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
@@ -0,0 +1,123 @@
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#
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# = bio/sequence/compat.rb - methods for backward compatibility
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#
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# Copyright:: Copyright (C) 2006
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# Toshiaki Katayama <k@bioruby.org>,
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# Ryan Raaum <ryan@raaum.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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module Bio
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class Sequence
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autoload :Common, 'bio/sequence/common'
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autoload :NA, 'bio/sequence/na'
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autoload :AA, 'bio/sequence/aa'
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# Return sequence as
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# String[http://corelib.rubyonrails.org/classes/String.html].
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# The original sequence is unchanged.
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#
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# seq = Bio::Sequence.new('atgc')
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# puts s.to_s #=> 'atgc'
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# puts s.to_s.class #=> String
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# puts s #=> 'atgc'
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# puts s.class #=> Bio::Sequence
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# ---
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# *Returns*:: String object
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def to_s
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String.new(self.seq)
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end
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alias to_str to_s
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module Common
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# *DEPRECIATED* Do not use! Use Bio::Sequence#output instead.
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#
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# Output the FASTA format string of the sequence. The 1st argument is
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# used as the comment string. If the 2nd option is given, the output
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# sequence will be folded.
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# ---
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# *Arguments*:
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# * (optional) _header_: String object
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# * (optional) _width_: Fixnum object (default nil)
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# *Returns*:: String
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def to_fasta(header = '', width = nil)
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warn "Bio::Sequence#to_fasta is obsolete. Use Bio::Sequence#output(:fasta) instead" if $DEBUG
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">#{header}\n" +
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if width
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self.to_s.gsub(Regexp.new(".{1,#{width}}"), "\\0\n")
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else
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self.to_s + "\n"
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end
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end
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end # Common
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class NA
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# Generate a new random sequence with the given frequency of bases.
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# The sequence length is determined by their cumulative sum.
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# (See also Bio::Sequence::Common#randomize which creates a new
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# randomized sequence object using the base composition of an existing
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# sequence instance).
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#
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# counts = {'a'=>1,'c'=>2,'g'=>3,'t'=>4}
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# puts Bio::Sequence::NA.randomize(counts) #=> "ggcttgttac" (for example)
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#
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# You may also feed the output of randomize into a block
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#
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# actual_counts = {'a'=>0, 'c'=>0, 'g'=>0, 't'=>0}
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# Bio::Sequence::NA.randomize(counts) {|x| actual_counts[x] += 1}
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# actual_counts #=> {"a"=>1, "c"=>2, "g"=>3, "t"=>4}
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# ---
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# *Arguments*:
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# * (optional) _hash_: Hash object
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# *Returns*:: Bio::Sequence::NA object
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def self.randomize(*arg, &block)
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self.new('').randomize(*arg, &block)
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end
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def pikachu #:nodoc:
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self.dna.tr("atgc", "pika") # joke, of course :-)
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end
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end # NA
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class AA
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# Generate a new random sequence with the given frequency of bases.
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# The sequence length is determined by their cumulative sum.
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# (See also Bio::Sequence::Common#randomize which creates a new
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# randomized sequence object using the base composition of an existing
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# sequence instance).
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#
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# counts = {'R'=>1,'L'=>2,'E'=>3,'A'=>4}
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# puts Bio::Sequence::AA.randomize(counts) #=> "AAEAELALRE" (for example)
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#
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# You may also feed the output of randomize into a block
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#
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# actual_counts = {'R'=>0,'L'=>0,'E'=>0,'A'=>0}
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# Bio::Sequence::AA.randomize(counts) {|x| actual_counts[x] += 1}
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# actual_counts #=> {"A"=>4, "L"=>2, "E"=>3, "R"=>1}
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# ---
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# *Arguments*:
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# * (optional) _hash_: Hash object
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# *Returns*:: Bio::Sequence::AA object
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def self.randomize(*arg, &block)
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self.new('').randomize(*arg, &block)
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end
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end # AA
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end # Sequence
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end # Bio
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#
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# = bio/sequence/dblink.rb - sequence ID with database name
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#
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# Copyright:: Copyright (C) 2008
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# Naohisa Goto <ng@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: dblink.rb,v 1.1.2.1 2008/06/17 15:44:22 ngoto Exp $
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#
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require 'bio/sequence'
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# Bio::Sequence::DBLink stores IDs with the database name.
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# Its main purpose is to store database cross-reference information
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# for a sequence entry.
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class Bio::Sequence::DBLink
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# creates a new DBLink object
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def initialize(database, primary_id, *secondary_ids)
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@database = database
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@id = primary_id
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@secondary_ids = secondary_ids
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end
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# Database name, or namespace identifier (String).
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attr_reader :database
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# Primary identifier (String)
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attr_reader :id
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# Secondary identifiers (Array of String)
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attr_reader :secondary_ids
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#--
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# class methods
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#++
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# Parses DR line in EMBL entry, and returns a DBLink object.
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def self.parse_embl_DR_line(str)
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str = str.sub(/\.\s*\z/, '')
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str.sub!(/\ADR /, '')
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self.new(*(str.split(/\s*\;\s*/, 3)))
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end
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# Parses DR line in UniProt entry, and returns a DBLink object.
|
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def self.parse_uniprot_DR_line(str)
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str = str.sub(/\.\s*\z/, '')
|
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str.sub!(/\ADR /, '')
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self.new(*(str.split(/\s*\;\s*/)))
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end
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end #class Bio::Sequence::DBLink
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#
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# = bio/sequence/format.rb - various output format of the biological sequence
|
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#
|
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# Copyright:: Copyright (C) 2006-2008
|
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# Toshiaki Katayama <k@bioruby.org>,
|
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# Naohisa Goto <ng@bioruby.org>,
|
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# Ryan Raaum <ryan@raaum.org>,
|
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# Jan Aerts <jan.aerts@bbsrc.ac.uk>
|
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# License:: The Ruby License
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#
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# = TODO
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#
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# porting from N. Goto's feature-output.rb on BioRuby list.
|
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#
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# $Id: format.rb,v 1.4.2.8 2008/06/17 15:50:05 ngoto Exp $
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#
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require 'erb'
|
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module Bio
|
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|
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class Sequence
|
23
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|
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# = DESCRIPTION
|
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# A Mixin[http://www.rubycentral.com/book/tut_modules.html]
|
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# of methods used by Bio::Sequence#output to output sequences in
|
27
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# common bioinformatic formats. These are not called in isolation.
|
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#
|
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# = USAGE
|
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# # Given a Bio::Sequence object,
|
31
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# puts s.output(:fasta)
|
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# puts s.output(:genbank)
|
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# puts s.output(:embl)
|
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module Format
|
35
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+
|
36
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# Repository of generic (or both nucleotide and protein) sequence
|
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# formatter classes
|
38
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module Formatter
|
39
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+
|
40
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# Raw format generatar
|
41
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autoload :Raw, 'bio/sequence/format_raw'
|
42
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+
|
43
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# Fasta format generater
|
44
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autoload :Fasta, 'bio/db/fasta/format_fasta'
|
45
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+
|
46
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# NCBI-style Fasta format generatar
|
47
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+
# (resemble to EMBOSS "ncbi" format)
|
48
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+
autoload :Fasta_ncbi, 'bio/db/fasta/format_fasta'
|
49
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+
|
50
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end #module Formatter
|
51
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+
|
52
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# Repository of nucleotide sequence formatter classes
|
53
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module NucFormatter
|
54
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+
|
55
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# GenBank format generater
|
56
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# Note that the name is 'Genbank' and NOT 'GenBank'
|
57
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autoload :Genbank, 'bio/db/genbank/format_genbank'
|
58
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+
|
59
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# EMBL format generater
|
60
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# Note that the name is 'Embl' and NOT 'EMBL'
|
61
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+
autoload :Embl, 'bio/db/embl/format_embl'
|
62
|
+
|
63
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+
end #module NucFormatter
|
64
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+
|
65
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+
# Repository of protein sequence formatter classes
|
66
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module AminoFormatter
|
67
|
+
# currently no formats available
|
68
|
+
end #module AminoFormatter
|
69
|
+
|
70
|
+
# Formatter base class.
|
71
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+
# Any formatter class should inherit this class.
|
72
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class FormatterBase
|
73
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+
|
74
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# Returns a formatterd string of the given sequence
|
75
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+
# ---
|
76
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+
# *Arguments*:
|
77
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+
# * (required) _sequence_: Bio::Sequence object
|
78
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+
# * (optional) _options_: a Hash object
|
79
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# *Returns*:: String object
|
80
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def self.output(sequence, options = {})
|
81
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+
self.new(sequence, options).output
|
82
|
+
end
|
83
|
+
|
84
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+
# register new Erb template
|
85
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+
def self.erb_template(str)
|
86
|
+
erb = ERB.new(str)
|
87
|
+
erb.def_method(self, 'output')
|
88
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+
true
|
89
|
+
end
|
90
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+
private_class_method :erb_template
|
91
|
+
|
92
|
+
# generates output data
|
93
|
+
# ---
|
94
|
+
# *Returns*:: String object
|
95
|
+
def output
|
96
|
+
raise NotImplementedError, 'should be implemented in subclass'
|
97
|
+
end
|
98
|
+
|
99
|
+
# creates a new formatter object for output
|
100
|
+
def initialize(sequence, options = {})
|
101
|
+
@sequence = sequence
|
102
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+
@options = options
|
103
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+
end
|
104
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+
|
105
|
+
private
|
106
|
+
|
107
|
+
# any unknown methods are delegated to the sequence object
|
108
|
+
def method_missing(sym, *args, &block) #:nodoc:
|
109
|
+
begin
|
110
|
+
@sequence.__send__(sym, *args, &block)
|
111
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+
rescue NoMethodError => evar
|
112
|
+
lineno = __LINE__ - 2
|
113
|
+
file = __FILE__
|
114
|
+
bt_here = [ "#{file}:#{lineno}:in \`__send__\'",
|
115
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+
"#{file}:#{lineno}:in \`method_missing\'"
|
116
|
+
]
|
117
|
+
if bt_here == evar.backtrace[0, 2] then
|
118
|
+
bt = evar.backtrace[2..-1]
|
119
|
+
evar = evar.class.new("undefined method \`#{sym.to_s}\' for #{self.inspect}")
|
120
|
+
evar.set_backtrace(bt)
|
121
|
+
end
|
122
|
+
raise(evar)
|
123
|
+
end
|
124
|
+
end
|
125
|
+
end #class FormatterBase
|
126
|
+
|
127
|
+
# Using Bio::Sequence::Format, return a String with the Bio::Sequence
|
128
|
+
# object formatted in the given style.
|
129
|
+
#
|
130
|
+
# Formats currently implemented are: 'fasta', 'genbank', and 'embl'
|
131
|
+
#
|
132
|
+
# s = Bio::Sequence.new('atgc')
|
133
|
+
# puts s.output(:fasta) #=> "> \natgc\n"
|
134
|
+
#
|
135
|
+
# The style argument is given as a Ruby
|
136
|
+
# Symbol(http://www.ruby-doc.org/core/classes/Symbol.html)
|
137
|
+
# ---
|
138
|
+
# *Arguments*:
|
139
|
+
# * (required) _format_: :fasta, :genbank, *or* :embl
|
140
|
+
# *Returns*:: String object
|
141
|
+
def output(format = :fasta, options = {})
|
142
|
+
formatter_const = format.to_s.capitalize.intern
|
143
|
+
|
144
|
+
formatter_class = nil
|
145
|
+
get_formatter_repositories.each do |mod|
|
146
|
+
begin
|
147
|
+
formatter_class = mod.const_get(formatter_const)
|
148
|
+
rescue NameError
|
149
|
+
end
|
150
|
+
break if formatter_class
|
151
|
+
end
|
152
|
+
unless formatter_class then
|
153
|
+
raise "unknown format name #{format.inspect}"
|
154
|
+
end
|
155
|
+
|
156
|
+
formatter_class.output(self, options)
|
157
|
+
end
|
158
|
+
|
159
|
+
# Returns a list of available output formats for the sequence
|
160
|
+
# ---
|
161
|
+
# *Arguments*:
|
162
|
+
# *Returns*:: Array of Symbols
|
163
|
+
def list_output_formats
|
164
|
+
a = get_formatter_repositories.collect { |mod| mod.constants }
|
165
|
+
a.flatten!
|
166
|
+
a.collect! { |x| x.to_s.downcase.intern }
|
167
|
+
a
|
168
|
+
end
|
169
|
+
|
170
|
+
private
|
171
|
+
|
172
|
+
# returns formatter repository modules
|
173
|
+
def get_formatter_repositories
|
174
|
+
if self.moltype == Bio::Sequence::NA then
|
175
|
+
[ NucFormatter, Formatter ]
|
176
|
+
elsif self.moltype == Bio::Sequence::AA then
|
177
|
+
[ AminoFormatter, Formatter ]
|
178
|
+
else
|
179
|
+
[ NucFormatter, AminoFormatter, Formatter ]
|
180
|
+
end
|
181
|
+
end
|
182
|
+
|
183
|
+
#---
|
184
|
+
|
185
|
+
# Not yet implemented :)
|
186
|
+
# Remove the nodoc command after implementation!
|
187
|
+
# ---
|
188
|
+
# *Returns*:: String object
|
189
|
+
#def format_gff #:nodoc:
|
190
|
+
# raise NotImplementedError
|
191
|
+
#end
|
192
|
+
|
193
|
+
#+++
|
194
|
+
|
195
|
+
# Formatting helper methods for INSD (NCBI, EMBL, DDBJ) feature table
|
196
|
+
module INSDFeatureHelper
|
197
|
+
private
|
198
|
+
|
199
|
+
# INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
|
200
|
+
# case, it would be difficult to successfully call this method outside
|
201
|
+
# its expected context).
|
202
|
+
#
|
203
|
+
# Output the Genbank feature format string of the sequence.
|
204
|
+
# Used in Bio::Sequence#output.
|
205
|
+
# ---
|
206
|
+
# *Returns*:: String object
|
207
|
+
def format_features_genbank(features)
|
208
|
+
prefix = ' ' * 5
|
209
|
+
indent = prefix + ' ' * 16
|
210
|
+
fwidth = 79 - indent.length
|
211
|
+
|
212
|
+
format_features(features, prefix, indent, fwidth)
|
213
|
+
end
|
214
|
+
|
215
|
+
# INTERNAL USE ONLY, YOU SHOULD NOT CALL THIS METHOD. (And in any
|
216
|
+
# case, it would be difficult to successfully call this method outside
|
217
|
+
# its expected context).
|
218
|
+
#
|
219
|
+
# Output the EMBL feature format string of the sequence.
|
220
|
+
# Used in Bio::Sequence#output.
|
221
|
+
# ---
|
222
|
+
# *Returns*:: String object
|
223
|
+
def format_features_embl(features)
|
224
|
+
prefix = 'FT '
|
225
|
+
indent = prefix + ' ' * 16
|
226
|
+
fwidth = 80 - indent.length
|
227
|
+
|
228
|
+
format_features(features, prefix, indent, fwidth)
|
229
|
+
end
|
230
|
+
|
231
|
+
# format INSD featurs
|
232
|
+
def format_features(features, prefix, indent, width)
|
233
|
+
result = []
|
234
|
+
features.each do |feature|
|
235
|
+
result.push format_feature(feature, prefix, indent, width)
|
236
|
+
end
|
237
|
+
return result.join('')
|
238
|
+
end
|
239
|
+
|
240
|
+
# format an INSD feature
|
241
|
+
def format_feature(feature, prefix, indent, width)
|
242
|
+
result = prefix + sprintf("%-16s", feature.feature)
|
243
|
+
|
244
|
+
position = feature.position
|
245
|
+
#position = feature.locations.to_s
|
246
|
+
|
247
|
+
result << wrap_and_split_lines(position, width).join("\n" + indent)
|
248
|
+
result << "\n"
|
249
|
+
result << format_qualifiers(feature.qualifiers, indent, width)
|
250
|
+
return result
|
251
|
+
end
|
252
|
+
|
253
|
+
# format qualifiers
|
254
|
+
def format_qualifiers(qualifiers, indent, width)
|
255
|
+
qualifiers.collect do |qualifier|
|
256
|
+
q = qualifier.qualifier
|
257
|
+
v = qualifier.value.to_s
|
258
|
+
|
259
|
+
if v == true
|
260
|
+
lines = wrap_with_newline('/' + q, width)
|
261
|
+
elsif q == 'translation'
|
262
|
+
lines = fold("/#{q}=\"#{v}\"", width)
|
263
|
+
else
|
264
|
+
if v[/\D/] or q == 'chromosome'
|
265
|
+
#v.delete!("\x00-\x1f\x7f-\xff")
|
266
|
+
v.gsub!(/"/, '""')
|
267
|
+
v = '"' + v + '"'
|
268
|
+
end
|
269
|
+
lines = wrap_with_newline('/' + q + '=' + v, width)
|
270
|
+
end
|
271
|
+
|
272
|
+
lines.gsub!(/^/, indent)
|
273
|
+
lines
|
274
|
+
end.join
|
275
|
+
end
|
276
|
+
|
277
|
+
def fold(str, width)
|
278
|
+
str.gsub(Regexp.new("(.{1,#{width}})"), "\\1\n")
|
279
|
+
end
|
280
|
+
|
281
|
+
def fold_and_split_lines(str, width)
|
282
|
+
str.scan(Regexp.new(".{1,#{width}}"))
|
283
|
+
end
|
284
|
+
|
285
|
+
def wrap_and_split_lines(str, width)
|
286
|
+
result = []
|
287
|
+
lefts = str.chomp.split(/(?:\r\n|\r|\n)/)
|
288
|
+
lefts.each do |left|
|
289
|
+
left.rstrip!
|
290
|
+
while left and left.length > width
|
291
|
+
line = nil
|
292
|
+
width.downto(1) do |i|
|
293
|
+
if left[i..i] == ' ' or /[\,\;]/ =~ left[(i-1)..(i-1)] then
|
294
|
+
line = left[0..(i-1)].sub(/ +\z/, '')
|
295
|
+
left = left[i..-1].sub(/\A +/, '')
|
296
|
+
break
|
297
|
+
end
|
298
|
+
end
|
299
|
+
if line.nil? then
|
300
|
+
line = left[0..(width-1)]
|
301
|
+
left = left[width..-1]
|
302
|
+
end
|
303
|
+
result << line
|
304
|
+
left = nil if left.to_s.empty?
|
305
|
+
end
|
306
|
+
result << left if left
|
307
|
+
end
|
308
|
+
return result
|
309
|
+
end
|
310
|
+
|
311
|
+
def wrap_with_newline(str, width)
|
312
|
+
result = wrap_and_split_lines(str, width)
|
313
|
+
result_string = result.join("\n")
|
314
|
+
result_string << "\n" unless result_string.empty?
|
315
|
+
return result_string
|
316
|
+
end
|
317
|
+
|
318
|
+
def wrap(str, width = 80, prefix = '')
|
319
|
+
actual_width = width - prefix.length
|
320
|
+
result = wrap_and_split_lines(str, actual_width)
|
321
|
+
result_string = result.join("\n#{prefix}")
|
322
|
+
result_string = prefix + result_string unless result_string.empty?
|
323
|
+
return result_string
|
324
|
+
end
|
325
|
+
|
326
|
+
#--
|
327
|
+
# internal use only
|
328
|
+
MonthStr = [ nil,
|
329
|
+
'JAN', 'FEB', 'MAR', 'APR', 'MAY', 'JUN',
|
330
|
+
'JUL', 'AUG', 'SEP', 'OCT', 'NOV', 'DEC'
|
331
|
+
].collect { |x| x.freeze }.freeze
|
332
|
+
#++
|
333
|
+
|
334
|
+
# formats a date from Date, DateTime, or Time object, or String.
|
335
|
+
def format_date(d)
|
336
|
+
begin
|
337
|
+
yy = d.year
|
338
|
+
mm = d.month
|
339
|
+
dd = d.day
|
340
|
+
rescue NoMethodError, NameError, ArgumentError, TypeError
|
341
|
+
return sprintf("%-11s", d)
|
342
|
+
end
|
343
|
+
sprintf("%02d-%-3s-%04d", dd, MonthStr[mm], yy)
|
344
|
+
end
|
345
|
+
|
346
|
+
# null date
|
347
|
+
def null_date
|
348
|
+
Date.new(0, 1, 1)
|
349
|
+
end
|
350
|
+
|
351
|
+
end #module INSDFeatureHelper
|
352
|
+
|
353
|
+
end #module Format
|
354
|
+
|
355
|
+
end #class Sequence
|
356
|
+
|
357
|
+
end #module Bio
|
358
|
+
|