bio 0.7.0
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- data/bin/bioruby +107 -0
- data/bin/br_biofetch.rb +59 -0
- data/bin/br_bioflat.rb +294 -0
- data/bin/br_biogetseq.rb +57 -0
- data/bin/br_pmfetch.rb +431 -0
- data/doc/BioRuby.rd.ja +225 -0
- data/doc/Changes-0.7.rd +236 -0
- data/doc/Design.rd.ja +341 -0
- data/doc/KEGG_API.rd +1437 -0
- data/doc/KEGG_API.rd.ja +1399 -0
- data/doc/TODO.rd.ja +138 -0
- data/doc/Tutorial.rd +1138 -0
- data/doc/Tutorial.rd.ja +2110 -0
- data/etc/bioinformatics/seqdatabase.ini +210 -0
- data/lib/bio.rb +256 -0
- data/lib/bio/alignment.rb +1906 -0
- data/lib/bio/appl/bl2seq/report.rb +350 -0
- data/lib/bio/appl/blast.rb +269 -0
- data/lib/bio/appl/blast/format0.rb +1402 -0
- data/lib/bio/appl/blast/format8.rb +95 -0
- data/lib/bio/appl/blast/report.rb +652 -0
- data/lib/bio/appl/blast/rexml.rb +151 -0
- data/lib/bio/appl/blast/wublast.rb +553 -0
- data/lib/bio/appl/blast/xmlparser.rb +222 -0
- data/lib/bio/appl/blat/report.rb +392 -0
- data/lib/bio/appl/clustalw.rb +191 -0
- data/lib/bio/appl/clustalw/report.rb +154 -0
- data/lib/bio/appl/emboss.rb +68 -0
- data/lib/bio/appl/fasta.rb +262 -0
- data/lib/bio/appl/fasta/format10.rb +428 -0
- data/lib/bio/appl/fasta/format6.rb +37 -0
- data/lib/bio/appl/genscan/report.rb +570 -0
- data/lib/bio/appl/hmmer.rb +129 -0
- data/lib/bio/appl/hmmer/report.rb +556 -0
- data/lib/bio/appl/mafft.rb +222 -0
- data/lib/bio/appl/mafft/report.rb +119 -0
- data/lib/bio/appl/psort.rb +555 -0
- data/lib/bio/appl/psort/report.rb +473 -0
- data/lib/bio/appl/sim4.rb +134 -0
- data/lib/bio/appl/sim4/report.rb +501 -0
- data/lib/bio/appl/sosui/report.rb +166 -0
- data/lib/bio/appl/spidey/report.rb +604 -0
- data/lib/bio/appl/targetp/report.rb +283 -0
- data/lib/bio/appl/tmhmm/report.rb +238 -0
- data/lib/bio/command.rb +166 -0
- data/lib/bio/data/aa.rb +354 -0
- data/lib/bio/data/codontable.rb +740 -0
- data/lib/bio/data/na.rb +226 -0
- data/lib/bio/db.rb +340 -0
- data/lib/bio/db/aaindex.rb +280 -0
- data/lib/bio/db/embl/common.rb +332 -0
- data/lib/bio/db/embl/embl.rb +446 -0
- data/lib/bio/db/embl/sptr.rb +954 -0
- data/lib/bio/db/embl/swissprot.rb +32 -0
- data/lib/bio/db/embl/trembl.rb +31 -0
- data/lib/bio/db/embl/uniprot.rb +32 -0
- data/lib/bio/db/fantom.rb +604 -0
- data/lib/bio/db/fasta.rb +869 -0
- data/lib/bio/db/genbank/common.rb +299 -0
- data/lib/bio/db/genbank/ddbj.rb +34 -0
- data/lib/bio/db/genbank/genbank.rb +354 -0
- data/lib/bio/db/genbank/genpept.rb +73 -0
- data/lib/bio/db/genbank/refseq.rb +31 -0
- data/lib/bio/db/gff.rb +106 -0
- data/lib/bio/db/go.rb +497 -0
- data/lib/bio/db/kegg/brite.rb +51 -0
- data/lib/bio/db/kegg/cell.rb +88 -0
- data/lib/bio/db/kegg/compound.rb +130 -0
- data/lib/bio/db/kegg/enzyme.rb +125 -0
- data/lib/bio/db/kegg/expression.rb +173 -0
- data/lib/bio/db/kegg/genes.rb +293 -0
- data/lib/bio/db/kegg/genome.rb +362 -0
- data/lib/bio/db/kegg/glycan.rb +213 -0
- data/lib/bio/db/kegg/keggtab.rb +418 -0
- data/lib/bio/db/kegg/kgml.rb +299 -0
- data/lib/bio/db/kegg/ko.rb +178 -0
- data/lib/bio/db/kegg/reaction.rb +97 -0
- data/lib/bio/db/litdb.rb +131 -0
- data/lib/bio/db/medline.rb +317 -0
- data/lib/bio/db/nbrf.rb +199 -0
- data/lib/bio/db/pdb.rb +38 -0
- data/lib/bio/db/pdb/atom.rb +60 -0
- data/lib/bio/db/pdb/chain.rb +117 -0
- data/lib/bio/db/pdb/model.rb +106 -0
- data/lib/bio/db/pdb/pdb.rb +1682 -0
- data/lib/bio/db/pdb/residue.rb +122 -0
- data/lib/bio/db/pdb/utils.rb +234 -0
- data/lib/bio/db/prosite.rb +616 -0
- data/lib/bio/db/rebase.rb +417 -0
- data/lib/bio/db/transfac.rb +387 -0
- data/lib/bio/feature.rb +201 -0
- data/lib/bio/io/brdb.rb +103 -0
- data/lib/bio/io/das.rb +471 -0
- data/lib/bio/io/dbget.rb +212 -0
- data/lib/bio/io/ddbjxml.rb +614 -0
- data/lib/bio/io/fastacmd.rb +123 -0
- data/lib/bio/io/fetch.rb +114 -0
- data/lib/bio/io/flatfile.rb +496 -0
- data/lib/bio/io/flatfile/bdb.rb +266 -0
- data/lib/bio/io/flatfile/index.rb +1308 -0
- data/lib/bio/io/flatfile/indexer.rb +778 -0
- data/lib/bio/io/higet.rb +92 -0
- data/lib/bio/io/keggapi.rb +863 -0
- data/lib/bio/io/pubmed.rb +189 -0
- data/lib/bio/io/registry.rb +308 -0
- data/lib/bio/io/soapwsdl.rb +114 -0
- data/lib/bio/io/sql.rb +428 -0
- data/lib/bio/location.rb +650 -0
- data/lib/bio/pathway.rb +991 -0
- data/lib/bio/reference.rb +308 -0
- data/lib/bio/sequence.rb +593 -0
- data/lib/bio/shell.rb +51 -0
- data/lib/bio/shell/core.rb +512 -0
- data/lib/bio/shell/plugin/codon.rb +228 -0
- data/lib/bio/shell/plugin/entry.rb +85 -0
- data/lib/bio/shell/plugin/flatfile.rb +119 -0
- data/lib/bio/shell/plugin/keggapi.rb +187 -0
- data/lib/bio/shell/plugin/midi.rb +448 -0
- data/lib/bio/shell/plugin/obda.rb +63 -0
- data/lib/bio/shell/plugin/seq.rb +238 -0
- data/lib/bio/shell/session.rb +214 -0
- data/lib/bio/util/color_scheme.rb +214 -0
- data/lib/bio/util/color_scheme/buried.rb +78 -0
- data/lib/bio/util/color_scheme/helix.rb +78 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +83 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +50 -0
- data/lib/bio/util/color_scheme/strand.rb +78 -0
- data/lib/bio/util/color_scheme/taylor.rb +69 -0
- data/lib/bio/util/color_scheme/turn.rb +78 -0
- data/lib/bio/util/color_scheme/zappo.rb +69 -0
- data/lib/bio/util/contingency_table.rb +337 -0
- data/lib/bio/util/sirna.rb +306 -0
- data/lib/bioruby.rb +34 -0
- data/sample/biofetch.rb +475 -0
- data/sample/color_scheme_na.rb +99 -0
- data/sample/dbget +37 -0
- data/sample/fasta2tab.rb +99 -0
- data/sample/fsplit.rb +51 -0
- data/sample/gb2fasta.rb +31 -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 +311 -0
- data/sample/gt2fasta.rb +47 -0
- data/sample/pmfetch.rb +42 -0
- data/sample/pmsearch.rb +42 -0
- data/sample/psortplot_html.rb +222 -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/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/blast/eco:b0002.faa +15 -0
- data/test/data/blast/eco:b0002.faa.m0 +128 -0
- data/test/data/blast/eco:b0002.faa.m7 +65 -0
- data/test/data/blast/eco:b0002.faa.m8 +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/runner.rb +10 -0
- data/test/unit/bio/appl/blast/test_report.rb +427 -0
- data/test/unit/bio/appl/blast/test_xmlparser.rb +400 -0
- data/test/unit/bio/appl/genscan/test_report.rb +195 -0
- data/test/unit/bio/appl/sosui/test_report.rb +94 -0
- data/test/unit/bio/appl/targetp/test_report.rb +159 -0
- data/test/unit/bio/appl/test_blast.rb +159 -0
- data/test/unit/bio/appl/test_fasta.rb +142 -0
- data/test/unit/bio/appl/tmhmm/test_report.rb +139 -0
- data/test/unit/bio/data/test_aa.rb +103 -0
- data/test/unit/bio/data/test_codontable.rb +120 -0
- data/test/unit/bio/data/test_na.rb +89 -0
- data/test/unit/bio/db/embl/test_common.rb +130 -0
- data/test/unit/bio/db/embl/test_embl.rb +227 -0
- data/test/unit/bio/db/embl/test_sptr.rb +268 -0
- data/test/unit/bio/db/embl/test_uniprot.rb +44 -0
- data/test/unit/bio/db/kegg/test_genes.rb +58 -0
- data/test/unit/bio/db/test_fasta.rb +263 -0
- data/test/unit/bio/db/test_gff.rb +140 -0
- data/test/unit/bio/db/test_prosite.rb +1450 -0
- data/test/unit/bio/io/test_ddbjxml.rb +87 -0
- data/test/unit/bio/io/test_soapwsdl.rb +45 -0
- data/test/unit/bio/shell/plugin/test_seq.rb +175 -0
- data/test/unit/bio/test_alignment.rb +1028 -0
- data/test/unit/bio/test_command.rb +71 -0
- data/test/unit/bio/test_db.rb +109 -0
- data/test/unit/bio/test_feature.rb +128 -0
- data/test/unit/bio/test_location.rb +51 -0
- data/test/unit/bio/test_pathway.rb +485 -0
- data/test/unit/bio/test_sequence.rb +386 -0
- data/test/unit/bio/test_shell.rb +31 -0
- data/test/unit/bio/util/test_color_scheme.rb +45 -0
- data/test/unit/bio/util/test_contingency_table.rb +106 -0
- data/test/unit/bio/util/test_sirna.rb +258 -0
- metadata +295 -0
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#
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# = bio/appl/psort/report.rb - PSORT systems report classes
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#
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# Copyright:: Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>
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# License:: LGPL
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#
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# $Id: report.rb,v 1.12 2005/11/03 10:50:58 nakao Exp $
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#
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# == A Report classes for PSORT Systems
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#
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#--
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#
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# This library is free software; you can redistribute it and/or
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# modify it under the terms of the GNU Lesser General Public
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# License as published by the Free Software Foundation; either
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# version 2 of the License, or (at your option) any later version.
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#
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# This library is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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# Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this library; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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#
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# ++
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#
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require 'bio/sequence'
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require 'bio/appl/psort'
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module Bio
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class PSORT
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class PSORT1
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# = Bio::PSORT::PSORT1::Report
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# Parser class for PSORT1 output report.
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#
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# == Example
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class Report
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# Returns aBio::PSORT::PSORT1::Report.
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def self.parser(output_report)
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self.default_parser(output_report)
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end
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# Returns aBio::PSORT::PSORT1::Report.
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def self.default_parser(output_report)
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rpt = self.new
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rpt.raw = output_report
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query_info = output_report.scan(/^Query Information\n\n(.+?)\n\n/m)[0][0].split(/\n/)
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result_info = output_report.scan(/^Result Information\n\n(.+?)\n\n\*/m)[0][0]
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step1 = output_report.scan(/^\*\*\* Reasoning Step: 1\n\n(.+?)\n\n/m)[0][0]
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step2 = output_report.scan(/^\*\*\* Reasoning Step: 2\n\n(.+?)\n\n/m)[0][0]
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final_result = output_report.scan(/\n\n----- Final Results -----\n\n(.+?)\n\n\n/m)[0][0]
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rpt.entry_id = query_info[2].scan(/^>(\S+) */).to_s
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rpt.origin = query_info[0].scan(/ORIGIN (\w+)/).to_s
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rpt.sequence = Bio::Sequence::AA.new(query_info[3..query_info.size].to_s)
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# rpt.reasoning
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rpt.final_result = final_result.split(/\n/).map {|x|
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x = x.strip.split(/---/).map {|y| y.strip }
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{ 'prediction' => x[0],
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'certainty' => x[1].scan(/Certainty= (\d\.\d{3})/).to_s,
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'comment' => x[1].scan(/\((\w+)\)/).to_s
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}
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}
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return rpt
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end
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attr_accessor :entry_id
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attr_accessor :origin
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attr_accessor :title
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attr_accessor :sequence
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attr_accessor :result_info
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attr_accessor :reasoning
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attr_accessor :final_result
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attr_accessor :raw
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# Constructs aBio::PSORT::PSORT1::Report object.
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def initialize(entry_id = '', origin = '', title = '', sequence = '',
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result_info = '', reasoning = {}, final_result = [])
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@entry_id = entry_id
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@origin = origin
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@title = title
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@sequence = sequence
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@result_info = result_info
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@reasoning = reasoning
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@final_result = final_result
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@raw = ''
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end
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end # class Report
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end # class PSORT1
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class PSORT2
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# Subcellular localization name codes used by PSORT2
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SclNames = {
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'csk' => 'cytoskeletal',
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'cyt' => 'cytoplasmic',
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'nuc' => 'nuclear',
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'mit' => 'mitochondrial',
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'ves' => 'vesicles of secretory system',
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'end' => 'endoplasmic reticulum',
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'gol' => 'Golgi',
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'vac' => 'vacuolar',
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'pla' => 'plasma membrane',
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'pox' => 'peroxisomal',
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'exc' => 'extracellular, including cell wall',
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'---' => 'other'
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}
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# Feature name codes
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Features = [
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'psg', # PSG: PSG score
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'gvh', # GvH: GvH score
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'alm', # ALOM: $xmax
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'tms', # ALOM: $count
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'top', # MTOP: Charge difference: $mtopscr
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'mit', # MITDISC: Score: $score
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'mip', # Gavel: motif at $isite
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'nuc', # NUCDISC: NLS Score: $score
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'erl', # KDEL: ($seg|none)
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'erm', # ER Membrane Retention Signals: ($cseg|none) $scr
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'pox', # SKL: ($pat|none) $scr
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'px2', # PTS2: (found|none) ($#match < 0) ? 0 : ($#match+1);
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'vac', # VAC: (found|none) ($#match < 0) ? 0 : ($#match+1);
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'rnp', # RNA-binding motif: (found|none) ($#match < 0) ? 0 : ($#match+1);
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'act', # Actinin-type actin-binding motif: (found|none) $hit
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'caa', # Prenylation motif: (2|1|0) CaaX,CXC,CC,nil
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'yqr', # memYQRL: (found|none) $scr
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'tyr', # Tyrosines in the tail: (none|\S+[,])
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# 10 * scalar(@ylist) / ($end - $start + 1);
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'leu', # Dileucine motif in the tail: (none|found) $scr
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'gpi', # >>> Seem to be GPI anchored
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'myr', # NMYR: (none|\w) $scr
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'dna', # checking 63 PROSITE DNA binding motifs: $hit
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'rib', # checking 71 PROSITE ribosomal protein motifs: $hit
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'bac', # checking 33 PROSITE prokaryotic DNA binding motifs: $hit
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'm1a', # $mtype eq '1a'
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'm1b', # $mtype eq '1b'
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'm2', # $mtype eq '2 '
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'mNt', # $mtype eq 'Nt'
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'm3a', # $mtype eq '3a'
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'm3b', # $mtype eq '3b'
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'm_', # $mtype eq '__' tms == 0
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'ncn', # NNCN: ($NetOutput[1] > $NetOutput[0]) ? $output : (-$output);
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'lps', # COIL: $count
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'len' # $leng
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]
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# Feature name codes (long version).
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FeaturesLong = {
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'psg' => 'PSG',
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'gvh' => 'GvH',
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'tms' => 'ALOM',
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'alm' => 'ALOM',
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'top' => 'MTOP',
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'mit' => 'MITDISC',
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'mip' => 'Gavel',
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173
|
+
'nuc' => 'NUCDISC',
|
174
|
+
'erl' => 'KDEL',
|
175
|
+
'erm' => 'ER Membrane Retention Signals',
|
176
|
+
'pox' => 'SKL',
|
177
|
+
'px2' => 'PTS2',
|
178
|
+
'vac' => 'VAC',
|
179
|
+
'rnp' => 'RNA-binding motif',
|
180
|
+
'act' => 'Actinin-type actin-binding motif',
|
181
|
+
'caa' => 'Prenylation motif',
|
182
|
+
'yqr' => 'memYQRL',
|
183
|
+
'tyr' => 'Tyrosines in the tail',
|
184
|
+
'leu' => 'Dileucine motif in the tail',
|
185
|
+
'gpi' => '>>> Seems to be GPI anchored',
|
186
|
+
'myr' => 'NMYR',
|
187
|
+
'dna' => 'checking 63 PROSITE DNA binding motifs',
|
188
|
+
'rib' => 'checking 71 PROSITE ribosomal protein motifs',
|
189
|
+
'bac' => 'ochecking 33 PROSITE prokaryotic DNA binding motifs:',
|
190
|
+
'm1a' => '',
|
191
|
+
'm1b' => '',
|
192
|
+
'm2' => '',
|
193
|
+
'mNt' => '',
|
194
|
+
'm3a' => '',
|
195
|
+
'm3b' => '',
|
196
|
+
'm_' => '',
|
197
|
+
'ncn' => 'NNCN',
|
198
|
+
'lps' => 'COIL',
|
199
|
+
'len' => 'AA' # length of input sequence
|
200
|
+
}
|
201
|
+
|
202
|
+
# = Bio::PSORT::PSORT2::Report
|
203
|
+
# Report parser classe for PSORT II(PSORT2).
|
204
|
+
# == Example
|
205
|
+
class Report
|
206
|
+
|
207
|
+
# Report boundary string.
|
208
|
+
BOUNDARY = '-' * 75
|
209
|
+
|
210
|
+
|
211
|
+
# Report delimiter.
|
212
|
+
RS = DELIMITER = "\)\n\n#{BOUNDARY}"
|
213
|
+
|
214
|
+
# entry_id of query sequence.
|
215
|
+
attr_accessor :entry_id
|
216
|
+
|
217
|
+
# Given subcellular localization (three letters code).
|
218
|
+
attr_accessor :scl
|
219
|
+
|
220
|
+
# Definition of query sequence.
|
221
|
+
attr_accessor :definition
|
222
|
+
|
223
|
+
# Sequence of query sequence.
|
224
|
+
attr_accessor :seq
|
225
|
+
|
226
|
+
# k parameter of k-nearest neighbors classifier.
|
227
|
+
attr_accessor :k
|
228
|
+
|
229
|
+
# Feature vector used the kNN prediction.
|
230
|
+
attr_accessor :features
|
231
|
+
|
232
|
+
# Probability vector of kNN prediction.
|
233
|
+
attr_accessor :prob
|
234
|
+
|
235
|
+
# Predicted subcellular localization (three letters code).
|
236
|
+
attr_accessor :pred
|
237
|
+
|
238
|
+
# Raw text of output report.
|
239
|
+
attr_accessor :raw
|
240
|
+
|
241
|
+
|
242
|
+
# Constructs aBio::PSORT::PSORT2::Report object.
|
243
|
+
def initialize(raw = '', entry_id = nil, scl = nil, definition = nil,
|
244
|
+
seq = nil, k = nil, features = {}, prob = {}, pred = nil)
|
245
|
+
@entry_id = entry_id
|
246
|
+
@scl = scl
|
247
|
+
@definition = definition
|
248
|
+
@seq = seq
|
249
|
+
@features = features
|
250
|
+
@prob = prob
|
251
|
+
@pred = pred
|
252
|
+
@k = k
|
253
|
+
@raw = raw
|
254
|
+
end
|
255
|
+
|
256
|
+
|
257
|
+
# Parses output report with output format detection automatically.
|
258
|
+
def self.parser(str, entry_id)
|
259
|
+
case str
|
260
|
+
when /^ psg:/ # default report
|
261
|
+
self.default_parser(str, entry_id)
|
262
|
+
when /^PSG:/ # -v report
|
263
|
+
self.v_parser(str, entry_id)
|
264
|
+
when /: too short length /
|
265
|
+
self.too_short_parser(str, entry_id)
|
266
|
+
when /PSORT II server/
|
267
|
+
tmp = self.new(ent, entry_id)
|
268
|
+
else
|
269
|
+
raise ArgumentError, "invalid format\n[#{str}]"
|
270
|
+
end
|
271
|
+
end
|
272
|
+
|
273
|
+
# Parser for ``too short length'' report.
|
274
|
+
#
|
275
|
+
# $id: too short length ($leng), skipped\n";
|
276
|
+
def self.too_short_parser(ent, entry_id = nil)
|
277
|
+
report = self.new(ent)
|
278
|
+
report.entry_id = entry_id
|
279
|
+
if ent =~ /^(.+)?: too short length/
|
280
|
+
report.entry_id = $1 unless report.entry_id
|
281
|
+
report.scl = '---'
|
282
|
+
end
|
283
|
+
report
|
284
|
+
end
|
285
|
+
|
286
|
+
|
287
|
+
# Parser for the default report format.
|
288
|
+
# ``psort report'' output.
|
289
|
+
def self.default_parser(ent, entry_id = nil)
|
290
|
+
report = self.new(ent, entry_id)
|
291
|
+
ent = ent.split(/\n\n/).map {|e| e.chomp }
|
292
|
+
|
293
|
+
report.set_header_line(ent[0])
|
294
|
+
|
295
|
+
# feature matrix
|
296
|
+
ent[1].gsub(/\n/,' ').strip.split(/ /).map {|fe|
|
297
|
+
pair = fe.split(/: /)
|
298
|
+
report.features[pair[0].strip] = pair[1].strip.to_f
|
299
|
+
}
|
300
|
+
|
301
|
+
report.prob = self.set_kNN_prob(ent[2])
|
302
|
+
report.set_prediction(ent[3])
|
303
|
+
|
304
|
+
return report
|
305
|
+
end
|
306
|
+
|
307
|
+
# Returns header information.
|
308
|
+
def set_header_line(str)
|
309
|
+
str.sub!(/^-+\n/,'')
|
310
|
+
tmp = str.split(/\t| /)
|
311
|
+
@entry_id = tmp.shift.sub(/^-+/,'').strip unless @entry_id
|
312
|
+
|
313
|
+
case tmp.join(' ').chomp
|
314
|
+
when /\(\d+ aa\) (.+)$/
|
315
|
+
@definition = $1
|
316
|
+
else
|
317
|
+
@definition = tmp.join(' ').chomp
|
318
|
+
end
|
319
|
+
scl = @definition.split(' ')[0]
|
320
|
+
|
321
|
+
@scl = scl if SclNames.keys.index(scl)
|
322
|
+
end
|
323
|
+
|
324
|
+
# Returns @prob value.
|
325
|
+
def self.set_kNN_prob(str)
|
326
|
+
prob = Hash.new
|
327
|
+
Bio::PSORT::PSORT2::SclNames.keys.each {|a|
|
328
|
+
prob.update( {a => 0.0} )
|
329
|
+
}
|
330
|
+
str.gsub(/\t/,'').split(/\n/).each {|a|
|
331
|
+
val,scl = a.strip.split(/ %: /)
|
332
|
+
key = Bio::PSORT::PSORT2::SclNames.index(scl)
|
333
|
+
prob[key] = val.to_f
|
334
|
+
}
|
335
|
+
return prob
|
336
|
+
end
|
337
|
+
|
338
|
+
# Returns @prob and @k values.
|
339
|
+
def set_prediction(str)
|
340
|
+
case str
|
341
|
+
when /prediction for (\S+?) is (\w{3}) \(k=(\d+)\)/
|
342
|
+
@entry_id ||= $1 unless @entry_id
|
343
|
+
@pred = $2
|
344
|
+
@k = $3
|
345
|
+
else
|
346
|
+
raise ArgumentError,
|
347
|
+
"Invalid format at(#{self.entry_id}):\n[#{str}]\n"
|
348
|
+
end
|
349
|
+
end
|
350
|
+
|
351
|
+
|
352
|
+
# Parser for the verbose output report format.
|
353
|
+
# ``psort -v report'' and WWW server output.
|
354
|
+
def self.v_parser(ent, entry_id = nil)
|
355
|
+
report = Bio::PSORT::PSORT2::Report.new(ent, entry_id)
|
356
|
+
|
357
|
+
ent = ent.split(/\n\n/).map {|e| e.chomp }
|
358
|
+
ent.each_with_index {|e, i|
|
359
|
+
unless /^(\w|-|\>|\t)/ =~ e
|
360
|
+
j = self.__send__(:search_j, i, ent)
|
361
|
+
ent[i - j] += e
|
362
|
+
ent[i] = nil
|
363
|
+
end
|
364
|
+
if /^none/ =~ e # psort output bug
|
365
|
+
j = self.__send__(:search_j, i, ent)
|
366
|
+
ent[i - j] += e
|
367
|
+
ent[i] = nil
|
368
|
+
end
|
369
|
+
}
|
370
|
+
ent.compact!
|
371
|
+
|
372
|
+
if /^ PSORT II server/ =~ ent[0] # for WWW version
|
373
|
+
ent.shift
|
374
|
+
delline = ''
|
375
|
+
ent.each {|e| delline = e if /^Results of Subprograms/ =~ e }
|
376
|
+
i = ent.index(delline)
|
377
|
+
ent.delete(delline)
|
378
|
+
ent.delete_at(i - 1)
|
379
|
+
end
|
380
|
+
|
381
|
+
report.set_header_line(ent.shift)
|
382
|
+
report.seq = Bio::Sequence::AA.new(ent.shift)
|
383
|
+
|
384
|
+
fent, pent = self.divent(ent)
|
385
|
+
report.set_features(fent)
|
386
|
+
report.prob = self.set_kNN_prob(pent[0].strip)
|
387
|
+
report.set_prediction(pent[1].strip)
|
388
|
+
|
389
|
+
return report
|
390
|
+
end
|
391
|
+
|
392
|
+
|
393
|
+
#
|
394
|
+
def self.search_j(i, ent)
|
395
|
+
j = 1
|
396
|
+
1.upto(ent.size) {|x|
|
397
|
+
if ent[i - x]
|
398
|
+
j = x
|
399
|
+
break
|
400
|
+
end
|
401
|
+
}
|
402
|
+
return j
|
403
|
+
end
|
404
|
+
private_class_method :search_j
|
405
|
+
|
406
|
+
|
407
|
+
# Divides entry body
|
408
|
+
def self.divent(entry)
|
409
|
+
boundary = entry.index(BOUNDARY)
|
410
|
+
return entry[0..(boundary - 1)], entry[(boundary + 2)..(entry.length)]
|
411
|
+
end
|
412
|
+
|
413
|
+
# Sets @features values.
|
414
|
+
def set_features(features_ary)
|
415
|
+
features_ary.each {|fent|
|
416
|
+
key = fent.split(/\:( |\n)/)[0].strip
|
417
|
+
self.features[key] = fent # unless /^\>/ =~ key
|
418
|
+
}
|
419
|
+
self.features['AA'] = self.seq.length
|
420
|
+
end
|
421
|
+
|
422
|
+
end # class Report
|
423
|
+
|
424
|
+
end # class PSORT2
|
425
|
+
|
426
|
+
end # class PSORT
|
427
|
+
|
428
|
+
end # module Bio
|
429
|
+
|
430
|
+
|
431
|
+
|
432
|
+
|
433
|
+
|
434
|
+
# testing code
|
435
|
+
|
436
|
+
if __FILE__ == $0
|
437
|
+
|
438
|
+
|
439
|
+
while entry = $<.gets(Bio::PSORT::PSORT2::Report::DELIMITER)
|
440
|
+
|
441
|
+
puts "\n ==> a = Bio::PSORT::PSORT2::Report.parser(entry)"
|
442
|
+
a = Bio::PSORT::PSORT2::Report.parser(entry)
|
443
|
+
|
444
|
+
puts "\n ==> a.entry_id "
|
445
|
+
p a.entry_id
|
446
|
+
puts "\n ==> a.scl "
|
447
|
+
p a.scl
|
448
|
+
puts "\n ==> a.pred "
|
449
|
+
p a.pred
|
450
|
+
puts "\n ==> a.prob "
|
451
|
+
p a.prob
|
452
|
+
p a.prob.keys.sort.map {|k| k.rjust(4)}.inspect.gsub('"','')
|
453
|
+
p a.prob.keys.sort.map {|k| a.prob[k].to_s.rjust(4) }.inspect.gsub('"','')
|
454
|
+
|
455
|
+
puts "\n ==> a.k "
|
456
|
+
p a.k
|
457
|
+
puts "\n ==> a.definition"
|
458
|
+
p a.definition
|
459
|
+
puts "\n ==> a.seq"
|
460
|
+
p a.seq
|
461
|
+
|
462
|
+
puts "\n ==> a.features.keys.sort "
|
463
|
+
p a.features.keys.sort
|
464
|
+
|
465
|
+
a.features.keys.sort.each do |key|
|
466
|
+
puts "\n ==> a.features['#{key}'] "
|
467
|
+
puts a.features[key]
|
468
|
+
end
|
469
|
+
|
470
|
+
|
471
|
+
end
|
472
|
+
|
473
|
+
end
|