jandot-bio 1.2.1
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- 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/bin/bioruby
ADDED
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#!/usr/bin/env ruby
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#
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# = BioRuby shell - command line interface for the BioRuby library
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#
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# Copyright:: Copyright (C) 2005, 2006, 2007
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# Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: bioruby,v 1.21 2007/07/26 10:46:46 k Exp $
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#
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begin
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require 'rubygems'
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gem 'bio', '>= 1.1.0'
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rescue LoadError
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require 'bio'
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end
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require 'bio/shell'
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# required to run commands (getseq, ls etc.)
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include Bio::Shell
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# setup command line options, working directory, and irb configurations
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|
+
Bio::Shell::Setup.new
|
25
|
+
|
26
|
+
# loading workspace and command history
|
27
|
+
Bio::Shell.load_session
|
28
|
+
|
29
|
+
# main loop
|
30
|
+
if Bio::Shell.cache[:rails]
|
31
|
+
Bio::Shell.cache[:rails].join
|
32
|
+
else
|
33
|
+
Signal.trap("SIGINT") do
|
34
|
+
Bio::Shell.cache[:irb].signal_handle
|
35
|
+
end
|
36
|
+
|
37
|
+
catch(:IRB_EXIT) do
|
38
|
+
Bio::Shell.cache[:irb].eval_input
|
39
|
+
end
|
40
|
+
end
|
41
|
+
|
42
|
+
# saving workspace, command history and configuration before exit
|
43
|
+
Bio::Shell.save_session
|
44
|
+
|
data/bin/br_biofetch.rb
ADDED
@@ -0,0 +1,47 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# = biofetch - BioFetch client
|
4
|
+
#
|
5
|
+
# Copyright:: Copyright (C) 2002
|
6
|
+
# Toshiaki Katayama <k@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: br_biofetch.rb,v 1.4 2007/04/05 23:35:39 trevor Exp $
|
10
|
+
#
|
11
|
+
|
12
|
+
require 'bio/io/fetch'
|
13
|
+
|
14
|
+
def usage
|
15
|
+
default_url = 'http://bioruby.org/cgi-bin/biofetch.rb'
|
16
|
+
another_url = 'http://www.ebi.ac.uk/cgi-bin/dbfetch'
|
17
|
+
puts "#{$0} [-s[erver] #{another_url}] db id [style] [format]"
|
18
|
+
puts " server : URL of the BioFetch CGI (default is #{default_url})"
|
19
|
+
puts " db : database name (embl, genbank, etc.)"
|
20
|
+
puts " id : entry id"
|
21
|
+
puts " style : 'raw' or 'html' (default is 'raw')"
|
22
|
+
puts " format : change the output format ('default', 'fasta', etc.)"
|
23
|
+
end
|
24
|
+
|
25
|
+
if ARGV.empty? or ARGV[0] =~ /^--?h/
|
26
|
+
usage
|
27
|
+
exit 1
|
28
|
+
end
|
29
|
+
|
30
|
+
case ARGV[0]
|
31
|
+
when /^--?s/ # User specified server
|
32
|
+
ARGV.shift
|
33
|
+
serv = Bio::Fetch.new(ARGV.shift)
|
34
|
+
puts serv.fetch(*ARGV)
|
35
|
+
when /^--?e/ # EBI server
|
36
|
+
ARGV.shift
|
37
|
+
serv = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch')
|
38
|
+
puts serv.fetch(*ARGV)
|
39
|
+
when /^--?r/ # BioRuby server
|
40
|
+
ARGV.shift
|
41
|
+
serv = Bio::Fetch.new('http://bioruby.org/cgi-bin/biofetch.rb')
|
42
|
+
puts serv.fetch(*ARGV)
|
43
|
+
else # Default server
|
44
|
+
puts Bio::Fetch.query(*ARGV)
|
45
|
+
end
|
46
|
+
|
47
|
+
|
data/bin/br_bioflat.rb
ADDED
@@ -0,0 +1,282 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# = bioflat - OBDA flat file indexer (executable)
|
4
|
+
#
|
5
|
+
# Copyright:: Copyright (C) 2002
|
6
|
+
# Naohisa Goto <ng@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: br_bioflat.rb,v 1.17 2007/04/05 23:35:39 trevor Exp $
|
10
|
+
#
|
11
|
+
|
12
|
+
require 'bio'
|
13
|
+
|
14
|
+
def usage
|
15
|
+
print <<EOM
|
16
|
+
Search:
|
17
|
+
#{$0} [--search] [options...] [DIR/]DBNAME KEYWORDS
|
18
|
+
or
|
19
|
+
#{$0} [--search] --location DIR --dbname DBNAME [options...] KEYWORDS
|
20
|
+
|
21
|
+
Search options:
|
22
|
+
--namespace NAME set serch namespace to NAME
|
23
|
+
(or --name NAME) You can set this option many times to specify
|
24
|
+
more than one namespace.
|
25
|
+
|
26
|
+
Create index:
|
27
|
+
#{$0} --create --location DIR --dbname DBNAME [--format <genbank|embl|fasta>] [options...] [--files] FILES
|
28
|
+
Update index:
|
29
|
+
#{$0} --update --location DIR --dbname DBNAME [options...] [--files] FILES
|
30
|
+
|
31
|
+
Create index options:
|
32
|
+
--primary=UNIQUE set primary namespece to UNIQUE
|
33
|
+
Default primary/secondary namespaces depend on
|
34
|
+
each format of flatfiles.
|
35
|
+
--secondary=KEY set secondary namespaces.
|
36
|
+
You may use this option many times to specify
|
37
|
+
more than one namespace.
|
38
|
+
--add-secondary=KEY add secondary namespaces to default specification.
|
39
|
+
You can use this option many times.
|
40
|
+
|
41
|
+
Options only valid for --create (or --update) --type flat:
|
42
|
+
--sort=/path/to/sort use external sort program (e.g. /usr/bin/sort)
|
43
|
+
--sort=BUILTIN use builtin sort routine
|
44
|
+
|
45
|
+
Options only valid for --update:
|
46
|
+
--renew re-read all flatfiles and update whole index
|
47
|
+
|
48
|
+
Backward compatibility:
|
49
|
+
--makeindex DIR/DBNAME
|
50
|
+
same as --create --type flat --location DIR --dbname DBNAME
|
51
|
+
--makeindexBDB DIR/DBNAME
|
52
|
+
same as --create --type bdb --location DIR --dbname DBNAME
|
53
|
+
--format=CLASS
|
54
|
+
instead of genbank|embl|fasta, specifing a class name is allowed
|
55
|
+
|
56
|
+
Show namespaces:
|
57
|
+
#{$0} --show-namespaces [--location DIR --dbname DBNAME] [DIR/DBNAME]
|
58
|
+
or
|
59
|
+
#{$0} --show-namespaces [--format=CLASS]
|
60
|
+
or
|
61
|
+
#{$0} --show-namespaces --files file
|
62
|
+
|
63
|
+
EOM
|
64
|
+
|
65
|
+
end
|
66
|
+
|
67
|
+
|
68
|
+
def do_index(mode = :create)
|
69
|
+
case ARGV[0]
|
70
|
+
when /^\-\-?make/
|
71
|
+
dbpath = ARGV[1]
|
72
|
+
args = ARGV[2..-1]
|
73
|
+
is_bdb = nil
|
74
|
+
when /^\-\-?make.*bdb/i
|
75
|
+
dbname = ARGV[1]
|
76
|
+
args = ARGV[2..-1]
|
77
|
+
is_bdb = Bio::FlatFileIndex::MAGIC_BDB
|
78
|
+
when /^\-\-create/, /^\-\-update/
|
79
|
+
args = ARGV[1..-1]
|
80
|
+
else
|
81
|
+
usage
|
82
|
+
end
|
83
|
+
|
84
|
+
options = {}
|
85
|
+
|
86
|
+
while args.first =~ /^\-/
|
87
|
+
case x = args.shift
|
88
|
+
|
89
|
+
# OBDA stuff
|
90
|
+
|
91
|
+
when /^\-\-?format/
|
92
|
+
args.shift
|
93
|
+
format = nil # throw this f*ckin' mess for auto detect :)
|
94
|
+
when /^\-\-?location/
|
95
|
+
location = args.shift.chomp('/')
|
96
|
+
when /^\-\-?dbname/
|
97
|
+
dbname = args.shift
|
98
|
+
when /^\-\-?(index)?type/
|
99
|
+
indextype = args.shift
|
100
|
+
case indextype
|
101
|
+
when /bdb/
|
102
|
+
is_bdb = Bio::FlatFileIndex::MAGIC_BDB
|
103
|
+
when /flat/
|
104
|
+
is_bdb = nil
|
105
|
+
else
|
106
|
+
usage
|
107
|
+
end
|
108
|
+
|
109
|
+
# BioRuby extension
|
110
|
+
|
111
|
+
when /^\-\-?files/i
|
112
|
+
break
|
113
|
+
|
114
|
+
when /^\-\-?format\=(.*)/i
|
115
|
+
format = $1
|
116
|
+
|
117
|
+
when /^\-\-?sort\=(.*)/i
|
118
|
+
options['sort_program'] = $1
|
119
|
+
options['onmemory'] = nil
|
120
|
+
when /^\-\-?no\-?te?mp/i
|
121
|
+
options['onmemory'] = true
|
122
|
+
|
123
|
+
when /^\-\-?primary.*\=(.*)/i
|
124
|
+
options['primary_namespace'] = $1
|
125
|
+
|
126
|
+
when /^\-\-?add-secondary.*\=(.*)/i
|
127
|
+
unless options['additional_secondary_namespaces'] then
|
128
|
+
options['additional_secondary_namespaces'] = []
|
129
|
+
end
|
130
|
+
options['additional_secondary_namespaces'] << $1 if $1.length > 0
|
131
|
+
|
132
|
+
when /^\-\-?secondary.*\=(.*)/i
|
133
|
+
unless options['secondary_namespaces'] then
|
134
|
+
options['secondary_namespaces'] = []
|
135
|
+
end
|
136
|
+
options['secondary_namespaces'] << $1 if $1.length > 0
|
137
|
+
|
138
|
+
when /^\-\-?renew/
|
139
|
+
options['renew'] = true
|
140
|
+
|
141
|
+
else
|
142
|
+
$stderr.print "Warning: ignoring invalid option #{x.inspect}\n"
|
143
|
+
end
|
144
|
+
end
|
145
|
+
|
146
|
+
dbpath = File.join(location, dbname) unless dbpath
|
147
|
+
if mode == :update then
|
148
|
+
Bio::FlatFileIndex::update_index(dbpath, format, options, *args)
|
149
|
+
else
|
150
|
+
Bio::FlatFileIndex::makeindex(is_bdb, dbpath, format, options, *args)
|
151
|
+
end
|
152
|
+
end
|
153
|
+
|
154
|
+
|
155
|
+
def do_search
|
156
|
+
dbname = nil
|
157
|
+
location = nil
|
158
|
+
names = []
|
159
|
+
while x = ARGV.shift
|
160
|
+
case x
|
161
|
+
when /\A\-\-?search/i
|
162
|
+
#do nothing
|
163
|
+
when /\A\-\-?location/i
|
164
|
+
location = ARGV.shift.to_s.chomp('/')
|
165
|
+
when /\A\-\-?dbname/i
|
166
|
+
dbname = ARGV.shift
|
167
|
+
when /\A\-\-?name(?:space)?(?:\=(.+))?/i
|
168
|
+
if $1 then
|
169
|
+
names << $1
|
170
|
+
elsif x = ARGV.shift
|
171
|
+
names << x
|
172
|
+
end
|
173
|
+
else
|
174
|
+
ARGV.unshift x
|
175
|
+
break
|
176
|
+
end
|
177
|
+
end
|
178
|
+
dbname = ARGV.shift unless dbname
|
179
|
+
dbname = File.join(location, dbname) unless location.to_s.empty?
|
180
|
+
db = Bio::FlatFileIndex.open(dbname)
|
181
|
+
ARGV.each do |key|
|
182
|
+
$stderr.print "Searching for \'#{key}\'...\n"
|
183
|
+
#r = db.search(key)
|
184
|
+
#$stderr.print "OK, #{r.size} entry found\n"
|
185
|
+
#if r.size > 0 then
|
186
|
+
# print r
|
187
|
+
#end
|
188
|
+
begin
|
189
|
+
if names.empty? then
|
190
|
+
r = db.include?(key)
|
191
|
+
else
|
192
|
+
r = db.include_in_namespaces?(key, *names)
|
193
|
+
end
|
194
|
+
rescue RuntimeError
|
195
|
+
$stderr.print "ERROR: #{$!}\n"
|
196
|
+
next
|
197
|
+
end
|
198
|
+
r = [] unless r
|
199
|
+
$stderr.print "OK, #{r.size} entry found\n"
|
200
|
+
r.each do |i|
|
201
|
+
print db.search_primary(i)
|
202
|
+
end
|
203
|
+
end
|
204
|
+
db.close
|
205
|
+
end
|
206
|
+
|
207
|
+
|
208
|
+
def do_show_namespaces
|
209
|
+
dbname = nil
|
210
|
+
location = nil
|
211
|
+
files = nil
|
212
|
+
format = nil
|
213
|
+
names = []
|
214
|
+
while x = ARGV.shift
|
215
|
+
case x
|
216
|
+
when /\A\-\-?(show\-)?name(space)?s/i
|
217
|
+
#do nothing
|
218
|
+
when /\A\-\-?location/i
|
219
|
+
location = ARGV.shift.to_s.chomp('/')
|
220
|
+
when /\A\-\-?dbname/i
|
221
|
+
dbname = ARGV.shift
|
222
|
+
when /\A\-\-?format(?:\=(.+))?/i
|
223
|
+
if $1 then
|
224
|
+
format = $1
|
225
|
+
elsif x = ARGV.shift
|
226
|
+
format = x
|
227
|
+
end
|
228
|
+
when /\A\-\-?files/i
|
229
|
+
files = ARGV
|
230
|
+
break
|
231
|
+
else
|
232
|
+
ARGV.unshift x
|
233
|
+
break
|
234
|
+
end
|
235
|
+
end
|
236
|
+
if files then
|
237
|
+
k = nil
|
238
|
+
files.each do |x|
|
239
|
+
k = Bio::FlatFile.autodetect_file(x)
|
240
|
+
break if k
|
241
|
+
end
|
242
|
+
if k then
|
243
|
+
$stderr.print "Format: #{k.to_s}\n"
|
244
|
+
format = k
|
245
|
+
else
|
246
|
+
$stderr.print "ERROR: couldn't determine file format\n"
|
247
|
+
return
|
248
|
+
end
|
249
|
+
end
|
250
|
+
$stderr.print "Namespaces: (first line: primary namespace)\n"
|
251
|
+
if format then
|
252
|
+
parser = Bio::FlatFileIndex::Indexer::Parser.new(format)
|
253
|
+
print parser.primary.name, "\n"
|
254
|
+
puts parser.secondary.keys
|
255
|
+
else
|
256
|
+
dbname = ARGV.shift unless dbname
|
257
|
+
dbname = File.join(location, dbname) unless location.to_s.empty?
|
258
|
+
db = Bio::FlatFileIndex.open(dbname)
|
259
|
+
puts db.namespaces
|
260
|
+
db.close
|
261
|
+
end
|
262
|
+
end
|
263
|
+
|
264
|
+
if ARGV.size > 1
|
265
|
+
case ARGV[0]
|
266
|
+
when /--make/, /--create/
|
267
|
+
Bio::FlatFileIndex::DEBUG.out = true
|
268
|
+
do_index
|
269
|
+
when /--update/
|
270
|
+
Bio::FlatFileIndex::DEBUG.out = true
|
271
|
+
do_index(:update)
|
272
|
+
when /\A\-\-?(show\-)?name(space)?s/i
|
273
|
+
do_show_namespaces
|
274
|
+
when /--search/
|
275
|
+
do_search
|
276
|
+
else #default is search
|
277
|
+
do_search
|
278
|
+
end
|
279
|
+
else
|
280
|
+
usage
|
281
|
+
end
|
282
|
+
|
data/bin/br_biogetseq.rb
ADDED
@@ -0,0 +1,45 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# = biogetseq - OBDA sequence data retrieval (executable)
|
4
|
+
#
|
5
|
+
# Copyright:: Copyright (C) 2003
|
6
|
+
# Toshiaki Katayama <k@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: br_biogetseq.rb,v 1.4 2007/04/05 23:35:39 trevor Exp $
|
10
|
+
#
|
11
|
+
|
12
|
+
require 'bio'
|
13
|
+
|
14
|
+
def usage
|
15
|
+
print <<END
|
16
|
+
#{$0} --dbname <dbname> [--namespace <namespace>] entry_id [entry_id]
|
17
|
+
END
|
18
|
+
exit 1
|
19
|
+
end
|
20
|
+
|
21
|
+
if ARGV.size < 3
|
22
|
+
usage
|
23
|
+
end
|
24
|
+
|
25
|
+
while ARGV.first =~ /^-/
|
26
|
+
case ARGV.shift
|
27
|
+
when /^\-\-format/
|
28
|
+
ARGV.shift
|
29
|
+
raise NotImplementedError
|
30
|
+
when /^\-\-dbname/
|
31
|
+
dbname = ARGV.shift
|
32
|
+
when /^\-\-namespace/
|
33
|
+
namespace = ARGV.shift
|
34
|
+
end
|
35
|
+
end
|
36
|
+
|
37
|
+
reg = Bio::Registry.new
|
38
|
+
db = reg.get_database(dbname)
|
39
|
+
if namespace
|
40
|
+
db['namespace'] = namespace
|
41
|
+
end
|
42
|
+
ARGV.each do |entry|
|
43
|
+
puts db.get_by_id(entry)
|
44
|
+
end
|
45
|
+
|
data/bin/br_pmfetch.rb
ADDED
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#!/usr/bin/env ruby
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#
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# = pmfetch - PubMed client
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#
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# Copyright:: Copyright (C) 2004, 2005
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# Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: br_pmfetch.rb,v 1.7 2007/04/05 23:35:39 trevor Exp $
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#
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PROG_VER = '$Id: br_pmfetch.rb,v 1.7 2007/04/05 23:35:39 trevor Exp $'
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PROG_NAME = File.basename($0)
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require 'getoptlong'
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require 'bio'
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### formatting
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class String
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def fill(fill_column = 80, prefix = '', separater = ' ')
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prefix = ' ' * prefix if prefix.is_a?(Integer)
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maxlen = fill_column - prefix.length
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raise "prefix is longer than fill_column" if maxlen <= 0
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cursor = pos = 0
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lines = []
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while cursor < self.length
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line = self[cursor, maxlen]
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pos = line.rindex(separater)
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pos = nil if line.length < maxlen
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if pos
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len = pos + separater.length
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lines << self[cursor, len]
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cursor += len
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else
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lines << self[cursor, maxlen]
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cursor += maxlen
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end
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end
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return lines.join("\n#{prefix}")
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end
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end
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module Bio
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class Reference
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def report
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if (num = @authors.size) > 10
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authors = "#{@authors[0]} et al. (#{num} authors)"
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elsif num > 4
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sep = ',' * (num - 1)
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authors = "#{@authors[0]}#{sep} #{@authors[-1]}"
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else
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authors = authors_join(' & ')
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end
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journal = "#{@journal} #{@year} #{@volume}(#{@issue}):#{@pages}"
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indent = 8
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prefix = ' ' * indent
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[
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"#{@pages[/\d+/]}".ljust(indent) + "#{@title}".fill(78, indent),
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authors,
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"#{journal} [PMID:#{@pubmed}]",
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].join("\n#{prefix}")
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end
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end
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end
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class PMFetch
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class Examples < StandardError; end
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class Version < StandardError; end
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class Usage < StandardError; end
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78
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79
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### default options
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def initialize
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@format = 'rd'
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@search_opts = {
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'retmax' => 20,
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}
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@query = nil
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@query_opts = []
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@pmid_list_only = false
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pmfetch
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end
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### main
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def pmfetch
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begin
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set_options
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parse_options
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check_query
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rescue PMFetch::Examples
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puts examples
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exit
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rescue PMFetch::Version
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puts version
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exit
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rescue PMFetch::Usage
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puts usage
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exit
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rescue GetoptLong::MissingArgument, GetoptLong::InvalidOption
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puts usage
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exit
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end
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list = pm_esearch
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if list.empty?
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;
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elsif @pmid_list_only
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puts list
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else
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pm_efetch(list)
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end
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end
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|
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### help
|
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|
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def usage
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%Q[
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Usage: #{PROG_NAME} [options...] "query string"
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or #{PROG_NAME} --query "query string" [other options...]
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Options:
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-q --query "genome AND virus" Query string for PubMed search
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-t --title "mobile elements" Title of the article to search
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-j --journal "genome res" Journal title to search
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-v --volume # Journal volume to search
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-i --issue # Journal issue to search
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-p --page # First page number of the article to search
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141
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-a --author "Altschul SF" Author name to search
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-m --mesh "SARS virus" MeSH term to search
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-f --format bibtex Summary output format
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--pmidlist Output only a list of PubMed IDs
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-n --retmax # Number of articles to retrieve at the maximum
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-N --retstart # Starting number of the articles to retrieve
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-s --sort pub+date Sort method for the summary output
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--reldate # Search articles published within recent # days
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--mindate YYYY/MM/DD Search articles published after the date
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--maxdate YYYY/MM/DD Search articles published before the date
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--help Output this help, then exit
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--examples Output examples, then exit
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--version Output version number, then exit
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Formats:
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endnote, medline, bibitem, bibtex, report, rd,
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nature, science, genome_res, genome_biol, nar, current, trends, cell
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Sort:
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author, journal, pub+date, page
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See the following pages for the PubMed search options:
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http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
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http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
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#{version}
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167
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]
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169
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end
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170
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171
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def version
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172
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PROG_VER
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173
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end
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174
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+
|
175
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def examples
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176
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DATA.read.gsub('PMFetch', PROG_NAME)
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177
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end
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178
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+
|
179
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+
|
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private
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181
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+
|
182
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+
|
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### options
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184
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|
185
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def set_options
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186
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@parser = GetoptLong.new
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187
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|
188
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@parser.set_options(
|
189
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[ '--query', '-q', GetoptLong::REQUIRED_ARGUMENT ],
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190
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[ '--title', '-t', GetoptLong::REQUIRED_ARGUMENT ],
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191
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[ '--journal', '-j', GetoptLong::REQUIRED_ARGUMENT ],
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192
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[ '--volume', '-v', GetoptLong::REQUIRED_ARGUMENT ],
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193
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[ '--issue', '-i', GetoptLong::REQUIRED_ARGUMENT ],
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194
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[ '--page', '-p', GetoptLong::REQUIRED_ARGUMENT ],
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195
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[ '--author', '-a', GetoptLong::REQUIRED_ARGUMENT ],
|
196
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[ '--mesh', '-m', GetoptLong::REQUIRED_ARGUMENT ],
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197
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[ '--format', '-f', GetoptLong::REQUIRED_ARGUMENT ],
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198
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[ '--pmidlist', GetoptLong::NO_ARGUMENT ],
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199
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[ '--retmax', '-n', GetoptLong::REQUIRED_ARGUMENT ],
|
200
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[ '--retstart', '-N', GetoptLong::REQUIRED_ARGUMENT ],
|
201
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[ '--sort', '-s', GetoptLong::REQUIRED_ARGUMENT ],
|
202
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[ '--reldate', GetoptLong::REQUIRED_ARGUMENT ],
|
203
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[ '--mindate', GetoptLong::REQUIRED_ARGUMENT ],
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204
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[ '--maxdate', GetoptLong::REQUIRED_ARGUMENT ],
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205
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[ '--examples', GetoptLong::NO_ARGUMENT ],
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206
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[ '--help', GetoptLong::NO_ARGUMENT ],
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207
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[ '--version', GetoptLong::NO_ARGUMENT ]
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208
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)
|
209
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end
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210
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|
211
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def parse_options
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212
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@parser.each_option do |optname, optarg|
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213
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case optname
|
214
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when /--query/
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215
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@query = optarg
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216
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when /--title/
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@query_opts << "#{optarg}[ti]"
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218
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when /--journal/
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@query_opts << "#{optarg}[ta]"
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when /--volume/
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@query_opts << "#{optarg}[vi]"
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when /--issue/
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@query_opts << "#{optarg}[ip]"
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when /--page/
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@query_opts << "#{optarg}[pg]"
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when /--author/
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@query_opts << "#{optarg}[au]"
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when /--mesh/
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@query_opts << "#{optarg}[mh]"
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when /--format/
|
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@format = optarg
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when /--pmidlist/
|
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@pmid_list_only = true
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when /--examples/
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raise PMFetch::Examples
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when /--help/
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raise PMFetch::Usage
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when /--version/
|
239
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raise PMFetch::Version
|
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when /--sort/
|
241
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@sort = optarg
|
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@search_opts["sort"] = @sort unless @sort == "page"
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else
|
244
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optname.delete!('-')
|
245
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@search_opts[optname] = optarg
|
246
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+
end
|
247
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+
end
|
248
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+
end
|
249
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+
|
250
|
+
|
251
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### check query
|
252
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+
|
253
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def check_query
|
254
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p @query if $DEBUG
|
255
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@query ||= ARGV.join(" ") unless ARGV.empty?
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256
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+
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257
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p @query if $DEBUG
|
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@query_str = [ @query, @query_opts ].flatten.compact.join(" AND ")
|
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|
260
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p @query_str if $DEBUG
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261
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if @query_str.empty?
|
262
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raise PMFetch::Usage
|
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+
end
|
264
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end
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265
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+
|
266
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+
|
267
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### search
|
268
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+
|
269
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def pm_esearch
|
270
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return Bio::PubMed.esearch(@query_str, @search_opts)
|
271
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+
end
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272
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+
|
273
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def pm_efetch(list)
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entries = Bio::PubMed.efetch(list)
|
275
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|
276
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if @format == 'medline'
|
277
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medline_format(entries)
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278
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else
|
279
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entries = parse_entries(entries)
|
280
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if @sort == 'page'
|
281
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entries = sort_entries(entries)
|
282
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+
end
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283
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if @format == 'report'
|
284
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report_format(entries)
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285
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+
else
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286
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other_format(entries)
|
287
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+
end
|
288
|
+
end
|
289
|
+
end
|
290
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+
|
291
|
+
|
292
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+
### output
|
293
|
+
|
294
|
+
def medline_format(entries)
|
295
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entries.each do |entry|
|
296
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puts entry
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297
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puts '//'
|
298
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+
end
|
299
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+
end
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300
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+
|
301
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def parse_entries(entries)
|
302
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entries.map { |entry| Bio::MEDLINE.new(entry) }
|
303
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+
end
|
304
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+
|
305
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def sort_entries(entries)
|
306
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if RUBY_VERSION > "1.8.0"
|
307
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entries.sort_by { |x|
|
308
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[ x.journal, x.volume.to_i, x.issue.to_i, x.pages.to_i ]
|
309
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+
}
|
310
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+
else
|
311
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entries.map { |x|
|
312
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[ x.journal, x.volume.to_i, x.issue.to_i, x.pages.to_i, x ]
|
313
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+
}.sort { |a, b|
|
314
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a[0..3] <=> b[0..3]
|
315
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+
}.map { |y|
|
316
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y.pop
|
317
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}
|
318
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+
end
|
319
|
+
end
|
320
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+
|
321
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+
def report_format(entries)
|
322
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entries.each do |entry|
|
323
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puts entry.reference.report
|
324
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puts
|
325
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+
end
|
326
|
+
end
|
327
|
+
|
328
|
+
def other_format(entries)
|
329
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entries.each do |entry|
|
330
|
+
puts entry.reference.format(@format)
|
331
|
+
puts
|
332
|
+
end
|
333
|
+
end
|
334
|
+
|
335
|
+
end
|
336
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+
|
337
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+
|
338
|
+
PMFetch.new
|
339
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+
|
340
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+
|
341
|
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__END__
|
342
|
+
|
343
|
+
= Examples : PubMed search
|
344
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+
|
345
|
+
These four lines will do the same job.
|
346
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+
|
347
|
+
% PMFetch transcription factor
|
348
|
+
% PMFetch "transcription factor"
|
349
|
+
% PMFetch --query "transcription factor"
|
350
|
+
% PMFetch -q "transcription factor"
|
351
|
+
|
352
|
+
|
353
|
+
Retrieve max 100 artiecles (20 is a NCBI's default) at a time, use --retmax as
|
354
|
+
|
355
|
+
% PMFetch -q "transcription factor" --retmax 100
|
356
|
+
|
357
|
+
and, to retrieve next 100 articles, use --retstart as
|
358
|
+
|
359
|
+
% PMFetch -q "transcription factor" --retmax 100 --retstart 100
|
360
|
+
|
361
|
+
|
362
|
+
You can narrow the search target for an issue of the journal.
|
363
|
+
|
364
|
+
% PMFetch --journal development --volume 131 --issue 3 transcription factor
|
365
|
+
|
366
|
+
|
367
|
+
Short options are also available.
|
368
|
+
|
369
|
+
% PMFetch -j development -v 131 -i 3 transcription factor
|
370
|
+
|
371
|
+
|
372
|
+
Search articles indexed in PubMed within these 90 days.
|
373
|
+
|
374
|
+
% PMFetch -q "transcription factor" --reldate 90
|
375
|
+
|
376
|
+
|
377
|
+
Search articles indexed in PubMed during the period of 2001/04/01 to 2001/08/31
|
378
|
+
|
379
|
+
% PMFetch -q "transcription factor" --mindate 2001/04/01 --maxdate 2001/08/31
|
380
|
+
|
381
|
+
|
382
|
+
Output format can be changed by --format option.
|
383
|
+
|
384
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f report
|
385
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f rd
|
386
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f endnote
|
387
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f medline
|
388
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f bibitem
|
389
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f bibtex
|
390
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f nature
|
391
|
+
% PMFetch -q "transcription factor" -j development -v 131 -i 3 -f science
|
392
|
+
|
393
|
+
|
394
|
+
Generate title listings for the journal report meeting (don't forget
|
395
|
+
to inclease the number of --retmax for fetching all titles).
|
396
|
+
|
397
|
+
% PMFetch -f report -j development -v 131 -i 3 -n 100
|
398
|
+
|
399
|
+
|
400
|
+
Search by author name.
|
401
|
+
|
402
|
+
% PMFetch -a "Karlin S"
|
403
|
+
% PMFetch -a "Koonin EV"
|
404
|
+
|
405
|
+
|
406
|
+
Search by MeSH term.
|
407
|
+
|
408
|
+
% PMFetch -m "computational biology"
|
409
|
+
% PMFetch -m "SARS virus"
|
410
|
+
|
411
|
+
|
412
|
+
Search by PubMed ID (PMID).
|
413
|
+
|
414
|
+
% PMFetch 12345
|
415
|
+
|
416
|
+
|
417
|
+
Output PMID only.
|
418
|
+
|
419
|
+
% PMFetch --pmidlist tardigrada
|
420
|
+
|
421
|
+
|