jandot-bio 1.2.1
Sign up to get free protection for your applications and to get access to all the features.
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +282 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/doc/Changes-0.7.rd +369 -0
- data/doc/KEGG_API.rd +1843 -0
- data/doc/KEGG_API.rd.ja +1834 -0
- data/doc/Tutorial.rd +1296 -0
- data/doc/Tutorial.rd.ja +2640 -0
- data/etc/bioinformatics/seqdatabase.ini +210 -0
- data/lib/bio.rb +279 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +351 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/report.rb +516 -0
- data/lib/bio/appl/blast/rexml.rb +135 -0
- data/lib/bio/appl/blast/rpsblast.rb +176 -0
- data/lib/bio/appl/blast/wublast.rb +550 -0
- data/lib/bio/appl/blast/xmlparser.rb +228 -0
- data/lib/bio/appl/blat/report.rb +489 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +237 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/phylip/alignment.rb +129 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/psort/report.rb +457 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +222 -0
- data/lib/bio/command.rb +337 -0
- data/lib/bio/data/aa.rb +349 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/embl/common.rb +336 -0
- data/lib/bio/db/embl/embl.rb +402 -0
- data/lib/bio/db/embl/sptr.rb +1283 -0
- data/lib/bio/db/embl/swissprot.rb +42 -0
- data/lib/bio/db/embl/trembl.rb +41 -0
- data/lib/bio/db/embl/uniprot.rb +42 -0
- data/lib/bio/db/fantom.rb +599 -0
- data/lib/bio/db/fasta.rb +907 -0
- data/lib/bio/db/genbank/common.rb +290 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/genbank.rb +215 -0
- data/lib/bio/db/genbank/genpept.rb +60 -0
- data/lib/bio/db/genbank/refseq.rb +18 -0
- data/lib/bio/db/gff.rb +174 -0
- data/lib/bio/db/go.rb +481 -0
- data/lib/bio/db/kegg/brite.rb +41 -0
- data/lib/bio/db/kegg/compound.rb +131 -0
- data/lib/bio/db/kegg/drug.rb +98 -0
- data/lib/bio/db/kegg/enzyme.rb +148 -0
- data/lib/bio/db/kegg/expression.rb +155 -0
- data/lib/bio/db/kegg/genes.rb +263 -0
- data/lib/bio/db/kegg/genome.rb +241 -0
- data/lib/bio/db/kegg/glycan.rb +170 -0
- data/lib/bio/db/kegg/keggtab.rb +357 -0
- data/lib/bio/db/kegg/kgml.rb +256 -0
- data/lib/bio/db/kegg/orthology.rb +136 -0
- data/lib/bio/db/kegg/reaction.rb +82 -0
- data/lib/bio/db/kegg/taxonomy.rb +331 -0
- data/lib/bio/db/lasergene.rb +209 -0
- data/lib/bio/db/litdb.rb +107 -0
- data/lib/bio/db/medline.rb +323 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +457 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/feature.rb +226 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +581 -0
- data/lib/bio/io/ebisoap.rb +158 -0
- data/lib/bio/io/ensembl.rb +229 -0
- data/lib/bio/io/fastacmd.rb +163 -0
- data/lib/bio/io/fetch.rb +181 -0
- data/lib/bio/io/flatfile.rb +1309 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/index.rb +1371 -0
- data/lib/bio/io/flatfile/indexer.rb +787 -0
- data/lib/bio/io/higet.rb +73 -0
- data/lib/bio/io/hinv.rb +442 -0
- data/lib/bio/io/keggapi.rb +805 -0
- data/lib/bio/io/ncbirest.rb +256 -0
- data/lib/bio/io/ncbisoap.rb +155 -0
- data/lib/bio/io/pubmed.rb +307 -0
- data/lib/bio/io/registry.rb +292 -0
- data/lib/bio/io/soapwsdl.rb +119 -0
- data/lib/bio/io/sql.rb +365 -0
- data/lib/bio/location.rb +772 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +854 -0
- data/lib/bio/reference.rb +623 -0
- data/lib/bio/sequence.rb +475 -0
- data/lib/bio/sequence/aa.rb +125 -0
- data/lib/bio/sequence/common.rb +333 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/format.rb +181 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +11 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +7 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +10 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +850 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +199 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/sample/any2fasta.rb +59 -0
- data/sample/biofetch.rb +475 -0
- data/sample/color_scheme_na.rb +91 -0
- data/sample/dbget +37 -0
- data/sample/enzymes.rb +78 -0
- data/sample/fasta2tab.rb +99 -0
- data/sample/fastagrep.rb +72 -0
- data/sample/fastasort.rb +54 -0
- data/sample/fsplit.rb +51 -0
- data/sample/gb2fasta.rb +30 -0
- data/sample/gb2tab.rb +325 -0
- data/sample/gbtab2mysql.rb +161 -0
- data/sample/genes2nuc.rb +33 -0
- data/sample/genes2pep.rb +33 -0
- data/sample/genes2tab.rb +81 -0
- data/sample/genome2rb.rb +29 -0
- data/sample/genome2tab.rb +76 -0
- data/sample/goslim.rb +303 -0
- data/sample/gt2fasta.rb +47 -0
- data/sample/na2aa.rb +34 -0
- data/sample/pmfetch.rb +42 -0
- data/sample/pmsearch.rb +42 -0
- data/sample/psortplot_html.rb +214 -0
- data/sample/ssearch2tab.rb +96 -0
- data/sample/tdiary.rb +158 -0
- data/sample/tfastx2tab.rb +100 -0
- data/sample/vs-genes.rb +212 -0
- data/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
- data/test/data/blast/b0002.faa.m0 +128 -0
- data/test/data/blast/b0002.faa.m7 +65 -0
- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/io/test_ensembl.rb +186 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_report.rb +417 -0
- data/test/unit/bio/appl/blast/test_xmlparser.rb +388 -0
- data/test/unit/bio/appl/genscan/test_report.rb +182 -0
- data/test/unit/bio/appl/hmmer/test_report.rb +342 -0
- data/test/unit/bio/appl/iprscan/test_report.rb +338 -0
- data/test/unit/bio/appl/mafft/test_report.rb +63 -0
- data/test/unit/bio/appl/sosui/test_report.rb +81 -0
- data/test/unit/bio/appl/targetp/test_report.rb +146 -0
- data/test/unit/bio/appl/test_blast.rb +163 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_pts1.rb +140 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +126 -0
- data/test/unit/bio/data/test_aa.rb +90 -0
- data/test/unit/bio/data/test_codontable.rb +107 -0
- data/test/unit/bio/data/test_na.rb +80 -0
- data/test/unit/bio/db/embl/test_common.rb +117 -0
- data/test/unit/bio/db/embl/test_embl.rb +214 -0
- data/test/unit/bio/db/embl/test_embl_rel89.rb +219 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1775 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +31 -0
- data/test/unit/bio/db/kegg/test_genes.rb +45 -0
- data/test/unit/bio/db/pdb/test_pdb.rb +152 -0
- data/test/unit/bio/db/test_aaindex.rb +197 -0
- data/test/unit/bio/db/test_fasta.rb +250 -0
- data/test/unit/bio/db/test_gff.rb +127 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +360 -0
- data/test/unit/bio/db/test_prosite.rb +1437 -0
- data/test/unit/bio/db/test_rebase.rb +101 -0
- data/test/unit/bio/db/test_soft.rb +138 -0
- data/test/unit/bio/io/test_ddbjxml.rb +75 -0
- data/test/unit/bio/io/test_ensembl.rb +109 -0
- data/test/unit/bio/io/test_fastacmd.rb +42 -0
- data/test/unit/bio/io/test_flatfile.rb +237 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +103 -0
- data/test/unit/bio/sequence/test_common.rb +174 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_na.rb +330 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +185 -0
- data/test/unit/bio/test_alignment.rb +1025 -0
- data/test/unit/bio/test_command.rb +288 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +116 -0
- data/test/unit/bio/test_location.rb +39 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +473 -0
- data/test/unit/bio/test_reference.rb +224 -0
- data/test/unit/bio/test_sequence.rb +329 -0
- data/test/unit/bio/test_shell.rb +18 -0
- data/test/unit/bio/test_tree.rb +593 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb +299 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb +103 -0
- data/test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb +240 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb +101 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb +75 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb +73 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb +53 -0
- data/test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb +104 -0
- data/test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb +83 -0
- data/test/unit/bio/util/restriction_enzyme/test_analysis.rb +246 -0
- data/test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb +44 -0
- data/test/unit/bio/util/restriction_enzyme/test_double_stranded.rb +115 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb +147 -0
- data/test/unit/bio/util/restriction_enzyme/test_string_formatting.rb +60 -0
- data/test/unit/bio/util/test_color_scheme.rb +33 -0
- data/test/unit/bio/util/test_contingency_table.rb +94 -0
- data/test/unit/bio/util/test_restriction_enzyme.rb +42 -0
- data/test/unit/bio/util/test_sirna.rb +245 -0
- metadata +479 -0
data/sample/gt2fasta.rb
ADDED
@@ -0,0 +1,47 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# gt2fasta.rb - convert GenBank translations into FASTA format (pep)
|
4
|
+
#
|
5
|
+
# Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
|
6
|
+
#
|
7
|
+
# This program is free software; you can redistribute it and/or modify
|
8
|
+
# it under the terms of the GNU General Public License as published by
|
9
|
+
# the Free Software Foundation; either version 2 of the License, or
|
10
|
+
# (at your option) any later version.
|
11
|
+
#
|
12
|
+
# This program is distributed in the hope that it will be useful,
|
13
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
14
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
15
|
+
# GNU General Public License for more details.
|
16
|
+
#
|
17
|
+
# $Id: gt2fasta.rb,v 0.3 2002/04/15 03:06:17 k Exp $
|
18
|
+
#
|
19
|
+
|
20
|
+
require 'bio/io/flatfile'
|
21
|
+
require 'bio/feature'
|
22
|
+
require 'bio/db/genbank'
|
23
|
+
|
24
|
+
include Bio
|
25
|
+
|
26
|
+
ff = FlatFile.new(GenBank, ARGF)
|
27
|
+
|
28
|
+
while gb = ff.next_entry
|
29
|
+
|
30
|
+
orf = 0
|
31
|
+
gb.features.each do |f|
|
32
|
+
f = f.assoc
|
33
|
+
if aaseq = f['translation']
|
34
|
+
orf += 1
|
35
|
+
gene = [
|
36
|
+
f['gene'],
|
37
|
+
f['product'],
|
38
|
+
f['note'],
|
39
|
+
f['function']
|
40
|
+
].compact.join(', ')
|
41
|
+
definition = "gp:#{gb.entry_id}_#{orf} #{gene} [#{gb.organism}]"
|
42
|
+
print aaseq.to_fasta(definition, 70)
|
43
|
+
end
|
44
|
+
end
|
45
|
+
|
46
|
+
end
|
47
|
+
|
data/sample/na2aa.rb
ADDED
@@ -0,0 +1,34 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# translate.rb - translate any NA input into AA FASTA format
|
4
|
+
#
|
5
|
+
# Copyright (C) 2008 KATAYAMA Toshiaki <k@bioruby.org> & Pjotr Prins
|
6
|
+
#
|
7
|
+
# This program is free software; you can redistribute it and/or modify
|
8
|
+
# it under the terms of the GNU General Public License as published by
|
9
|
+
# the Free Software Foundation; either version 2 of the License, or
|
10
|
+
# (at your option) any later version.
|
11
|
+
#
|
12
|
+
# This program is distributed in the hope that it will be useful,
|
13
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
14
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
15
|
+
# GNU General Public License for more details.
|
16
|
+
#
|
17
|
+
# $Id: na2aa.rb,v 1.1 2008/02/06 16:25:53 pjotr Exp $
|
18
|
+
#
|
19
|
+
|
20
|
+
require 'bio'
|
21
|
+
require 'pp'
|
22
|
+
|
23
|
+
include Bio
|
24
|
+
|
25
|
+
ARGV.each do | fn |
|
26
|
+
Bio::FlatFile.auto(fn).each do | item |
|
27
|
+
seq = Sequence::NA.new(item.data)
|
28
|
+
aa = seq.translate
|
29
|
+
aa.gsub!(/X/,'-')
|
30
|
+
rec = Bio::FastaFormat.new('> '+item.definition+"\n"+aa)
|
31
|
+
print rec
|
32
|
+
end
|
33
|
+
end
|
34
|
+
|
data/sample/pmfetch.rb
ADDED
@@ -0,0 +1,42 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# pmfetch.rb - generate BibTeX format reference list by PubMed ID list
|
4
|
+
#
|
5
|
+
# Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
|
6
|
+
#
|
7
|
+
# This program is free software; you can redistribute it and/or modify
|
8
|
+
# it under the terms of the GNU General Public License as published by
|
9
|
+
# the Free Software Foundation; either version 2 of the License, or
|
10
|
+
# (at your option) any later version.
|
11
|
+
#
|
12
|
+
# This program is distributed in the hope that it will be useful,
|
13
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
14
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
15
|
+
# GNU General Public License for more details.
|
16
|
+
#
|
17
|
+
# You should have received a copy of the GNU General Public License
|
18
|
+
# along with this program; if not, write to the Free Software
|
19
|
+
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
20
|
+
#
|
21
|
+
# $Id: pmfetch.rb,v 1.2 2002/07/23 04:52:03 k Exp $
|
22
|
+
#
|
23
|
+
|
24
|
+
require 'bio'
|
25
|
+
|
26
|
+
if ARGV[0] =~ /-f/
|
27
|
+
ARGV.shift
|
28
|
+
form = ARGV.shift
|
29
|
+
else
|
30
|
+
form = 'bibtex'
|
31
|
+
end
|
32
|
+
|
33
|
+
ARGV.each do |id|
|
34
|
+
entry = Bio::PubMed.query(id)
|
35
|
+
case form
|
36
|
+
when 'medline'
|
37
|
+
puts entry
|
38
|
+
else
|
39
|
+
puts Bio::MEDLINE.new(entry).reference.send(form)
|
40
|
+
end
|
41
|
+
end
|
42
|
+
|
data/sample/pmsearch.rb
ADDED
@@ -0,0 +1,42 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# pmsearch.rb - generate BibTeX format reference list by PubMed keyword search
|
4
|
+
#
|
5
|
+
# Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
|
6
|
+
#
|
7
|
+
# This program is free software; you can redistribute it and/or modify
|
8
|
+
# it under the terms of the GNU General Public License as published by
|
9
|
+
# the Free Software Foundation; either version 2 of the License, or
|
10
|
+
# (at your option) any later version.
|
11
|
+
#
|
12
|
+
# This program is distributed in the hope that it will be useful,
|
13
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
14
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
15
|
+
# GNU General Public License for more details.
|
16
|
+
#
|
17
|
+
# You should have received a copy of the GNU General Public License
|
18
|
+
# along with this program; if not, write to the Free Software
|
19
|
+
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
20
|
+
#
|
21
|
+
# $Id: pmsearch.rb,v 1.2 2002/07/23 04:52:03 k Exp $
|
22
|
+
#
|
23
|
+
|
24
|
+
require 'bio'
|
25
|
+
|
26
|
+
if ARGV[0] =~ /-f/
|
27
|
+
ARGV.shift
|
28
|
+
form = ARGV.shift
|
29
|
+
else
|
30
|
+
form = 'bibtex'
|
31
|
+
end
|
32
|
+
|
33
|
+
entries = Bio::PubMed.search(ARGV.join(' '))
|
34
|
+
entries.each do |entry|
|
35
|
+
case form
|
36
|
+
when 'medline'
|
37
|
+
puts entry
|
38
|
+
else
|
39
|
+
puts Bio::MEDLINE.new(entry).reference.send(form)
|
40
|
+
end
|
41
|
+
end
|
42
|
+
|
@@ -0,0 +1,214 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# psortplot_html.rb - A KEGG API demo script. Generates a HTML file of
|
4
|
+
# genes marked by PSORT II predictions onto a
|
5
|
+
# KEGG/PATHWAY map.
|
6
|
+
#
|
7
|
+
# Usage:
|
8
|
+
#
|
9
|
+
# % ruby psortplot_html.rb
|
10
|
+
# % cat sce00010_psort2.html
|
11
|
+
# % ruby psortplot_html.rb path:eco00010
|
12
|
+
# % cat eco00010_psort2.html
|
13
|
+
#
|
14
|
+
# Copyright:: Copyright (C) 2005
|
15
|
+
# Mitsuteru C. Nakao <n@bioruby.org>
|
16
|
+
# License:: The Ruby License
|
17
|
+
#
|
18
|
+
# $Id: psortplot_html.rb,v 1.3 2007/04/05 23:35:42 trevor Exp $
|
19
|
+
#
|
20
|
+
|
21
|
+
require 'bio'
|
22
|
+
|
23
|
+
class KEGG
|
24
|
+
DBGET_BASEURI = 'http://kegg.com/dbget-bin'
|
25
|
+
WWW_BGET_BASEURI = DBGET_BASEURI + '/www_bget'
|
26
|
+
WWW_PATHWAY_BASEURI = DBGET_BASEURI + '/get_pathway'
|
27
|
+
|
28
|
+
# path := path:sce00010
|
29
|
+
def self.link_pathway(path0)
|
30
|
+
path, path = path0.split(':')
|
31
|
+
org_name = path.scan(/(^\w{3})/).to_s
|
32
|
+
mapno = path.sub(org_name, '')
|
33
|
+
str = "<a href='#{WWW_PATHWAY_BASEURI}?org_name=#{org_name}&mapno=#{mapno}'>#{path0}</a>"
|
34
|
+
end
|
35
|
+
|
36
|
+
# ec_num := ec:1.2.3.4
|
37
|
+
def self.link_ec(ec_num)
|
38
|
+
ec = ec_num.sub(/^ec:/, '')
|
39
|
+
str = "<a href='#{WWW_BGET_BASEURI}?enzyme+#{ec}'>#{ec_num}</a>"
|
40
|
+
return str
|
41
|
+
end
|
42
|
+
|
43
|
+
# gene := eco:b0002
|
44
|
+
def self.link_genes(gene)
|
45
|
+
org_name, gene_name = gene.split(':')
|
46
|
+
str = "<a href='#{WWW_BGET_BASEURI}?#{org_name}+#{gene_name}'>#{gene}</a>"
|
47
|
+
return str
|
48
|
+
end
|
49
|
+
end
|
50
|
+
|
51
|
+
|
52
|
+
class PSORT
|
53
|
+
COLOR_Palette = {
|
54
|
+
'csk' => "#FF0000", # 'cytoskeletal'
|
55
|
+
'cyt' => "#FF8000", # 'cytoplasmic'
|
56
|
+
'nuc' => "#FFFF00", # 'nuclear'
|
57
|
+
'mit' => "#80FF00", # 'mitochondrial'
|
58
|
+
'ves' => "#00FF00", # 'vesicles of secretory system'
|
59
|
+
'end' => "#00FF80", # 'endoplasmic reticulum'
|
60
|
+
'gol' => "#00FFFF", # 'Golgi'
|
61
|
+
'vac' => "#0080FF", # 'vacuolar'
|
62
|
+
'pla' => "#0000FF", # 'plasma membrane'
|
63
|
+
'pox' => "#8000FF", # 'peroxisomal'
|
64
|
+
'exc' => "#FF00FF", # 'extracellular, including cell wall'
|
65
|
+
'---' => "#FF0080" # 'other'
|
66
|
+
}
|
67
|
+
end
|
68
|
+
|
69
|
+
|
70
|
+
|
71
|
+
|
72
|
+
keggapi = Bio::KEGG::API.new
|
73
|
+
psort2serv = Bio::PSORT::PSORT2.imsut
|
74
|
+
|
75
|
+
# Obtains a list of genes on specified pathway
|
76
|
+
pathway = ARGV.shift || "path:sce00010"
|
77
|
+
genes = keggapi.get_genes_by_pathway(pathway)
|
78
|
+
|
79
|
+
scl = Hash.new # protein subcelluler localizations
|
80
|
+
ec = Hash.new # EC numbers
|
81
|
+
|
82
|
+
serial = 0
|
83
|
+
sync_default = $stdout.sync
|
84
|
+
$stdout.sync = true
|
85
|
+
genes.each do |gene|
|
86
|
+
print "#{(serial += 1).to_s.rjust(genes.size.to_s.size)}\t#{gene}\t"
|
87
|
+
# Obtains amino acid sequence from KEGG GENES entry
|
88
|
+
aaseq = keggapi.get_aaseqs([gene])
|
89
|
+
|
90
|
+
# Predicts protein subcellualr localization
|
91
|
+
result = psort2serv.exec(aaseq)
|
92
|
+
scl[gene] = result.pred
|
93
|
+
print "#{scl[gene]}\t"
|
94
|
+
|
95
|
+
# Obtains the EC number from KEGG GENES entry
|
96
|
+
ec[gene] = keggapi.get_enzymes_by_gene(gene)
|
97
|
+
puts "#{ec[gene].inspect}"
|
98
|
+
end
|
99
|
+
$stdout.sync = sync_default
|
100
|
+
|
101
|
+
|
102
|
+
|
103
|
+
|
104
|
+
fg_list = Array.new
|
105
|
+
bg_list = Array.new
|
106
|
+
|
107
|
+
genes.each do |gene|
|
108
|
+
fg_list << "#FF0000"
|
109
|
+
bg_list << PSORT::COLOR_Palette[scl[gene]]
|
110
|
+
end
|
111
|
+
|
112
|
+
# coloring KEGG pathway according to gene's localization
|
113
|
+
url = keggapi.color_pathway_by_objects(pathway, genes, fg_list, bg_list)
|
114
|
+
puts "#{url} downloaded."
|
115
|
+
|
116
|
+
# remove "path:" prefix from pathway_id
|
117
|
+
path_code = pathway.sub(/^path:/, '')
|
118
|
+
|
119
|
+
# save the result image
|
120
|
+
image_file = "#{path_code}_psort2.gif"
|
121
|
+
begin
|
122
|
+
keggapi.save_image(url, image_file)
|
123
|
+
end
|
124
|
+
|
125
|
+
|
126
|
+
# create html with a color palette
|
127
|
+
html = <<END
|
128
|
+
<html>
|
129
|
+
<head>
|
130
|
+
<title>PSORT II prediction protein subcellular localization map of KEGG/PATHWAY (#{pathway})</title>
|
131
|
+
<style>
|
132
|
+
table { border-collapse: collapse; }
|
133
|
+
td { border: 1px solid black; padding: 5px; }
|
134
|
+
td.outer { border: none; vertical-align: top; }
|
135
|
+
</style>
|
136
|
+
</head>
|
137
|
+
<body>
|
138
|
+
<h1><li><a href="http://psort.ims.u-tokyo.ac.jp/helpwww2.html">PSORT II</a> prediction protein subcellular localization map of <a href="http://kegg.com/kegg/pathway.html">KEGG/PATHWAY</a> (<a href="">#{KEGG.link_pathway(pathway)})</h1>
|
139
|
+
|
140
|
+
<table>
|
141
|
+
<tr>
|
142
|
+
<td class=outer>
|
143
|
+
<table>
|
144
|
+
<tr>
|
145
|
+
<th></th>
|
146
|
+
<th>EC</th>
|
147
|
+
<th>Gene</th>
|
148
|
+
<th>Localization</th>
|
149
|
+
</tr>
|
150
|
+
END
|
151
|
+
|
152
|
+
|
153
|
+
# generate gene table with localization
|
154
|
+
names = Bio::PSORT::PSORT2::SclNames
|
155
|
+
multi_genes = Hash.new(0)
|
156
|
+
|
157
|
+
ec.values.flatten.sort.uniq.each do |ec_num|
|
158
|
+
ec.find_all {|x| x[1].include?(ec_num) }.each do |gene|
|
159
|
+
gene = gene[0]
|
160
|
+
loc = scl[gene]
|
161
|
+
color = PSORT::COLOR_Palette[loc]
|
162
|
+
name = names[loc]
|
163
|
+
multi_genes[gene] += 1
|
164
|
+
|
165
|
+
html += <<END
|
166
|
+
<tr>
|
167
|
+
<td>#{multi_genes[gene]}</td>
|
168
|
+
<td>#{KEGG.link_ec(ec_num)}</td>
|
169
|
+
<td>#{KEGG.link_genes(gene)}</td>
|
170
|
+
<td bgcolor="#{color}">#{name}</td>
|
171
|
+
</tr>
|
172
|
+
END
|
173
|
+
end
|
174
|
+
end
|
175
|
+
|
176
|
+
html += <<END
|
177
|
+
</table>
|
178
|
+
</td>
|
179
|
+
<td class=outer>
|
180
|
+
<table>
|
181
|
+
<tr>
|
182
|
+
<th>Code</th>
|
183
|
+
<th>Color</th>
|
184
|
+
</tr>
|
185
|
+
END
|
186
|
+
|
187
|
+
# generate color code table also
|
188
|
+
PSORT::COLOR_Palette.sort.each do |code, color|
|
189
|
+
html += <<END
|
190
|
+
<tr>
|
191
|
+
<td>#{code}</td>
|
192
|
+
<td bgcolor="#{color}">#{names[code]}</td>
|
193
|
+
</tr>
|
194
|
+
END
|
195
|
+
end
|
196
|
+
|
197
|
+
html += <<END
|
198
|
+
</table>
|
199
|
+
</td>
|
200
|
+
</tr>
|
201
|
+
</table>
|
202
|
+
<br>
|
203
|
+
<img src="#{image_file}">
|
204
|
+
</body>
|
205
|
+
</html>
|
206
|
+
END
|
207
|
+
|
208
|
+
# save generated HTML file
|
209
|
+
html_file = "#{path_code}_psort2.html"
|
210
|
+
File.open(html_file, "w+") do |file|
|
211
|
+
file.puts html
|
212
|
+
end
|
213
|
+
|
214
|
+
puts "Open #{html_file}"
|
@@ -0,0 +1,96 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# ssearch2tab.rb - convert SSEARCH output into tab delimited data for MySQL
|
4
|
+
#
|
5
|
+
# Usage:
|
6
|
+
#
|
7
|
+
# % ssearch2tab.rb SSEARCH-output-file[s] > ssearch_results.tab
|
8
|
+
# % mysql < ssearch_results.sql (use sample at the end of this file)
|
9
|
+
#
|
10
|
+
# Format accepted:
|
11
|
+
#
|
12
|
+
# % ssearch3[3][_t] -Q -H -m 6 query.f target.f > SSEARCH-output-file
|
13
|
+
#
|
14
|
+
# Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
|
15
|
+
#
|
16
|
+
# This program is free software; you can redistribute it and/or modify
|
17
|
+
# it under the terms of the GNU General Public License as published by
|
18
|
+
# the Free Software Foundation; either version 2 of the License, or
|
19
|
+
# (at your option) any later version.
|
20
|
+
#
|
21
|
+
# This program is distributed in the hope that it will be useful,
|
22
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
23
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
24
|
+
# GNU General Public License for more details.
|
25
|
+
#
|
26
|
+
# $Id: ssearch2tab.rb,v 0.1 2001/06/21 08:25:58 katayama Exp $
|
27
|
+
#
|
28
|
+
|
29
|
+
while gets
|
30
|
+
|
31
|
+
# query
|
32
|
+
if /^\S+: (\d+) aa$/
|
33
|
+
q_len = $1
|
34
|
+
end
|
35
|
+
|
36
|
+
# each hit
|
37
|
+
if /^>>([^>]\S+).*\((\d+) aa\)$/
|
38
|
+
target = $1
|
39
|
+
t_len = $2
|
40
|
+
|
41
|
+
# d = dummy variable
|
42
|
+
d, d, d, swopt, d, zscore, d, bits, d, evalue =
|
43
|
+
gets.split(/\s+/)
|
44
|
+
d, d, sw, ident, d, ugident, d, d, overlap, d, d, lap =
|
45
|
+
gets.split(/\s+/)
|
46
|
+
|
47
|
+
# query-hit pair
|
48
|
+
print "#{$FILENAME}\t#{q_len}\t#{target}\t#{t_len}"
|
49
|
+
|
50
|
+
# pick up values
|
51
|
+
ary = [
|
52
|
+
swopt,
|
53
|
+
zscore,
|
54
|
+
bits,
|
55
|
+
evalue,
|
56
|
+
sw,
|
57
|
+
ident,
|
58
|
+
ugident,
|
59
|
+
overlap,
|
60
|
+
lap
|
61
|
+
]
|
62
|
+
|
63
|
+
# print values
|
64
|
+
for i in ary
|
65
|
+
i.tr!('^0-9.:e\-','')
|
66
|
+
print "\t#{i}"
|
67
|
+
end
|
68
|
+
|
69
|
+
print "\n"
|
70
|
+
|
71
|
+
end
|
72
|
+
end
|
73
|
+
|
74
|
+
=begin MySQL ssearch_results.sql sample
|
75
|
+
|
76
|
+
CREATE DATABASE IF NOT EXISTS db_name;
|
77
|
+
CREATE TABLE IF NOT EXISTS db_name.table_name (
|
78
|
+
query varchar(25) not NULL,
|
79
|
+
q_len integer unsigned default 0,
|
80
|
+
target varchar(25) not NULL,
|
81
|
+
t_len integer unsigned default 0,
|
82
|
+
swopt integer unsigned default 0,
|
83
|
+
zscore float default 0.0,
|
84
|
+
bits float default 0.0,
|
85
|
+
evalue float default 0.0,
|
86
|
+
sw integer unsigned default 0,
|
87
|
+
ident float default 0.0,
|
88
|
+
ugident float default 0.0,
|
89
|
+
overlap integer unsigned default 0,
|
90
|
+
lap_at varchar(25) default NULL
|
91
|
+
);
|
92
|
+
LOAD DATA LOCAL INFILE 'ssearch_results.tab' INTO TABLE db_name.table_name;
|
93
|
+
|
94
|
+
=end
|
95
|
+
|
96
|
+
|