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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# = bio/reference.rb - Journal reference classes
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#
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# Copyright:: Copyright (C) 2001, 2006, 2008
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# Toshiaki Katayama <k@bioruby.org>,
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# Ryan Raaum <ryan@raaum.org>,
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# Jan Aerts <jandot@bioruby.org>
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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 'enumerator'
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module Bio
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# = DESCRIPTION
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#
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# A class for journal reference information.
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#
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# = USAGE
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#
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# hash = {'authors' => [ "Hoge, J.P.", "Fuga, F.B." ],
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# 'title' => "Title of the study.",
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# 'journal' => "Theor. J. Hoge",
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# 'volume' => 12,
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# 'issue' => 3,
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# 'pages' => "123-145",
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# 'year' => 2001,
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# 'pubmed' => 12345678,
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# 'medline' => 98765432,
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# 'abstract' => "Hoge fuga. ...",
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# 'url' => "http://example.com",
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# 'mesh' => [],
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# 'affiliations' => []}
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# ref = Bio::Reference.new(hash)
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#
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# # Formats in the BiBTeX style.
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# ref.format("bibtex")
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#
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# # Short-cut for Bio::Reference#format("bibtex")
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# ref.bibtex
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#
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class Reference
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# Author names in an Array, [ "Hoge, J.P.", "Fuga, F.B." ].
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attr_reader :authors
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# String with title of the study
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attr_reader :title
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# String with journal name
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attr_reader :journal
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# volume number (typically Fixnum)
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attr_reader :volume
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# issue number (typically Fixnum)
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attr_reader :issue
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# page range (typically String, e.g. "123-145")
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attr_reader :pages
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# year of publication (typically Fixnum)
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attr_reader :year
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# pubmed identifier (typically Fixnum)
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attr_reader :pubmed
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# medline identifier (typically Fixnum)
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attr_reader :medline
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# DOI identifier (typically String, e.g. "10.1126/science.1110418")
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attr_reader :doi
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# Abstract text in String.
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attr_reader :abstract
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# An URL String.
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attr_reader :url
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# MeSH terms in an Array.
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attr_reader :mesh
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# Affiliations in an Array.
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attr_reader :affiliations
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# Sequence number in EMBL/GenBank records
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attr_reader :embl_gb_record_number
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# Position in a sequence that this reference refers to
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attr_reader :sequence_position
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# Comments for the reference (typically Array of String, or nil)
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attr_reader :comments
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# Create a new Bio::Reference object from a Hash of values.
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# Data is extracted from the values for keys:
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#
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# * authors - expected value: Array of Strings
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# * title - expected value: String
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# * journal - expected value: String
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# * volume - expected value: Fixnum or String
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# * issue - expected value: Fixnum or String
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# * pages - expected value: String
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# * year - expected value: Fixnum or String
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# * pubmed - expected value: Fixnum or String
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# * medline - expected value: Fixnum or String
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# * abstract - expected value: String
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# * url - expected value: String
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# * mesh - expected value: Array of Strings
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# * affiliations - expected value: Array of Strings
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#
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#
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# hash = {'authors' => [ "Hoge, J.P.", "Fuga, F.B." ],
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# 'title' => "Title of the study.",
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# 'journal' => "Theor. J. Hoge",
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# 'volume' => 12,
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# 'issue' => 3,
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# 'pages' => "123-145",
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# 'year' => 2001,
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# 'pubmed' => 12345678,
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# 'medline' => 98765432,
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# 'abstract' => "Hoge fuga. ...",
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# 'url' => "http://example.com",
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# 'mesh' => [],
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# 'affiliations' => []}
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# ref = Bio::Reference.new(hash)
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# ---
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# *Arguments*:
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# * (required) _hash_: Hash
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# *Returns*:: Bio::Reference object
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def initialize(hash)
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@authors = hash['authors'] || [] # [ "Hoge, J.P.", "Fuga, F.B." ]
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@title = hash['title'] || '' # "Title of the study."
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@journal = hash['journal'] || '' # "Theor. J. Hoge"
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@volume = hash['volume'] || '' # 12
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@issue = hash['issue'] || '' # 3
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@pages = hash['pages'] || '' # 123-145
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@year = hash['year'] || '' # 2001
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@pubmed = hash['pubmed'] || '' # 12345678
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@medline = hash['medline'] || '' # 98765432
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@doi = hash['doi']
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@abstract = hash['abstract'] || ''
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@url = hash['url']
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@mesh = hash['mesh'] || []
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@embl_gb_record_number = hash['embl_gb_record_number'] || nil
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@sequence_position = hash['sequence_position'] || nil
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@comments = hash['comments']
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@affiliations = hash['affiliations'] || []
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end
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# Formats the reference in a given style.
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#
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# Styles:
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# 0. nil - general
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# 1. endnote - Endnote
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# 2. bibitem - Bibitem (option available)
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# 3. bibtex - BiBTeX (option available)
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# 4. rd - rd (option available)
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# 5. nature - Nature (option available)
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# 6. science - Science
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# 7. genome_biol - Genome Biology
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# 8. genome_res - Genome Research
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# 9. nar - Nucleic Acids Research
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# 10. current - Current Biology
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# 11. trends - Trends in *
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# 12. cell - Cell Press
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#
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# See individual methods for details. Basic usage is:
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#
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# # ref is Bio::Reference object
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# # using simplest possible call (for general style)
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# puts ref.format
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#
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# # output in Nature style
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# puts ref.format("nature") # alternatively, puts ref.nature
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#
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# # output in Nature short style (see Bio::Reference#nature)
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# puts ref.format("nature",true) # alternatively, puts ref.nature(true)
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# ---
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# *Arguments*:
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# * (optional) _style_: String with style identifier
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# * (optional) _options_: Options for styles accepting one
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# *Returns*:: String
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def format(style = nil, *options)
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case style
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when 'embl'
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return embl
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when 'endnote'
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return endnote
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when 'bibitem'
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return bibitem(*options)
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when 'bibtex'
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return bibtex(*options)
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when 'rd'
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return rd(*options)
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when /^nature$/i
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return nature(*options)
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when /^science$/i
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return science
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when /^genome\s*_*biol/i
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return genome_biol
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when /^genome\s*_*res/i
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return genome_res
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when /^nar$/i
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return nar
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when /^current/i
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return current
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when /^trends/i
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return trends
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when /^cell$/i
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return cell
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else
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return general
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end
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end
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# Returns reference formatted in the Endnote style.
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#
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# # ref is a Bio::Reference object
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# puts ref.endnote
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#
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# %0 Journal Article
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# %A Hoge, J.P.
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# %A Fuga, F.B.
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# %D 2001
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# %T Title of the study.
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# %J Theor. J. Hoge
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# %V 12
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# %N 3
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# %P 123-145
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# %M 12345678
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# %U http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12345678
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# %X Hoge fuga. ...
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# ---
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# *Returns*:: String
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def endnote
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lines = []
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lines << "%0 Journal Article"
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@authors.each do |author|
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lines << "%A #{author}"
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end
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lines << "%D #{@year}" unless @year.to_s.empty?
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lines << "%T #{@title}" unless @title.empty?
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lines << "%J #{@journal}" unless @journal.empty?
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lines << "%V #{@volume}" unless @volume.to_s.empty?
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lines << "%N #{@issue}" unless @issue.to_s.empty?
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lines << "%P #{@pages}" unless @pages.empty?
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lines << "%M #{@pubmed}" unless @pubmed.to_s.empty?
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u = @url.empty? ? pubmed_url : @url
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lines << "%U #{u}" unless u.empty?
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lines << "%X #{@abstract}" unless @abstract.empty?
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@mesh.each do |term|
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lines << "%K #{term}"
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end
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lines << "%+ #{@affiliations.join(' ')}" unless @affiliations.empty?
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return lines.join("\n")
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end
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# Returns reference formatted in the EMBL style.
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#
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# # ref is a Bio::Reference object
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# puts ref.embl
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#
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# RP 1-1859
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# RX PUBMED; 1907511.
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# RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
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# RT "Nucleotide and derived amino acid sequence of the cyanogenic
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# RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)";
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# RL Plant Mol. Biol. 17(2):209-219(1991).
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def embl
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r = self
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Bio::Sequence::Format::NucFormatter::Embl.new('').instance_eval {
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reference_format_embl(r)
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}
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end
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# Returns reference formatted in the bibitem style
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#
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# # ref is a Bio::Reference object
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# puts ref.bibitem
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#
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# \bibitem{PMID:12345678}
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# Hoge, J.P., Fuga, F.B.
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# Title of the study.,
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# {\em Theor. J. Hoge}, 12(3):123--145, 2001.
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# ---
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# *Arguments*:
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# * (optional) _item_: label string (default: <tt>"PMID:#{pubmed}"</tt>).
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# *Returns*:: String
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def bibitem(item = nil)
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item = "PMID:#{@pubmed}" unless item
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pages = @pages.sub('-', '--')
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return <<-"END".enum_for(:each_line).collect {|line| line.strip}.join("\n")
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\\bibitem{#{item}}
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#{@authors.join(', ')}
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#{@title},
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{\\em #{@journal}}, #{@volume}(#{@issue}):#{pages}, #{@year}.
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END
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end
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# Returns reference formatted in the BiBTeX style.
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#
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# # ref is a Bio::Reference object
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# puts ref.bibtex
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#
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# @article{PMID:12345678,
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# author = {Hoge, J.P. and Fuga, F.B.},
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# title = {Title of the study.},
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# journal = {Theor. J. Hoge},
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# year = {2001},
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# volume = {12},
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# number = {3},
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# pages = {123--145},
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# }
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#
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# # using a different section (e.g. "book")
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# # (but not really configured for anything other than articles)
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# puts ref.bibtex("book")
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#
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# @book{PMID:12345678,
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# author = {Hoge, J.P. and Fuga, F.B.},
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# title = {Title of the study.},
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# journal = {Theor. J. Hoge},
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# year = {2001},
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# volume = {12},
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# number = {3},
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# pages = {123--145},
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# }
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# ---
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# *Arguments*:
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333
|
+
# * (optional) _section_: BiBTeX section as String
|
334
|
+
# * (optional) _label_: Label string cited by LaTeX documents.
|
335
|
+
# Default is <tt>"PMID:#{pubmed}"</tt>.
|
336
|
+
# * (optional) _keywords_: Hash of additional keywords,
|
337
|
+
# e.g. { 'abstract' => 'This is abstract.' }.
|
338
|
+
# You can also override default keywords.
|
339
|
+
# To disable default keywords, specify false as
|
340
|
+
# value, e.g. { 'url' => false, 'year' => false }.
|
341
|
+
# *Returns*:: String
|
342
|
+
def bibtex(section = nil, label = nil, keywords = {})
|
343
|
+
section = "article" unless section
|
344
|
+
authors = authors_join(' and ', ' and ')
|
345
|
+
thepages = pages.to_s.empty? ? nil : pages.sub(/\-/, '--')
|
346
|
+
unless label then
|
347
|
+
label = "PMID:#{pubmed}"
|
348
|
+
end
|
349
|
+
theurl = if !(url.to_s.empty?) then
|
350
|
+
url
|
351
|
+
elsif pmurl = pubmed_url and !(pmurl.to_s.empty?) then
|
352
|
+
pmurl
|
353
|
+
else
|
354
|
+
nil
|
355
|
+
end
|
356
|
+
hash = {
|
357
|
+
'author' => authors.empty? ? nil : authors,
|
358
|
+
'title' => title.to_s.empty? ? nil : title,
|
359
|
+
'number' => issue.to_s.empty? ? nil : issue,
|
360
|
+
'pages' => thepages,
|
361
|
+
'url' => theurl
|
362
|
+
}
|
363
|
+
keys = %w( author title journal year volume number pages url )
|
364
|
+
keys.each do |k|
|
365
|
+
hash[k] = self.__send__(k.intern) unless hash.has_key?(k)
|
366
|
+
end
|
367
|
+
hash.merge!(keywords) { |k, v1, v2| v2.nil? ? v1 : v2 }
|
368
|
+
bib = [ "@#{section}{#{label}," ]
|
369
|
+
keys.concat((hash.keys - keys).sort)
|
370
|
+
keys.each do |kw|
|
371
|
+
ref = hash[kw]
|
372
|
+
bib.push " #{kw.ljust(12)} = {#{ref}}," if ref
|
373
|
+
end
|
374
|
+
bib.push "}\n"
|
375
|
+
return bib.join("\n")
|
376
|
+
end
|
377
|
+
|
378
|
+
# Returns reference formatted in a general/generic style.
|
379
|
+
#
|
380
|
+
# # ref is a Bio::Reference object
|
381
|
+
# puts ref.general
|
382
|
+
#
|
383
|
+
# Hoge, J.P., Fuga, F.B. (2001). "Title of the study." Theor. J. Hoge 12:123-145.
|
384
|
+
# ---
|
385
|
+
# *Returns*:: String
|
386
|
+
def general
|
387
|
+
authors = @authors.join(', ')
|
388
|
+
"#{authors} (#{@year}). \"#{@title}\" #{@journal} #{@volume}:#{@pages}."
|
389
|
+
end
|
390
|
+
|
391
|
+
# Return reference formatted in the RD style.
|
392
|
+
#
|
393
|
+
# # ref is a Bio::Reference object
|
394
|
+
# puts ref.rd
|
395
|
+
#
|
396
|
+
# == Title of the study.
|
397
|
+
#
|
398
|
+
# * Hoge, J.P. and Fuga, F.B.
|
399
|
+
#
|
400
|
+
# * Theor. J. Hoge 2001 12:123-145 [PMID:12345678]
|
401
|
+
#
|
402
|
+
# Hoge fuga. ...
|
403
|
+
#
|
404
|
+
# An optional string argument can be supplied, but does nothing.
|
405
|
+
# ---
|
406
|
+
# *Arguments*:
|
407
|
+
# * (optional) str: String (default nil)
|
408
|
+
# *Returns*:: String
|
409
|
+
def rd(str = nil)
|
410
|
+
@abstract ||= str
|
411
|
+
lines = []
|
412
|
+
lines << "== " + @title
|
413
|
+
lines << "* " + authors_join(' and ')
|
414
|
+
lines << "* #{@journal} #{@year} #{@volume}:#{@pages} [PMID:#{@pubmed}]"
|
415
|
+
lines << @abstract
|
416
|
+
return lines.join("\n\n")
|
417
|
+
end
|
418
|
+
|
419
|
+
# Formats in the Nature Publishing Group
|
420
|
+
# (http://www.nature.com) style.
|
421
|
+
#
|
422
|
+
# # ref is a Bio::Reference object
|
423
|
+
# puts ref.nature
|
424
|
+
#
|
425
|
+
# Hoge, J.P. & Fuga, F.B. Title of the study. Theor. J. Hoge 12, 123-145 (2001).
|
426
|
+
#
|
427
|
+
# # optionally, output short version
|
428
|
+
# puts ref.nature(true) # or puts ref.nature(short=true)
|
429
|
+
#
|
430
|
+
# Hoge, J.P. & Fuga, F.B. Theor. J. Hoge 12, 123-145 (2001).
|
431
|
+
# ---
|
432
|
+
# *Arguments*:
|
433
|
+
# * (optional) _short_: Boolean (default false)
|
434
|
+
# *Returns*:: String
|
435
|
+
def nature(short = false)
|
436
|
+
if short
|
437
|
+
if @authors.size > 4
|
438
|
+
authors = "#{@authors[0]} et al."
|
439
|
+
elsif @authors.size == 1
|
440
|
+
authors = "#{@authors[0]}"
|
441
|
+
else
|
442
|
+
authors = authors_join(' & ')
|
443
|
+
end
|
444
|
+
"#{authors} #{@journal} #{@volume}, #{@pages} (#{@year})."
|
445
|
+
else
|
446
|
+
authors = authors_join(' & ')
|
447
|
+
"#{authors} #{@title} #{@journal} #{@volume}, #{@pages} (#{@year})."
|
448
|
+
end
|
449
|
+
end
|
450
|
+
|
451
|
+
# Returns reference formatted in the
|
452
|
+
# Science[http://www.sciencemag.org] style.
|
453
|
+
#
|
454
|
+
# # ref is a Bio::Reference object
|
455
|
+
# puts ref.science
|
456
|
+
#
|
457
|
+
# J.P. Hoge, F.B. Fuga, Theor. J. Hoge 12 123 (2001).
|
458
|
+
# ---
|
459
|
+
# *Returns*:: String
|
460
|
+
def science
|
461
|
+
if @authors.size > 4
|
462
|
+
authors = rev_name(@authors[0]) + " et al."
|
463
|
+
else
|
464
|
+
authors = @authors.collect {|name| rev_name(name)}.join(', ')
|
465
|
+
end
|
466
|
+
page_from, = @pages.split('-')
|
467
|
+
"#{authors}, #{@journal} #{@volume} #{page_from} (#{@year})."
|
468
|
+
end
|
469
|
+
|
470
|
+
# Returns reference formatted in the Genome Biology
|
471
|
+
# (http://genomebiology.com) style.
|
472
|
+
#
|
473
|
+
# # ref is a Bio::Reference object
|
474
|
+
# puts ref.genome_biol
|
475
|
+
#
|
476
|
+
# Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.
|
477
|
+
# ---
|
478
|
+
# *Returns*:: String
|
479
|
+
def genome_biol
|
480
|
+
authors = @authors.collect {|name| strip_dots(name)}.join(', ')
|
481
|
+
journal = strip_dots(@journal)
|
482
|
+
"#{authors}: #{@title} #{journal} #{@year}, #{@volume}:#{@pages}."
|
483
|
+
end
|
484
|
+
|
485
|
+
# Returns reference formatted in the Current Biology
|
486
|
+
# (http://current-biology.com) style. (Same as the Genome Biology style)
|
487
|
+
#
|
488
|
+
# # ref is a Bio::Reference object
|
489
|
+
# puts ref.current
|
490
|
+
#
|
491
|
+
# Hoge JP, Fuga FB: Title of the study. Theor J Hoge 2001, 12:123-145.
|
492
|
+
# ---
|
493
|
+
# *Returns*:: String
|
494
|
+
def current
|
495
|
+
self.genome_biol
|
496
|
+
end
|
497
|
+
|
498
|
+
# Returns reference formatted in the Genome Research
|
499
|
+
# (http://genome.org) style.
|
500
|
+
#
|
501
|
+
# # ref is a Bio::Reference object
|
502
|
+
# puts ref.genome_res
|
503
|
+
#
|
504
|
+
# Hoge, J.P. and Fuga, F.B. 2001.
|
505
|
+
# Title of the study. Theor. J. Hoge 12: 123-145.
|
506
|
+
# ---
|
507
|
+
# *Returns*:: String
|
508
|
+
def genome_res
|
509
|
+
authors = authors_join(' and ')
|
510
|
+
"#{authors} #{@year}.\n #{@title} #{@journal} #{@volume}: #{@pages}."
|
511
|
+
end
|
512
|
+
|
513
|
+
# Returns reference formatted in the Nucleic Acids Reseach
|
514
|
+
# (http://nar.oxfordjournals.org) style.
|
515
|
+
#
|
516
|
+
# # ref is a Bio::Reference object
|
517
|
+
# puts ref.nar
|
518
|
+
#
|
519
|
+
# Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge, 12, 123-145.
|
520
|
+
# ---
|
521
|
+
# *Returns*:: String
|
522
|
+
def nar
|
523
|
+
authors = authors_join(' and ')
|
524
|
+
"#{authors} (#{@year}) #{@title} #{@journal}, #{@volume}, #{@pages}."
|
525
|
+
end
|
526
|
+
|
527
|
+
# Returns reference formatted in the
|
528
|
+
# CELL[http://www.cell.com] Press style.
|
529
|
+
#
|
530
|
+
# # ref is a Bio::Reference object
|
531
|
+
# puts ref.cell
|
532
|
+
#
|
533
|
+
# Hoge, J.P. and Fuga, F.B. (2001). Title of the study. Theor. J. Hoge 12, 123-145.
|
534
|
+
# ---
|
535
|
+
# *Returns*:: String
|
536
|
+
def cell
|
537
|
+
authors = authors_join(' and ')
|
538
|
+
"#{authors} (#{@year}). #{@title} #{@journal} #{@volume}, #{pages}."
|
539
|
+
end
|
540
|
+
|
541
|
+
# Returns reference formatted in the
|
542
|
+
# TRENDS[http://www.trends.com] style.
|
543
|
+
#
|
544
|
+
# # ref is a Bio::Reference object
|
545
|
+
# puts ref.trends
|
546
|
+
#
|
547
|
+
# Hoge, J.P. and Fuga, F.B. (2001) Title of the study. Theor. J. Hoge 12, 123-145
|
548
|
+
# ---
|
549
|
+
# *Returns*:: String
|
550
|
+
def trends
|
551
|
+
if @authors.size > 2
|
552
|
+
authors = "#{@authors[0]} et al."
|
553
|
+
elsif @authors.size == 1
|
554
|
+
authors = "#{@authors[0]}"
|
555
|
+
else
|
556
|
+
authors = authors_join(' and ')
|
557
|
+
end
|
558
|
+
"#{authors} (#{@year}) #{@title} #{@journal} #{@volume}, #{@pages}"
|
559
|
+
end
|
560
|
+
|
561
|
+
# Returns a valid URL for pubmed records
|
562
|
+
#
|
563
|
+
# *Returns*:: String
|
564
|
+
def pubmed_url
|
565
|
+
unless @pubmed.to_s.empty?
|
566
|
+
cgi = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
|
567
|
+
opts = "cmd=Retrieve&db=PubMed&dopt=Citation&list_uids"
|
568
|
+
return "#{cgi}?#{opts}=#{@pubmed}"
|
569
|
+
end
|
570
|
+
''
|
571
|
+
end
|
572
|
+
|
573
|
+
private
|
574
|
+
|
575
|
+
def strip_dots(data)
|
576
|
+
data.tr(',.', '') if data
|
577
|
+
end
|
578
|
+
|
579
|
+
def authors_join(amp, sep = ', ')
|
580
|
+
authors = @authors.clone
|
581
|
+
if authors.length > 1
|
582
|
+
last = authors.pop
|
583
|
+
authors = authors.join(sep) + "#{amp}" + last
|
584
|
+
elsif authors.length == 1
|
585
|
+
authors = authors.pop
|
586
|
+
else
|
587
|
+
authors = ""
|
588
|
+
end
|
589
|
+
end
|
590
|
+
|
591
|
+
def rev_name(name)
|
592
|
+
if name =~ /,/
|
593
|
+
name, initial = name.split(/,\s+/)
|
594
|
+
name = "#{initial} #{name}"
|
595
|
+
end
|
596
|
+
return name
|
597
|
+
end
|
598
|
+
|
599
|
+
end
|
600
|
+
|
601
|
+
end
|
602
|
+
|