ngoto-bio 1.2.9.9001
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- data/ChangeLog +2046 -0
- data/README.rdoc +223 -0
- data/README_DEV.rdoc +285 -0
- data/Rakefile +70 -0
- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +293 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/bioruby.gemspec +463 -0
- data/bioruby.gemspec.erb +79 -0
- data/doc/Changes-0.7.rd +369 -0
- data/doc/Changes-1.3.rdoc +195 -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/extconf.rb +2 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast/ddbj.rb +142 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/genomenet.rb +263 -0
- data/lib/bio/appl/blast/ncbioptions.rb +220 -0
- data/lib/bio/appl/blast/remote.rb +105 -0
- data/lib/bio/appl/blast/report.rb +767 -0
- data/lib/bio/appl/blast/rexml.rb +144 -0
- data/lib/bio/appl/blast/rpsblast.rb +277 -0
- data/lib/bio/appl/blast/wublast.rb +671 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/fasta.rb +235 -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/report.rb +683 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/codeml/rates.rb +67 -0
- data/lib/bio/appl/paml/codeml/report.rb +67 -0
- data/lib/bio/appl/paml/codeml.rb +242 -0
- data/lib/bio/appl/paml/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/paml/yn00.rb +103 -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/report.rb +457 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sim4.rb +124 -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 +231 -0
- data/lib/bio/command.rb +593 -0
- data/lib/bio/compat/features.rb +157 -0
- data/lib/bio/compat/references.rb +128 -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/aaindex.rb +357 -0
- data/lib/bio/db/biosql/biosql_to_biosequence.rb +67 -0
- data/lib/bio/db/biosql/sequence.rb +508 -0
- data/lib/bio/db/embl/common.rb +352 -0
- data/lib/bio/db/embl/embl.rb +500 -0
- data/lib/bio/db/embl/embl_to_biosequence.rb +85 -0
- data/lib/bio/db/embl/format_embl.rb +190 -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 +597 -0
- data/lib/bio/db/fasta/defline.rb +532 -0
- data/lib/bio/db/fasta/fasta_to_biosequence.rb +63 -0
- data/lib/bio/db/fasta/format_fasta.rb +97 -0
- data/lib/bio/db/fasta.rb +410 -0
- data/lib/bio/db/genbank/common.rb +307 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/format_genbank.rb +187 -0
- data/lib/bio/db/genbank/genbank.rb +250 -0
- data/lib/bio/db/genbank/genbank_to_biosequence.rb +86 -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 +1846 -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 +166 -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 +326 -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/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/pdb.rb +29 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db.rb +329 -0
- data/lib/bio/feature.rb +139 -0
- data/lib/bio/io/biosql/biodatabase.rb +64 -0
- data/lib/bio/io/biosql/bioentry.rb +29 -0
- data/lib/bio/io/biosql/bioentry_dbxref.rb +11 -0
- data/lib/bio/io/biosql/bioentry_path.rb +12 -0
- data/lib/bio/io/biosql/bioentry_qualifier_value.rb +10 -0
- data/lib/bio/io/biosql/bioentry_reference.rb +10 -0
- data/lib/bio/io/biosql/bioentry_relationship.rb +10 -0
- data/lib/bio/io/biosql/biosequence.rb +11 -0
- data/lib/bio/io/biosql/comment.rb +7 -0
- data/lib/bio/io/biosql/config/database.yml +20 -0
- data/lib/bio/io/biosql/dbxref.rb +13 -0
- data/lib/bio/io/biosql/dbxref_qualifier_value.rb +12 -0
- data/lib/bio/io/biosql/location.rb +32 -0
- data/lib/bio/io/biosql/location_qualifier_value.rb +11 -0
- data/lib/bio/io/biosql/ontology.rb +10 -0
- data/lib/bio/io/biosql/reference.rb +9 -0
- data/lib/bio/io/biosql/seqfeature.rb +32 -0
- data/lib/bio/io/biosql/seqfeature_dbxref.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_path.rb +11 -0
- data/lib/bio/io/biosql/seqfeature_qualifier_value.rb +20 -0
- data/lib/bio/io/biosql/seqfeature_relationship.rb +11 -0
- data/lib/bio/io/biosql/taxon.rb +12 -0
- data/lib/bio/io/biosql/taxon_name.rb +9 -0
- data/lib/bio/io/biosql/term.rb +27 -0
- data/lib/bio/io/biosql/term_dbxref.rb +11 -0
- data/lib/bio/io/biosql/term_path.rb +12 -0
- data/lib/bio/io/biosql/term_relationship.rb +13 -0
- data/lib/bio/io/biosql/term_relationship_term.rb +11 -0
- data/lib/bio/io/biosql/term_synonym.rb +10 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +638 -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 +195 -0
- data/lib/bio/io/flatfile/autodetection.rb +545 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/buffer.rb +237 -0
- data/lib/bio/io/flatfile/index.rb +1381 -0
- data/lib/bio/io/flatfile/indexer.rb +805 -0
- data/lib/bio/io/flatfile/splitter.rb +297 -0
- data/lib/bio/io/flatfile.rb +473 -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 +733 -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 +186 -0
- data/lib/bio/location.rb +867 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +960 -0
- data/lib/bio/reference.rb +602 -0
- data/lib/bio/sequence/aa.rb +125 -0
- data/lib/bio/sequence/adapter.rb +108 -0
- data/lib/bio/sequence/common.rb +310 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/dblink.rb +54 -0
- data/lib/bio/sequence/format.rb +358 -0
- data/lib/bio/sequence/format_raw.rb +23 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/sequence.rb +456 -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
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- 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
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- 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/shell.rb +44 -0
- data/lib/bio/tree.rb +852 -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/color_scheme.rb +191 -0
- data/lib/bio/util/contingency_table.rb +370 -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/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/double_stranded.rb +321 -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/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/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -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.rb +200 -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/restriction_enzyme.rb +228 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/lib/bio.rb +300 -0
- data/rdoc.zsh +8 -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/demo_sequence.rb +158 -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/setup.rb +1596 -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
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- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
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- data/test/data/fasta/example1.txt +75 -0
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- data/test/data/genscan/sample.report +63 -0
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- data/test/data/paml/codeml/control_file.txt +30 -0
- data/test/data/paml/codeml/output.txt +78 -0
- data/test/data/paml/codeml/rates +217 -0
- data/test/data/prosite/prosite.dat +2233 -0
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- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
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- data/test/functional/bio/io/test_ensembl.rb +229 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/functional/bio/sequence/test_output_embl.rb +51 -0
- data/test/functional/bio/test_command.rb +301 -0
- data/test/runner.rb +23 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_ncbioptions.rb +112 -0
- data/test/unit/bio/appl/blast/test_report.rb +1135 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +398 -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/paml/codeml/test_rates.rb +45 -0
- data/test/unit/bio/appl/paml/codeml/test_report.rb +45 -0
- data/test/unit/bio/appl/paml/test_codeml.rb +174 -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 +277 -0
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- data/test/unit/bio/appl/test_pts1.rb +77 -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_embl_to_bioseq.rb +203 -0
- data/test/unit/bio/db/embl/test_sptr.rb +1812 -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 +1190 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_medline.rb +127 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +364 -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/flatfile/test_autodetection.rb +375 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +251 -0
- data/test/unit/bio/io/flatfile/test_splitter.rb +369 -0
- data/test/unit/bio/io/test_ddbjxml.rb +80 -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 +488 -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 +373 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -0
- data/test/unit/bio/sequence/test_dblink.rb +58 -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 +349 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +144 -0
- data/test/unit/bio/test_location.rb +599 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +499 -0
- data/test/unit/bio/test_reference.rb +252 -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 +484 -0
data/bin/br_pmfetch.rb
ADDED
@@ -0,0 +1,421 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# = pmfetch - PubMed client
|
4
|
+
#
|
5
|
+
# Copyright:: Copyright (C) 2004, 2005
|
6
|
+
# Toshiaki Katayama <k@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id: br_pmfetch.rb,v 1.7 2007/04/05 23:35:39 trevor Exp $
|
10
|
+
#
|
11
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+
|
12
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+
PROG_VER = '$Id: br_pmfetch.rb,v 1.7 2007/04/05 23:35:39 trevor Exp $'
|
13
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+
PROG_NAME = File.basename($0)
|
14
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+
|
15
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+
|
16
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+
require 'getoptlong'
|
17
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+
require 'bio'
|
18
|
+
|
19
|
+
|
20
|
+
### formatting
|
21
|
+
|
22
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+
class String
|
23
|
+
def fill(fill_column = 80, prefix = '', separater = ' ')
|
24
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+
prefix = ' ' * prefix if prefix.is_a?(Integer)
|
25
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+
maxlen = fill_column - prefix.length
|
26
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+
raise "prefix is longer than fill_column" if maxlen <= 0
|
27
|
+
|
28
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+
cursor = pos = 0
|
29
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+
lines = []
|
30
|
+
while cursor < self.length
|
31
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+
line = self[cursor, maxlen]
|
32
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+
pos = line.rindex(separater)
|
33
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+
pos = nil if line.length < maxlen
|
34
|
+
if pos
|
35
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+
len = pos + separater.length
|
36
|
+
lines << self[cursor, len]
|
37
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+
cursor += len
|
38
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+
else
|
39
|
+
lines << self[cursor, maxlen]
|
40
|
+
cursor += maxlen
|
41
|
+
end
|
42
|
+
end
|
43
|
+
return lines.join("\n#{prefix}")
|
44
|
+
end
|
45
|
+
end
|
46
|
+
|
47
|
+
|
48
|
+
module Bio
|
49
|
+
class Reference
|
50
|
+
def report
|
51
|
+
if (num = @authors.size) > 10
|
52
|
+
authors = "#{@authors[0]} et al. (#{num} authors)"
|
53
|
+
elsif num > 4
|
54
|
+
sep = ',' * (num - 1)
|
55
|
+
authors = "#{@authors[0]}#{sep} #{@authors[-1]}"
|
56
|
+
else
|
57
|
+
authors = authors_join(' & ')
|
58
|
+
end
|
59
|
+
journal = "#{@journal} #{@year} #{@volume}(#{@issue}):#{@pages}"
|
60
|
+
|
61
|
+
indent = 8
|
62
|
+
prefix = ' ' * indent
|
63
|
+
[
|
64
|
+
"#{@pages[/\d+/]}".ljust(indent) + "#{@title}".fill(78, indent),
|
65
|
+
authors,
|
66
|
+
"#{journal} [PMID:#{@pubmed}]",
|
67
|
+
].join("\n#{prefix}")
|
68
|
+
end
|
69
|
+
end
|
70
|
+
end
|
71
|
+
|
72
|
+
|
73
|
+
class PMFetch
|
74
|
+
|
75
|
+
class Examples < StandardError; end
|
76
|
+
class Version < StandardError; end
|
77
|
+
class Usage < StandardError; end
|
78
|
+
|
79
|
+
### default options
|
80
|
+
|
81
|
+
def initialize
|
82
|
+
@format = 'rd'
|
83
|
+
@search_opts = {
|
84
|
+
'retmax' => 20,
|
85
|
+
}
|
86
|
+
@query = nil
|
87
|
+
@query_opts = []
|
88
|
+
@pmid_list_only = false
|
89
|
+
|
90
|
+
pmfetch
|
91
|
+
end
|
92
|
+
|
93
|
+
|
94
|
+
### main
|
95
|
+
|
96
|
+
def pmfetch
|
97
|
+
begin
|
98
|
+
set_options
|
99
|
+
parse_options
|
100
|
+
check_query
|
101
|
+
rescue PMFetch::Examples
|
102
|
+
puts examples
|
103
|
+
exit
|
104
|
+
rescue PMFetch::Version
|
105
|
+
puts version
|
106
|
+
exit
|
107
|
+
rescue PMFetch::Usage
|
108
|
+
puts usage
|
109
|
+
exit
|
110
|
+
rescue GetoptLong::MissingArgument, GetoptLong::InvalidOption
|
111
|
+
puts usage
|
112
|
+
exit
|
113
|
+
end
|
114
|
+
|
115
|
+
list = pm_esearch
|
116
|
+
|
117
|
+
if list.empty?
|
118
|
+
;
|
119
|
+
elsif @pmid_list_only
|
120
|
+
puts list
|
121
|
+
else
|
122
|
+
pm_efetch(list)
|
123
|
+
end
|
124
|
+
end
|
125
|
+
|
126
|
+
|
127
|
+
### help
|
128
|
+
|
129
|
+
def usage
|
130
|
+
%Q[
|
131
|
+
Usage: #{PROG_NAME} [options...] "query string"
|
132
|
+
or #{PROG_NAME} --query "query string" [other options...]
|
133
|
+
|
134
|
+
Options:
|
135
|
+
-q --query "genome AND virus" Query string for PubMed search
|
136
|
+
-t --title "mobile elements" Title of the article to search
|
137
|
+
-j --journal "genome res" Journal title to search
|
138
|
+
-v --volume # Journal volume to search
|
139
|
+
-i --issue # Journal issue to search
|
140
|
+
-p --page # First page number of the article to search
|
141
|
+
-a --author "Altschul SF" Author name to search
|
142
|
+
-m --mesh "SARS virus" MeSH term to search
|
143
|
+
-f --format bibtex Summary output format
|
144
|
+
--pmidlist Output only a list of PubMed IDs
|
145
|
+
-n --retmax # Number of articles to retrieve at the maximum
|
146
|
+
-N --retstart # Starting number of the articles to retrieve
|
147
|
+
-s --sort pub+date Sort method for the summary output
|
148
|
+
--reldate # Search articles published within recent # days
|
149
|
+
--mindate YYYY/MM/DD Search articles published after the date
|
150
|
+
--maxdate YYYY/MM/DD Search articles published before the date
|
151
|
+
--help Output this help, then exit
|
152
|
+
--examples Output examples, then exit
|
153
|
+
--version Output version number, then exit
|
154
|
+
|
155
|
+
Formats:
|
156
|
+
endnote, medline, bibitem, bibtex, report, rd,
|
157
|
+
nature, science, genome_res, genome_biol, nar, current, trends, cell
|
158
|
+
|
159
|
+
Sort:
|
160
|
+
author, journal, pub+date, page
|
161
|
+
|
162
|
+
See the following pages for the PubMed search options:
|
163
|
+
http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
|
164
|
+
http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
|
165
|
+
|
166
|
+
#{version}
|
167
|
+
|
168
|
+
]
|
169
|
+
end
|
170
|
+
|
171
|
+
def version
|
172
|
+
PROG_VER
|
173
|
+
end
|
174
|
+
|
175
|
+
def examples
|
176
|
+
DATA.read.gsub('PMFetch', PROG_NAME)
|
177
|
+
end
|
178
|
+
|
179
|
+
|
180
|
+
private
|
181
|
+
|
182
|
+
|
183
|
+
### options
|
184
|
+
|
185
|
+
def set_options
|
186
|
+
@parser = GetoptLong.new
|
187
|
+
|
188
|
+
@parser.set_options(
|
189
|
+
[ '--query', '-q', GetoptLong::REQUIRED_ARGUMENT ],
|
190
|
+
[ '--title', '-t', GetoptLong::REQUIRED_ARGUMENT ],
|
191
|
+
[ '--journal', '-j', GetoptLong::REQUIRED_ARGUMENT ],
|
192
|
+
[ '--volume', '-v', GetoptLong::REQUIRED_ARGUMENT ],
|
193
|
+
[ '--issue', '-i', GetoptLong::REQUIRED_ARGUMENT ],
|
194
|
+
[ '--page', '-p', GetoptLong::REQUIRED_ARGUMENT ],
|
195
|
+
[ '--author', '-a', GetoptLong::REQUIRED_ARGUMENT ],
|
196
|
+
[ '--mesh', '-m', GetoptLong::REQUIRED_ARGUMENT ],
|
197
|
+
[ '--format', '-f', GetoptLong::REQUIRED_ARGUMENT ],
|
198
|
+
[ '--pmidlist', GetoptLong::NO_ARGUMENT ],
|
199
|
+
[ '--retmax', '-n', GetoptLong::REQUIRED_ARGUMENT ],
|
200
|
+
[ '--retstart', '-N', GetoptLong::REQUIRED_ARGUMENT ],
|
201
|
+
[ '--sort', '-s', GetoptLong::REQUIRED_ARGUMENT ],
|
202
|
+
[ '--reldate', GetoptLong::REQUIRED_ARGUMENT ],
|
203
|
+
[ '--mindate', GetoptLong::REQUIRED_ARGUMENT ],
|
204
|
+
[ '--maxdate', GetoptLong::REQUIRED_ARGUMENT ],
|
205
|
+
[ '--examples', GetoptLong::NO_ARGUMENT ],
|
206
|
+
[ '--help', GetoptLong::NO_ARGUMENT ],
|
207
|
+
[ '--version', GetoptLong::NO_ARGUMENT ]
|
208
|
+
)
|
209
|
+
end
|
210
|
+
|
211
|
+
def parse_options
|
212
|
+
@parser.each_option do |optname, optarg|
|
213
|
+
case optname
|
214
|
+
when /--query/
|
215
|
+
@query = optarg
|
216
|
+
when /--title/
|
217
|
+
@query_opts << "#{optarg}[ti]"
|
218
|
+
when /--journal/
|
219
|
+
@query_opts << "#{optarg}[ta]"
|
220
|
+
when /--volume/
|
221
|
+
@query_opts << "#{optarg}[vi]"
|
222
|
+
when /--issue/
|
223
|
+
@query_opts << "#{optarg}[ip]"
|
224
|
+
when /--page/
|
225
|
+
@query_opts << "#{optarg}[pg]"
|
226
|
+
when /--author/
|
227
|
+
@query_opts << "#{optarg}[au]"
|
228
|
+
when /--mesh/
|
229
|
+
@query_opts << "#{optarg}[mh]"
|
230
|
+
when /--format/
|
231
|
+
@format = optarg
|
232
|
+
when /--pmidlist/
|
233
|
+
@pmid_list_only = true
|
234
|
+
when /--examples/
|
235
|
+
raise PMFetch::Examples
|
236
|
+
when /--help/
|
237
|
+
raise PMFetch::Usage
|
238
|
+
when /--version/
|
239
|
+
raise PMFetch::Version
|
240
|
+
when /--sort/
|
241
|
+
@sort = optarg
|
242
|
+
@search_opts["sort"] = @sort unless @sort == "page"
|
243
|
+
else
|
244
|
+
optname.delete!('-')
|
245
|
+
@search_opts[optname] = optarg
|
246
|
+
end
|
247
|
+
end
|
248
|
+
end
|
249
|
+
|
250
|
+
|
251
|
+
### check query
|
252
|
+
|
253
|
+
def check_query
|
254
|
+
p @query if $DEBUG
|
255
|
+
@query ||= ARGV.join(" ") unless ARGV.empty?
|
256
|
+
|
257
|
+
p @query if $DEBUG
|
258
|
+
@query_str = [ @query, @query_opts ].flatten.compact.join(" AND ")
|
259
|
+
|
260
|
+
p @query_str if $DEBUG
|
261
|
+
if @query_str.empty?
|
262
|
+
raise PMFetch::Usage
|
263
|
+
end
|
264
|
+
end
|
265
|
+
|
266
|
+
|
267
|
+
### search
|
268
|
+
|
269
|
+
def pm_esearch
|
270
|
+
return Bio::PubMed.esearch(@query_str, @search_opts)
|
271
|
+
end
|
272
|
+
|
273
|
+
def pm_efetch(list)
|
274
|
+
entries = Bio::PubMed.efetch(list)
|
275
|
+
|
276
|
+
if @format == 'medline'
|
277
|
+
medline_format(entries)
|
278
|
+
else
|
279
|
+
entries = parse_entries(entries)
|
280
|
+
if @sort == 'page'
|
281
|
+
entries = sort_entries(entries)
|
282
|
+
end
|
283
|
+
if @format == 'report'
|
284
|
+
report_format(entries)
|
285
|
+
else
|
286
|
+
other_format(entries)
|
287
|
+
end
|
288
|
+
end
|
289
|
+
end
|
290
|
+
|
291
|
+
|
292
|
+
### output
|
293
|
+
|
294
|
+
def medline_format(entries)
|
295
|
+
entries.each do |entry|
|
296
|
+
puts entry
|
297
|
+
puts '//'
|
298
|
+
end
|
299
|
+
end
|
300
|
+
|
301
|
+
def parse_entries(entries)
|
302
|
+
entries.map { |entry| Bio::MEDLINE.new(entry) }
|
303
|
+
end
|
304
|
+
|
305
|
+
def sort_entries(entries)
|
306
|
+
if RUBY_VERSION > "1.8.0"
|
307
|
+
entries.sort_by { |x|
|
308
|
+
[ x.journal, x.volume.to_i, x.issue.to_i, x.pages.to_i ]
|
309
|
+
}
|
310
|
+
else
|
311
|
+
entries.map { |x|
|
312
|
+
[ x.journal, x.volume.to_i, x.issue.to_i, x.pages.to_i, x ]
|
313
|
+
}.sort { |a, b|
|
314
|
+
a[0..3] <=> b[0..3]
|
315
|
+
}.map { |y|
|
316
|
+
y.pop
|
317
|
+
}
|
318
|
+
end
|
319
|
+
end
|
320
|
+
|
321
|
+
def report_format(entries)
|
322
|
+
entries.each do |entry|
|
323
|
+
puts entry.reference.report
|
324
|
+
puts
|
325
|
+
end
|
326
|
+
end
|
327
|
+
|
328
|
+
def other_format(entries)
|
329
|
+
entries.each do |entry|
|
330
|
+
puts entry.reference.format(@format)
|
331
|
+
puts
|
332
|
+
end
|
333
|
+
end
|
334
|
+
|
335
|
+
end
|
336
|
+
|
337
|
+
|
338
|
+
PMFetch.new
|
339
|
+
|
340
|
+
|
341
|
+
__END__
|
342
|
+
|
343
|
+
= Examples : PubMed search
|
344
|
+
|
345
|
+
These four lines will do the same job.
|
346
|
+
|
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
|
+
|