|
25
|
-
# * It may take long time to run this script.
|
26
|
-
# * It can not be run with Ruby 1.9 because SOAP4R (SOAP support for Ruby)
|
27
|
-
# currently does not support Ruby 1.9.
|
28
|
-
#
|
29
|
-
# == Development information
|
30
|
-
#
|
31
|
-
# The code was moved from lib/bio/io/keggapi.rb, and modified as below:
|
32
|
-
#
|
33
|
-
# * Commented out deprecated methods: get_neighbors_by_gene,
|
34
|
-
# get_similarity_between_genes, get_ko_members, get_oc_members_by_gene,
|
35
|
-
# get_pc_members_by_gene.
|
36
|
-
# * Commented out some methods internally using the deprecated methods:
|
37
|
-
# get_all_neighbors_by_gene, get_all_oc_members_by_gene,
|
38
|
-
# get_all_pc_members_by_gene.
|
39
|
-
#
|
40
|
-
|
41
|
-
require 'bio'
|
42
|
-
|
43
|
-
#if __FILE__ == $0
|
44
|
-
|
45
|
-
begin
|
46
|
-
require 'pp'
|
47
|
-
alias p pp
|
48
|
-
rescue LoadError
|
49
|
-
end
|
50
|
-
|
51
|
-
puts ">>> KEGG API"
|
52
|
-
serv = Bio::KEGG::API.new
|
53
|
-
# serv.log = STDERR
|
54
|
-
|
55
|
-
puts "# * parameters"
|
56
|
-
puts " wsdl : #{serv.wsdl}"
|
57
|
-
puts " log : #{serv.log}"
|
58
|
-
puts " start : #{serv.start}"
|
59
|
-
puts " max_results : #{serv.max_results}"
|
60
|
-
|
61
|
-
puts "=== META"
|
62
|
-
|
63
|
-
puts "### list_databases"
|
64
|
-
list = serv.list_databases
|
65
|
-
list.each do |db|
|
66
|
-
print db.entry_id, "\t", db.definition, "\n"
|
67
|
-
end
|
68
|
-
|
69
|
-
puts "### list_organisms"
|
70
|
-
list = serv.list_organisms
|
71
|
-
list.each do |org|
|
72
|
-
print org.entry_id, "\t", org.definition, "\n"
|
73
|
-
end
|
74
|
-
|
75
|
-
puts "### list_pathways('map') : reference pathway"
|
76
|
-
list = serv.list_pathways("map")
|
77
|
-
list.each do |path|
|
78
|
-
print path.entry_id, "\t", path.definition, "\n"
|
79
|
-
end
|
80
|
-
|
81
|
-
puts "### list_pathways('eco') : E. coli pathway"
|
82
|
-
list = serv.list_pathways("eco")
|
83
|
-
list.each do |path|
|
84
|
-
print path.entry_id, "\t", path.definition, "\n"
|
85
|
-
end
|
86
|
-
|
87
|
-
puts "=== DBGET"
|
88
|
-
|
89
|
-
puts "### binfo('all')"
|
90
|
-
puts serv.binfo("all")
|
91
|
-
|
92
|
-
puts "### binfo('genbank')"
|
93
|
-
puts serv.binfo("genbank")
|
94
|
-
|
95
|
-
puts "### bfind('genbank kinase cell cycle human')"
|
96
|
-
puts serv.bfind("genbank kinase cell cycle human")
|
97
|
-
|
98
|
-
puts "### bget('gb:AJ617376')"
|
99
|
-
puts serv.bget("gb:AJ617376")
|
100
|
-
|
101
|
-
puts "### bget('eco:b0002 eco:b0003')"
|
102
|
-
puts serv.bget("eco:b0002 eco:b0003")
|
103
|
-
|
104
|
-
puts "### btit('eco:b0002 eco:b0003')"
|
105
|
-
puts serv.btit("eco:b0002 eco:b0003")
|
106
|
-
|
107
|
-
puts "# * get_entries(['eco:b0002', 'eco:b0003'])"
|
108
|
-
puts serv.get_entries(["eco:b0002", "eco:b0003"])
|
109
|
-
|
110
|
-
puts "# * get_aaseqs(['eco:b0002', 'eco:b0003'])"
|
111
|
-
puts serv.get_aaseqs(["eco:b0002", "eco:b0003"])
|
112
|
-
|
113
|
-
puts "# * get_naseqs(['eco:b0002', 'eco:b0003'])"
|
114
|
-
puts serv.get_naseqs(["eco:b0002", "eco:b0003"])
|
115
|
-
|
116
|
-
puts "# * get_definitions(['eco:b0002', 'eco:b0003'])"
|
117
|
-
puts serv.get_definitions(["eco:b0002", "eco:b0003"])
|
118
|
-
|
119
|
-
puts "# * get_definitions(('eco:b0001'..'eco:b0200').to_a)"
|
120
|
-
puts serv.get_definitions(("eco:b0001".."eco:b0200").to_a)
|
121
|
-
|
122
|
-
puts "=== LinkDB"
|
123
|
-
|
124
|
-
puts "### get_linkdb_by_entry('eco:b0002', 'pathway', 1, 5)"
|
125
|
-
list = serv.get_linkdb_by_entry("eco:b0002", "pathway", 1, 5)
|
126
|
-
list.each do |link|
|
127
|
-
puts [ link.entry_id1, link.entry_id2, link.type, link.path ].join("\t")
|
128
|
-
end
|
129
|
-
|
130
|
-
puts "# * get_all_linkdb_by_entry('eco:b0002', 'pathway')"
|
131
|
-
list = serv.get_all_linkdb_by_entry("eco:b0002", "pathway")
|
132
|
-
list.each do |link|
|
133
|
-
puts [ link.entry_id1, link.entry_id2, link.type, link.path ].join("\t")
|
134
|
-
end
|
135
|
-
|
136
|
-
puts "=== SSDB"
|
137
|
-
|
138
|
-
# The method "get_neighbors_by_gene" is deprecated in 2005-02-20.
|
139
|
-
#
|
140
|
-
#puts "### get_neighbors_by_gene('eco:b0002', 'all', 1, 5)"
|
141
|
-
#list = serv.get_neighbors_by_gene("eco:b0002", "all", 1, 5)
|
142
|
-
#list.each do |hit|
|
143
|
-
# puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
144
|
-
#end
|
145
|
-
|
146
|
-
# The method "get_all_neighbors_by_gene" can not be used because
|
147
|
-
# it internally uses the deprecated "get_neighbors_by_gene" method.
|
148
|
-
#
|
149
|
-
#puts "# * get_all_neighbors_by_gene('eco:b0002', 'bsu')"
|
150
|
-
#list = serv.get_all_neighbors_by_gene("eco:b0002", "bsu")
|
151
|
-
#list.each do |hit|
|
152
|
-
# puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
153
|
-
#end
|
154
|
-
|
155
|
-
puts "### get_best_best_neighbors_by_gene('eco:b0002', 1, 5)"
|
156
|
-
list = serv.get_best_best_neighbors_by_gene("eco:b0002", 1, 5)
|
157
|
-
list.each do |hit|
|
158
|
-
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
159
|
-
end
|
160
|
-
|
161
|
-
puts "# * get_all_best_best_neighbors_by_gene('eco:b0002')"
|
162
|
-
list = serv.get_all_best_best_neighbors_by_gene("eco:b0002")
|
163
|
-
list.each do |hit|
|
164
|
-
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
165
|
-
end
|
166
|
-
|
167
|
-
puts "### get_best_neighbors_by_gene('eco:b0002', 1, 5)"
|
168
|
-
list = serv.get_best_neighbors_by_gene("eco:b0002", 1, 5)
|
169
|
-
list.each do |hit|
|
170
|
-
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
171
|
-
end
|
172
|
-
|
173
|
-
puts "# * get_all_best_neighbors_by_gene('eco:b0002')"
|
174
|
-
list = serv.get_all_best_neighbors_by_gene("eco:b0002")
|
175
|
-
list.each do |hit|
|
176
|
-
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
177
|
-
end
|
178
|
-
|
179
|
-
puts "### get_reverse_best_neighbors_by_gene('eco:b0002', 1, 5)"
|
180
|
-
list = serv.get_reverse_best_neighbors_by_gene("eco:b0002", 1, 5)
|
181
|
-
list.each do |hit|
|
182
|
-
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
183
|
-
end
|
184
|
-
|
185
|
-
puts "# * get_all_reverse_best_neighbors_by_gene('eco:b0002')"
|
186
|
-
list = serv.get_all_reverse_best_neighbors_by_gene("eco:b0002")
|
187
|
-
list.each do |hit|
|
188
|
-
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
189
|
-
end
|
190
|
-
|
191
|
-
puts "### get_paralogs_by_gene('eco:b0002', 1, 5)"
|
192
|
-
list = serv.get_paralogs_by_gene("eco:b0002", 1, 5)
|
193
|
-
list.each do |hit|
|
194
|
-
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
195
|
-
end
|
196
|
-
|
197
|
-
puts "# * get_all_paralogs_by_gene('eco:b0002')"
|
198
|
-
list = serv.get_all_paralogs_by_gene("eco:b0002")
|
199
|
-
list.each do |hit|
|
200
|
-
puts [ hit.genes_id1, hit.genes_id2, hit.sw_score ].join("\t")
|
201
|
-
end
|
202
|
-
|
203
|
-
# The method "get_similarity_between_genes" is deprecated in 2005-02-20.
|
204
|
-
#
|
205
|
-
#puts "### get_similarity_between_genes('eco:b0002', 'bsu:BG10350')"
|
206
|
-
#relation = serv.get_similarity_between_genes("eco:b0002", "bsu:BG10350")
|
207
|
-
#puts " genes_id1 : #{relation.genes_id1}" # string
|
208
|
-
#puts " genes_id2 : #{relation.genes_id2}" # string
|
209
|
-
#puts " sw_score : #{relation.sw_score}" # int
|
210
|
-
#puts " bit_score : #{relation.bit_score}" # float
|
211
|
-
#puts " identity : #{relation.identity}" # float
|
212
|
-
#puts " overlap : #{relation.overlap}" # int
|
213
|
-
#puts " start_position1 : #{relation.start_position1}" # int
|
214
|
-
#puts " end_position1 : #{relation.end_position1}" # int
|
215
|
-
#puts " start_position2 : #{relation.start_position2}" # int
|
216
|
-
#puts " end_position2 : #{relation.end_position2}" # int
|
217
|
-
#puts " best_flag_1to2 : #{relation.best_flag_1to2}" # boolean
|
218
|
-
#puts " best_flag_2to1 : #{relation.best_flag_2to1}" # boolean
|
219
|
-
#puts " definition1 : #{relation.definition1}" # string
|
220
|
-
#puts " definition2 : #{relation.definition2}" # string
|
221
|
-
#puts " length1 : #{relation.length1}" # int
|
222
|
-
#puts " length2 : #{relation.length2}" # int
|
223
|
-
|
224
|
-
puts "=== MOTIF"
|
225
|
-
|
226
|
-
puts "### get_motifs_by_gene('eco:b0002', 'pfam')"
|
227
|
-
list = serv.get_motifs_by_gene("eco:b0002", "pfam")
|
228
|
-
list.each do |motif|
|
229
|
-
puts motif.motif_id
|
230
|
-
end if list
|
231
|
-
|
232
|
-
puts "### get_motifs_by_gene('eco:b0002', 'tfam')"
|
233
|
-
list = serv.get_motifs_by_gene("eco:b0002", "tfam")
|
234
|
-
list.each do |motif|
|
235
|
-
puts motif.motif_id
|
236
|
-
end if list
|
237
|
-
|
238
|
-
puts "### get_motifs_by_gene('eco:b0002', 'pspt')"
|
239
|
-
list = serv.get_motifs_by_gene("eco:b0002", "pspt")
|
240
|
-
list.each do |motif|
|
241
|
-
puts motif.motif_id
|
242
|
-
end if list
|
243
|
-
|
244
|
-
puts "### get_motifs_by_gene('eco:b0002', 'pspf')"
|
245
|
-
list = serv.get_motifs_by_gene("eco:b0002", "pspf")
|
246
|
-
list.each do |motif|
|
247
|
-
puts motif.motif_id
|
248
|
-
end if list
|
249
|
-
|
250
|
-
puts "### get_motifs_by_gene('eco:b0002', 'all')"
|
251
|
-
list = serv.get_motifs_by_gene("eco:b0002", "all")
|
252
|
-
list.each do |motif|
|
253
|
-
puts "# * motif result"
|
254
|
-
puts " motif_id : #{motif.motif_id}"
|
255
|
-
puts " definition : #{motif.definition}"
|
256
|
-
puts " genes_id : #{motif.genes_id}"
|
257
|
-
puts " start_position : #{motif.start_position}"
|
258
|
-
puts " end_position : #{motif.end_position}"
|
259
|
-
puts " score : #{motif.score}"
|
260
|
-
puts " evalue : #{motif.evalue}"
|
261
|
-
end
|
262
|
-
|
263
|
-
puts "### get_genes_by_motifs(['pf:ACT', 'ps:ASPARTOKINASE'], 1, 5)"
|
264
|
-
list = serv.get_genes_by_motifs(["pf:ACT", "ps:ASPARTOKINASE"], 1, 5)
|
265
|
-
list.each do |gene|
|
266
|
-
puts [ gene.entry_id, gene.definition ].join("\t")
|
267
|
-
end
|
268
|
-
|
269
|
-
puts "# * get_all_genes_by_motifs(['pf:ACT', 'ps:ASPARTOKINASE'])"
|
270
|
-
list = serv.get_all_genes_by_motifs(["pf:ACT", "ps:ASPARTOKINASE"])
|
271
|
-
list.each do |gene|
|
272
|
-
puts [ gene.entry_id, gene.definition ].join("\t")
|
273
|
-
end
|
274
|
-
|
275
|
-
puts "=== KO, OC, PC"
|
276
|
-
|
277
|
-
puts "### get_ko_by_gene('eco:b0002')"
|
278
|
-
list = serv.get_ko_by_gene("eco:b0002")
|
279
|
-
list.each do |ko|
|
280
|
-
puts ko
|
281
|
-
end
|
282
|
-
|
283
|
-
# The method "get_ko_members" is removed in 2005-06-01.
|
284
|
-
#
|
285
|
-
#puts "### get_ko_members('ko:K00003')"
|
286
|
-
#list = serv.get_ko_members("ko:K00003")
|
287
|
-
#list.each do |gene|
|
288
|
-
# puts gene
|
289
|
-
#end
|
290
|
-
|
291
|
-
# The method "get_oc_members_by_gene" is removed in 2006-10-04.
|
292
|
-
#
|
293
|
-
#puts "### get_oc_members_by_gene('eco:b0002', 1, 5)"
|
294
|
-
#list = serv.get_oc_members_by_gene("eco:b0002", 1, 5)
|
295
|
-
#list.each do |gene|
|
296
|
-
# puts gene
|
297
|
-
#end
|
298
|
-
|
299
|
-
# The method "get_all_oc_members_by_gene" can not be used because
|
300
|
-
# it internally uses the deprecated "get_oc_members_by_gene" method.
|
301
|
-
#
|
302
|
-
#puts "# * get_all_oc_members_by_gene('eco:b0002')"
|
303
|
-
#list = serv.get_all_oc_members_by_gene("eco:b0002")
|
304
|
-
#list.each do |gene|
|
305
|
-
# puts gene
|
306
|
-
#end
|
307
|
-
|
308
|
-
# The method "get_pc_members_by_gene" is removed in 2006-10-04.
|
309
|
-
#
|
310
|
-
#puts "### get_pc_members_by_gene('eco:b0002', 1, 5)"
|
311
|
-
#list = serv.get_pc_members_by_gene("eco:b0002", 1, 5)
|
312
|
-
#list.each do |gene|
|
313
|
-
# puts gene
|
314
|
-
#end
|
315
|
-
|
316
|
-
# The method "get_all_pc_members_by_gene" can not be used because
|
317
|
-
# it internally uses the deprecated "get_pc_members_by_gene" method.
|
318
|
-
#
|
319
|
-
#puts "# * get_all_pc_members_by_gene('eco:b0002')"
|
320
|
-
#list = serv.get_all_pc_members_by_gene("eco:b0002")
|
321
|
-
#list.each do |gene|
|
322
|
-
# puts gene
|
323
|
-
#end
|
324
|
-
|
325
|
-
puts "=== PATHWAY"
|
326
|
-
|
327
|
-
puts "==== coloring pathway"
|
328
|
-
|
329
|
-
puts "### mark_pathway_by_objects('path:eco00260', obj_list)"
|
330
|
-
puts " obj_list = ['eco:b0002', 'cpd:C00263']"
|
331
|
-
obj_list = ["eco:b0002", "cpd:C00263"]
|
332
|
-
url = serv.mark_pathway_by_objects("path:eco00260", obj_list)
|
333
|
-
puts url
|
334
|
-
|
335
|
-
puts "### color_pathway_by_objects('path:eco00053', obj_list, fg_list, bg_list)"
|
336
|
-
puts " obj_list = ['eco:b0207', 'eco:b1300']"
|
337
|
-
puts " fg_list = ['blue', '#00ff00']"
|
338
|
-
puts " bg_list = ['#ff0000', 'yellow']"
|
339
|
-
obj_list = ["eco:b0207", "eco:b1300"]
|
340
|
-
fg_list = ["blue", "#00ff00"]
|
341
|
-
bg_list = ["#ff0000", "yellow"]
|
342
|
-
url = serv.color_pathway_by_objects("path:eco00053", obj_list, fg_list, bg_list)
|
343
|
-
puts url
|
344
|
-
|
345
|
-
#puts "# * save_image(#{url})"
|
346
|
-
#filename = serv.save_image(url, "test.gif")
|
347
|
-
#filename = serv.save_image(url)
|
348
|
-
#puts filename
|
349
|
-
|
350
|
-
puts "==== objects on pathway"
|
351
|
-
|
352
|
-
puts "### get_genes_by_pathway('path:map00010')"
|
353
|
-
list = serv.get_genes_by_pathway("path:map00010")
|
354
|
-
list.each do |gene|
|
355
|
-
puts gene
|
356
|
-
end
|
357
|
-
|
358
|
-
puts "### get_genes_by_pathway('path:eco00010')"
|
359
|
-
list = serv.get_genes_by_pathway("path:eco00010")
|
360
|
-
list.each do |gene|
|
361
|
-
puts gene
|
362
|
-
end
|
363
|
-
|
364
|
-
puts "### get_enzymes_by_pathway('path:map00010')"
|
365
|
-
list = serv.get_enzymes_by_pathway("path:map00010")
|
366
|
-
list.each do |enzyme|
|
367
|
-
puts enzyme
|
368
|
-
end
|
369
|
-
|
370
|
-
puts "### get_enzymes_by_pathway('path:eco00010')"
|
371
|
-
list = serv.get_enzymes_by_pathway("path:eco00010")
|
372
|
-
list.each do |enzyme|
|
373
|
-
puts enzyme
|
374
|
-
end
|
375
|
-
|
376
|
-
puts "### get_compounds_by_pathway('path:map00010')"
|
377
|
-
list = serv.get_compounds_by_pathway("path:map00010")
|
378
|
-
list.each do |compound|
|
379
|
-
puts compound
|
380
|
-
end
|
381
|
-
|
382
|
-
puts "### get_compounds_by_pathway('path:eco00010')"
|
383
|
-
list = serv.get_compounds_by_pathway("path:eco00010")
|
384
|
-
list.each do |compound|
|
385
|
-
puts compound
|
386
|
-
end
|
387
|
-
|
388
|
-
puts "### get_reactions_by_pathway('path:map00010')"
|
389
|
-
list = serv.get_reactions_by_pathway("path:map00010")
|
390
|
-
list.each do |reaction|
|
391
|
-
puts reaction
|
392
|
-
end
|
393
|
-
|
394
|
-
puts "### get_reactions_by_pathway('path:eco00010')"
|
395
|
-
list = serv.get_reactions_by_pathway("path:eco00010")
|
396
|
-
list.each do |reaction|
|
397
|
-
puts reaction
|
398
|
-
end
|
399
|
-
|
400
|
-
puts "==== pathway by objects"
|
401
|
-
|
402
|
-
puts "### get_pathways_by_genes(['eco:b0756', 'eco:b1002'])"
|
403
|
-
list = serv.get_pathways_by_genes(["eco:b0756", "eco:b1002"])
|
404
|
-
list.each do |path|
|
405
|
-
puts path
|
406
|
-
end
|
407
|
-
|
408
|
-
puts "### get_pathways_by_enzymes(['ec:5.1.3.3', 'ec:3.1.3.10'])"
|
409
|
-
list = serv.get_pathways_by_enzymes(["ec:5.1.3.3", "ec:3.1.3.10"])
|
410
|
-
list.each do |path|
|
411
|
-
puts path
|
412
|
-
end
|
413
|
-
|
414
|
-
puts "### get_pathways_by_compounds(['cpd:C00221', 'cpd:C00267'])"
|
415
|
-
list = serv.get_pathways_by_compounds(["cpd:C00221", "cpd:C00267"])
|
416
|
-
list.each do |path|
|
417
|
-
puts path
|
418
|
-
end
|
419
|
-
|
420
|
-
puts "### get_pathways_by_reactions(['rn:R00014', 'rn:R00710'])"
|
421
|
-
list = serv.get_pathways_by_reactions(["rn:R00014", "rn:R00710"])
|
422
|
-
list.each do |path|
|
423
|
-
puts path
|
424
|
-
end
|
425
|
-
|
426
|
-
puts "==== relation between objects"
|
427
|
-
|
428
|
-
puts "### get_linked_pathways('path:eco00620')"
|
429
|
-
list = serv.get_linked_pathways('path:eco00620')
|
430
|
-
list.each do |path|
|
431
|
-
puts path
|
432
|
-
end
|
433
|
-
|
434
|
-
puts "### get_genes_by_enzyme('ec:1.1.1.1', 'eco')"
|
435
|
-
list = serv.get_genes_by_enzyme("ec:1.1.1.1", "eco")
|
436
|
-
list.each do |gene|
|
437
|
-
puts gene
|
438
|
-
end
|
439
|
-
|
440
|
-
puts "### get_enzymes_by_gene('eco:b0002')"
|
441
|
-
list = serv.get_enzymes_by_gene("eco:b0002")
|
442
|
-
list.each do |enzyme|
|
443
|
-
puts enzyme
|
444
|
-
end
|
445
|
-
|
446
|
-
puts "### get_enzymes_by_compound('cpd:C00345')"
|
447
|
-
list = serv.get_enzymes_by_compound("cpd:C00345")
|
448
|
-
list.each do |enzyme|
|
449
|
-
puts enzyme
|
450
|
-
end
|
451
|
-
|
452
|
-
puts "### get_enzymes_by_reaction('rn:R00100')"
|
453
|
-
list = serv.get_enzymes_by_reaction("rn:R00100")
|
454
|
-
list.each do |enzyme|
|
455
|
-
puts enzyme
|
456
|
-
end
|
457
|
-
|
458
|
-
puts "### get_compounds_by_enzyme('ec:2.7.1.12')"
|
459
|
-
list = serv.get_compounds_by_enzyme("ec:2.7.1.12")
|
460
|
-
list.each do |compound|
|
461
|
-
puts compound
|
462
|
-
end
|
463
|
-
|
464
|
-
puts "### get_compounds_by_reaction('rn:R00100')"
|
465
|
-
list = serv.get_compounds_by_reaction("rn:R00100")
|
466
|
-
list.each do |compound|
|
467
|
-
puts compound
|
468
|
-
end
|
469
|
-
|
470
|
-
puts "### get_reactions_by_enzyme('ec:2.7.1.12')"
|
471
|
-
list = serv.get_reactions_by_enzyme("ec:2.7.1.12")
|
472
|
-
list.each do |reaction|
|
473
|
-
puts reaction
|
474
|
-
end
|
475
|
-
|
476
|
-
puts "### get_reactions_by_compound('cpd:C00199')"
|
477
|
-
list = serv.get_reactions_by_compound("cpd:C00199")
|
478
|
-
list.each do |reaction|
|
479
|
-
puts reaction
|
480
|
-
end
|
481
|
-
|
482
|
-
puts "=== GENES"
|
483
|
-
|
484
|
-
puts "### get_genes_by_organism('mge', 1, 5)"
|
485
|
-
list = serv.get_genes_by_organism("mge", 1, 5)
|
486
|
-
list.each do |gene|
|
487
|
-
puts gene
|
488
|
-
end
|
489
|
-
|
490
|
-
puts "# * get_all_genes_by_organism('mge')"
|
491
|
-
list = serv.get_all_genes_by_organism("mge")
|
492
|
-
list.each do |gene|
|
493
|
-
puts gene
|
494
|
-
end
|
495
|
-
|
496
|
-
puts "=== GENOME"
|
497
|
-
|
498
|
-
puts "### get_number_of_genes_by_organism(org)"
|
499
|
-
puts serv.get_number_of_genes_by_organism("mge")
|
500
|
-
|
501
|
-
#end
|
502
|
-
|