wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -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/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -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 +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -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 +235 -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/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -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/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -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 +542 -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 +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 +353 -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/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.rb +410 -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/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.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 +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -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.rb +482 -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/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.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -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/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
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -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
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- 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 +852 -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 +200 -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/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
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +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/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
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -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/appl/test_pts1.rb +115 -0
- 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 +14 -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
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- 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/db/test_url.rb +36 -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 +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -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 +543 -0
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#
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# bio/db/rebase.rb - Interface for EMBOSS formatted REBASE files
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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#
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# $Id:$
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#
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require 'yaml'
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require 'bio/reference'
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module Bio
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#
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# bio/db/rebase.rb - Interface for EMBOSS formatted REBASE files
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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#
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#
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# = Description
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#
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# Bio::REBASE provides utilties for interacting with REBASE data in EMBOSS
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# format. REBASE is the Restriction Enzyme Database, more information
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# can be found here:
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#
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# * http://rebase.neb.com
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#
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# EMBOSS formatted files located at:
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#
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# * http://rebase.neb.com/rebase/rebase.f37.html
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#
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# These files are the same as the "emboss_?.???" files located at:
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#
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# * ftp://ftp.neb.com/pub/rebase/
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#
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# To easily get started with the data you can simply type this command
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# at your shell prompt:
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#
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# % wget ftp://ftp.neb.com/pub/rebase/emboss*
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#
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#
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# = Usage
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#
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# require 'bio'
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# require 'pp'
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#
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# enz = File.read('emboss_e')
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# ref = File.read('emboss_r')
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# sup = File.read('emboss_s')
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#
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# # When creating a new instance of Bio::REBASE
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# # the contents of the enzyme file must be passed.
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# # The references and suppiers file contents
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# # may also be passed.
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# rebase = Bio::REBASE.new( enz )
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# rebase = Bio::REBASE.new( enz, ref )
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# rebase = Bio::REBASE.new( enz, ref, sup )
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#
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# # The 'read' class method allows you to read in files
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# # that are REBASE EMBOSS formatted
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# rebase = Bio::REBASE.read( 'emboss_e' )
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# rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r' )
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# rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r', 'emboss_s' )
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#
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# # The data loaded may be saved in YAML format
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# rebase.save_yaml( 'enz.yaml' )
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# rebase.save_yaml( 'enz.yaml', 'ref.yaml' )
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# rebase.save_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )
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#
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# # YAML formatted files can also be read with the
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# # class method 'load_yaml'
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# rebase = Bio::REBASE.load_yaml( 'enz.yaml' )
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# rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml' )
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# rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )
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#
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# pp rebase.enzymes[0..4] # ["AarI", "AasI", "AatI", "AatII", "Acc16I"]
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# pp rebase.enzyme_name?('aasi') # true
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# pp rebase['AarI'].pattern # "CACCTGC"
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# pp rebase['AarI'].blunt? # false
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# pp rebase['AarI'].organism # "Arthrobacter aurescens SS2-322"
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# pp rebase['AarI'].source # "A. Janulaitis"
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# pp rebase['AarI'].primary_strand_cut1 # 11
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# pp rebase['AarI'].primary_strand_cut2 # 0
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# pp rebase['AarI'].complementary_strand_cut1 # 15
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# pp rebase['AarI'].complementary_strand_cut2 # 0
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# pp rebase['AarI'].suppliers # ["F"]
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# pp rebase['AarI'].supplier_names # ["Fermentas International Inc."]
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#
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# pp rebase['AarI'].isoschizomers # Currently none stored in the references file
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# pp rebase['AarI'].methylation # ""
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#
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# pp rebase['EcoRII'].methylation # "2(5)"
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# pp rebase['EcoRII'].suppliers # ["F", "J", "M", "O", "S"]
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# pp rebase['EcoRII'].supplier_names # ["Fermentas International Inc.", "Nippon Gene Co., Ltd.",
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# # "Roche Applied Science", "Toyobo Biochemicals",
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# # "Sigma Chemical Corporation"]
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#
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# # Number of enzymes in the database
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# pp rebase.size # 673
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# pp rebase.enzymes.size # 673
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#
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# rebase.each do |name, info|
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# pp "#{name}: #{info.methylation}" unless info.methylation.empty?
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# end
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#
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class REBASE
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class DynamicMethod_Hash < Hash #:nodoc:
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# Define a writer or reader
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# * Allows hash[:kay]= to be accessed like hash.key=
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# * Allows hash[:key] to be accessed like hash.key
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def method_missing(method_id, *args)
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k = self.class
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if method_id.to_s[-1].chr == '='
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k.class_eval do
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define_method(method_id) { |s| self[ method_id.to_s[0..-2].to_sym ] = s }
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end
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k.instance_method(method_id).bind(self).call(args[0])
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else
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k.class_eval do
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define_method(method_id) { self[method_id] }
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end
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k.instance_method(method_id).bind(self).call
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end
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end
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end
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class EnzymeEntry < DynamicMethod_Hash #:nodoc:
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@@supplier_data = {}
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def self.supplier_data=(d); @@supplier_data = d; end
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def supplier_names
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ret = []
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self.suppliers.each { |s| ret << @@supplier_data[s] }
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ret
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end
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end
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# Calls _block_ once for each element in <tt>@data</tt> hash, passing that element as a parameter.
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#
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# ---
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# *Arguments*
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# * Accepts a block
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# *Returns*:: results of _block_ operations
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def each
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@data.each { |item| yield item }
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end
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# Make the instantiated class act like a Hash on @data
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# Does the equivalent and more of this:
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# def []( key ); @data[ key ]; end
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# def size; @data.size; end
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def method_missing(method_id, *args) #:nodoc:
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self.class.class_eval do
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define_method(method_id) { |a| Hash.instance_method(method_id).bind(@data).call(a) }
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end
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Hash.instance_method(method_id).bind(@data).call(*args)
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end
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# Constructor
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#
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# ---
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# *Arguments*
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# * +enzyme_lines+: (_required_) contents of EMBOSS formatted enzymes file
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# * +reference_lines+: (_optional_) contents of EMBOSS formatted references file
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# * +supplier_lines+: (_optional_) contents of EMBOSS formatted suppliers files
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# * +yaml+: (_optional_, _default_ +false+) enzyme_lines, reference_lines, and supplier_lines are read as YAML if set to true
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# *Returns*:: Bio::REBASE
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def initialize( enzyme_lines, reference_lines = nil, supplier_lines = nil, yaml = false )
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# All your REBASE are belong to us.
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if yaml
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@enzyme_data = enzyme_lines
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@reference_data = reference_lines
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@supplier_data = supplier_lines
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else
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@enzyme_data = parse_enzymes(enzyme_lines)
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@reference_data = parse_references(reference_lines)
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@supplier_data = parse_suppliers(supplier_lines)
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end
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EnzymeEntry.supplier_data = @supplier_data
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setup_enzyme_data
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end
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# List the enzymes available
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#
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# ---
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# *Arguments*
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# * _none_
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# *Returns*:: +Array+ sorted enzyme names
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def enzymes
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@data.keys.sort
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end
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# Check if supplied name is the name of an available enzyme
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#
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# ---
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# *Arguments*
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# * +name+: Enzyme name
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# *Returns*:: +true/false+
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def enzyme_name?(name)
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enzymes.each do |e|
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return true if e.downcase == name.downcase
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end
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return false
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end
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# Save the current data
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# rebase.save_yaml( 'enz.yaml' )
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# rebase.save_yaml( 'enz.yaml', 'ref.yaml' )
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# rebase.save_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )
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#
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# ---
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# *Arguments*
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# * +f_enzyme+: (_required_) Filename to save YAML formatted output of enzyme data
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# * +f_reference+: (_optional_) Filename to save YAML formatted output of reference data
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# * +f_supplier+: (_optional_) Filename to save YAML formatted output of supplier data
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# *Returns*:: nothing
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def save_yaml( f_enzyme, f_reference=nil, f_supplier=nil )
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File.open(f_enzyme, 'w') { |f| f.puts YAML.dump(@enzyme_data) }
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File.open(f_reference, 'w') { |f| f.puts YAML.dump(@reference_data) } if f_reference
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File.open(f_supplier, 'w') { |f| f.puts YAML.dump(@supplier_data) } if f_supplier
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return
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end
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# Read REBASE EMBOSS-formatted files
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# rebase = Bio::REBASE.read( 'emboss_e' )
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# rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r' )
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# rebase = Bio::REBASE.read( 'emboss_e', 'emboss_r', 'emboss_s' )
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#
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# ---
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# *Arguments*
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# * +f_enzyme+: (_required_) Filename to read enzyme data
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# * +f_reference+: (_optional_) Filename to read reference data
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# * +f_supplier+: (_optional_) Filename to read supplier data
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# *Returns*:: Bio::REBASE object
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def self.read( f_enzyme, f_reference=nil, f_supplier=nil )
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e = IO.readlines(f_enzyme)
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r = f_reference ? IO.readlines(f_reference) : nil
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s = f_supplier ? IO.readlines(f_supplier) : nil
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self.new(e,r,s)
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end
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# Read YAML formatted files
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# rebase = Bio::REBASE.load_yaml( 'enz.yaml' )
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# rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml' )
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# rebase = Bio::REBASE.load_yaml( 'enz.yaml', 'ref.yaml', 'sup.yaml' )
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#
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# ---
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# *Arguments*
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# * +f_enzyme+: (_required_) Filename to read YAML-formatted enzyme data
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# * +f_reference+: (_optional_) Filename to read YAML-formatted reference data
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# * +f_supplier+: (_optional_) Filename to read YAML-formatted supplier data
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# *Returns*:: Bio::REBASE object
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def self.load_yaml( f_enzyme, f_reference=nil, f_supplier=nil )
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e = YAML.load_file(f_enzyme)
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r = f_reference ? YAML.load_file(f_reference) : nil
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s = f_supplier ? YAML.load_file(f_supplier) : nil
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self.new(e,r,s,true)
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end
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#########
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protected
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#########
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def setup_enzyme_data
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@data = {}
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@enzyme_data.each do |name, hash|
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@data[name] = EnzymeEntry.new
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d = @data[name]
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d.pattern = hash[:pattern]
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# d.blunt?= is a syntax error
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d[:blunt?] = (hash[:blunt].to_i == 1 ? true : false)
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d.primary_strand_cut1 = hash[:c1].to_i
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d.complementary_strand_cut1 = hash[:c2].to_i
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d.primary_strand_cut2 = hash[:c3].to_i
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d.complementary_strand_cut2 = hash[:c4].to_i
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# Set up keys just in case there's no reference data supplied
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[:organism, :isoschizomers,
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:methylation, :source].each { |k| d[k] = '' }
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d.suppliers = []
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d.references = []
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end
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setup_enzyme_and_reference_association
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end
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def setup_enzyme_and_reference_association
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return unless @reference_data
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@reference_data.each do |name, hash|
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d = @data[name]
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[:organism, :isoschizomers,
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|
+
:methylation, :source].each { |k| d[k] = hash[k] }
|
302
|
+
d.suppliers = hash[:suppliers].split('')
|
303
|
+
d.references = []
|
304
|
+
hash[:references].each { |k| d.references << raw_to_reference(k) }
|
305
|
+
end
|
306
|
+
end
|
307
|
+
|
308
|
+
# data is a hash indexed by the :name of each entry which is also a hash
|
309
|
+
# * data[enzyme_name] has the following keys:
|
310
|
+
# :name, :pattern, :len, :ncuts, :blunt, :c1, :c2, :c3, :c4
|
311
|
+
# :c1 => First 5' cut
|
312
|
+
# :c2 => First 3' cut
|
313
|
+
# :c3 => Second 5' cut
|
314
|
+
# :c4 => Seocnd 3' cut
|
315
|
+
def parse_enzymes( lines )
|
316
|
+
data = {}
|
317
|
+
return data if lines == nil
|
318
|
+
lines.each_line do |line|
|
319
|
+
next if line[0].chr == '#'
|
320
|
+
line.chomp!
|
321
|
+
|
322
|
+
a = line.split("\s")
|
323
|
+
|
324
|
+
data[ a[0] ] = {
|
325
|
+
:name => a[0],
|
326
|
+
:pattern => a[1],
|
327
|
+
:len => a[2],
|
328
|
+
:ncuts => a[3],
|
329
|
+
:blunt => a[4],
|
330
|
+
:c1 => a[5],
|
331
|
+
:c2 => a[6],
|
332
|
+
:c3 => a[7],
|
333
|
+
:c4 => a[8]
|
334
|
+
}
|
335
|
+
end # lines.each
|
336
|
+
data
|
337
|
+
end
|
338
|
+
|
339
|
+
# data is a hash indexed by the :name of each entry which is also a hash
|
340
|
+
# * data[enzyme_name] has the following keys:
|
341
|
+
# :organism, :isoschizomers, :references, :source, :methylation, :suppliers, :name, :number_of_references
|
342
|
+
def parse_references( lines )
|
343
|
+
data = {}
|
344
|
+
return data if lines == nil
|
345
|
+
index = 1
|
346
|
+
h = {}
|
347
|
+
references_left = 0
|
348
|
+
|
349
|
+
lines.each_line do |line|
|
350
|
+
next if line[0].chr == '#' # Comment
|
351
|
+
next if line[0..1] == '//' # End of entry marker
|
352
|
+
line.chomp!
|
353
|
+
|
354
|
+
if (1..7).include?( index )
|
355
|
+
h[index] = line
|
356
|
+
references_left = h[index].to_i if index == 7
|
357
|
+
index += 1
|
358
|
+
next
|
359
|
+
end
|
360
|
+
|
361
|
+
if index == 8
|
362
|
+
h[index] ||= []
|
363
|
+
h[index] << line
|
364
|
+
references_left -= 1
|
365
|
+
end
|
366
|
+
|
367
|
+
if references_left == 0
|
368
|
+
data[ h[1] ] = {
|
369
|
+
:name => h[1],
|
370
|
+
:organism => h[2],
|
371
|
+
:isoschizomers => h[3],
|
372
|
+
:methylation => h[4],
|
373
|
+
:source => h[5],
|
374
|
+
:suppliers => h[6],
|
375
|
+
:number_of_references => h[7],
|
376
|
+
:references => h[8]
|
377
|
+
}
|
378
|
+
index = 1
|
379
|
+
h = {}
|
380
|
+
end
|
381
|
+
end # lines.each
|
382
|
+
data
|
383
|
+
end
|
384
|
+
|
385
|
+
# data is a hash indexed by the supplier code
|
386
|
+
# data[supplier_code]
|
387
|
+
# returns the suppliers name
|
388
|
+
def parse_suppliers( lines )
|
389
|
+
data = {}
|
390
|
+
return data if lines == nil
|
391
|
+
lines.each_line do |line|
|
392
|
+
next if line[0].chr == '#'
|
393
|
+
data[$1] = $2 if line =~ %r{(.+?)\s(.+)}
|
394
|
+
end
|
395
|
+
data
|
396
|
+
end
|
397
|
+
|
398
|
+
# Takes a string in one of the three formats listed below and returns a
|
399
|
+
# Bio::Reference object
|
400
|
+
# * Possible input styles:
|
401
|
+
# a = 'Inagaki, K., Hikita, T., Yanagidani, S., Nomura, Y., Kishimoto, N., Tano, T., Tanaka, H., (1993) Biosci. Biotechnol. Biochem., vol. 57, pp. 1716-1721.'
|
402
|
+
# b = 'Nekrasiene, D., Lapcinskaja, S., Kiuduliene, L., Vitkute, J., Janulaitis, A., Unpublished observations.'
|
403
|
+
# c = "Grigaite, R., Maneliene, Z., Janulaitis, A., (2002) Nucleic Acids Res., vol. 30."
|
404
|
+
def raw_to_reference( line )
|
405
|
+
a = line.split(', ')
|
406
|
+
|
407
|
+
if a[-1] == 'Unpublished observations.'
|
408
|
+
title = a.pop.chop
|
409
|
+
pages = volume = year = journal = ''
|
410
|
+
else
|
411
|
+
title = ''
|
412
|
+
|
413
|
+
pages_or_volume = a.pop.chop
|
414
|
+
if pages_or_volume =~ %r{pp\.\s}
|
415
|
+
pages = pages_or_volume
|
416
|
+
pages.gsub!('pp. ', '')
|
417
|
+
volume = a.pop
|
418
|
+
else
|
419
|
+
pages = ''
|
420
|
+
volume = pages_or_volume
|
421
|
+
end
|
422
|
+
|
423
|
+
volume.gsub!('vol. ', '')
|
424
|
+
|
425
|
+
year_and_journal = a.pop
|
426
|
+
year_and_journal =~ %r{\((\d+)\)\s(.+)}
|
427
|
+
year = $1
|
428
|
+
journal = $2
|
429
|
+
end
|
430
|
+
|
431
|
+
authors = []
|
432
|
+
|
433
|
+
last_name = nil
|
434
|
+
a.each do |e|
|
435
|
+
if last_name
|
436
|
+
authors << "#{last_name}, #{e}"
|
437
|
+
last_name = nil
|
438
|
+
else
|
439
|
+
last_name = e
|
440
|
+
end
|
441
|
+
end
|
442
|
+
|
443
|
+
ref = {
|
444
|
+
'title' => title,
|
445
|
+
'pages' => pages,
|
446
|
+
'volume' => volume,
|
447
|
+
'year' => year,
|
448
|
+
'journal' => journal,
|
449
|
+
'authors' => authors,
|
450
|
+
}
|
451
|
+
|
452
|
+
Bio::Reference.new(ref)
|
453
|
+
end
|
454
|
+
|
455
|
+
end # REBASE
|
456
|
+
end # Bio
|