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 +1,67 @@
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#
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# = bio/appl/paml/codeml/rates.rb - Codeml rates report file parser
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#
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# Copyright:: Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
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#
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# License:: The Ruby License
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#
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# == Description
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#
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# This file contains a class that implement a simple interface to Codeml rates estimation file
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#
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# == References
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#
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# * http://abacus.gene.ucl.ac.uk/software/paml.html
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#
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require 'delegate'
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require 'bio/appl/paml/codeml'
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module Bio::PAML
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class Codeml
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# == Description
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#
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# A simple class for parsing the codeml rates file.
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#
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# WARNING: The order of the parsed data should be correct, however will
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# not necessarily correspond to the position in the alignment. For instance
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# codeml ignores columns that contains gaps, and therefore there will not
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# be any estimated rate data.
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#
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# == Usage
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#
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# site_rates = Bio::PAML::Codeml::Rates.new(File.open(@tmp_dir + "/rates").read)
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# site_rate.first[:freq] # => Number of times that column appears
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# site_rate.[5][:rate] # => Estimated rate of evolution
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# site_rate.last[:data] # => The content of the column, as a string
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#
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# # This class delegates to an array, so will respond to all array methods
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# site_rates.max {|x,y| x[:rate] <=> y[:rate] } # => Fastest evolving column
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# site_rates.detect {|x| x[:freq] > 1 } # => Columns appearing more than once
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class Rates < DelegateClass(Array)
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def initialize(rates)
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super(parse_rates(rates))
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end
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private
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def parse_rates(text)
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re = /\s+(\d+)\s+(\d+)\s+([A-Z\*]+)\s+(\d+\.\d+)\s+(\d)/
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array = Array.new
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text.each_line do |line|
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if re =~ line
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match = Regexp.last_match
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array[match[1].to_i] = {
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:freq => match[2].to_i,
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:data => match[3],
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:rate => match[4].to_f }
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end
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end
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array.compact
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end
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end
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end
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end
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#
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# = bio/appl/paml/codeml/report.rb - Codeml report parser
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#
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# Copyright:: Copyright (C) 2008 Michael D. Barton <mail@michaelbarton.me.uk>
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#
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# License:: The Ruby License
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#
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# == Description
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#
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# This file contains a class that implement a simple interface to Codeml output file
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#
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# == References
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#
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# * http://abacus.gene.ucl.ac.uk/software/paml.html
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#
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require 'bio/appl/paml/codeml'
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module Bio::PAML
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class Codeml
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# == Description
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#
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# A simple class for parsing codeml output.
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#
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# WARNING: This data is parsed using a regex from the output file, and
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# so will take the first result found. If using multiple tree's, your
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# milage may vary. See the source for the regular expressions.
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#
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# require 'bio'
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#
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# report = Bio::PAML::Codeml::Report.new(File.open(codeml_output_file).read)
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# report.gene_rate # => Rate of gene evolution as defined be alpha
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# report.tree_lengh # => Estimated phylogetic tree length
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class Report < Bio::PAML::Common::Report
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attr_reader :tree_log_likelihood, :tree_length, :alpha, :tree
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def initialize(codeml_report)
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@tree_log_likelihood = pull_tree_log_likelihood(codeml_report)
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@tree_length = pull_tree_length(codeml_report)
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@alpha = pull_alpha(codeml_report)
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@tree = pull_tree(codeml_report)
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end
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private
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def pull_tree_log_likelihood(text)
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text[/lnL\(.+\):\s+(-?\d+(\.\d+)?)/,1].to_f
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end
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def pull_tree_length(text)
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text[/tree length\s+=\s+ (-?\d+(\.\d+)?)/,1].to_f
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end
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def pull_alpha(text)
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text[/alpha .+ =\s+(-?\d+(\.\d+)?)/,1].to_f
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end
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def pull_tree(text)
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text[/([^\n]+)\n\nDetailed/m,1]
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end
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end # End Report
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end # End Codeml
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end # End Bio::PAML
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#
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# = bio/appl/paml/common.rb - Basic wrapper class common to PAML programs
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#
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# Copyright:: Copyright (C) 2008
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# Michael D. Barton <mail@michaelbarton.me.uk>,
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# Naohisa Goto <ng@bioruby.org>
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#
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# License:: The Ruby License
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#
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# == Description
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#
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# This file contains Bio::PAML::Common, a basic wrapper class for
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# running PAML programs.
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#
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# == References
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#
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# * http://abacus.gene.ucl.ac.uk/software/paml.html
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#
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require 'tempfile'
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require 'bio/command'
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require 'bio/alignment'
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module Bio
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module PAML
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autoload :Codeml, 'bio/appl/paml/codeml'
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autoload :Baseml, 'bio/appl/paml/baseml'
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autoload :Yn00, 'bio/appl/paml/yn00'
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#--
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# The autoload of Common::Report, Codeml::Report, Codeml::Rates,
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# Baseml::Report, Yn00::Report are described inside the classes.
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#++
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# == Description
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#
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# Bio::PAML::Common is a basic wrapper class for PAML programs.
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# The class provides methods for generating the necessary configuration
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# file, and running a program.
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#
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class Common
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autoload :Report, 'bio/appl/paml/common_report'
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# Default parameters. Should be redefined in subclass.
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DEFAULT_PARAMETERS = {}
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# Default program. Should be redifined in subclass.
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DEFAULT_PROGRAM = nil
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# Parameters described in the control file. (Hash)
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# Each key of the hash must be a Symbol object, and each value
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# must be a String object or nil.
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attr_accessor :parameters
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# Preferred order of parameters.
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DEFAULT_PARAMETERS_ORDER = %w( seqfile outfile treefile
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noisy verbose runmode seqtype CodonFreq ndata clock
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aaDist aaRatefile model NSsites icode Mgene
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fix_kappa kappa fix_omega omega fix_alpha alpha Malpha ncatG
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fix_rho rho nparK nhomo getSE RateAncestor
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Small_Diff cleandata fix_blength method ).collect { |x| x.to_sym }
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|
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# Creates a wrapper instance, which will run using the specified
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# binary location or the command in the PATH.
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# If program is specified as nil, DEFAULT_PROGRAM is used.
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# Default parameters are automatically loaded and merged with
|
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# the specified parameters.
|
69
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# ---
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# *Arguments*:
|
71
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# * (optional) _program_: path to the program, or command name (String)
|
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# * (optional) _params_: parameters (Hash)
|
73
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def initialize(program = nil, params = {})
|
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@program = program || self.class::DEFAULT_PROGRAM
|
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set_default_parameters
|
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self.parameters.update(params)
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end
|
78
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|
79
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# Runs the program on the parameters in the passed control file.
|
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# No parameters checks are performed.
|
81
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# All internal parameters are ignored and are kept untouched.
|
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# The output and report attributes are cleared in this method.
|
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#
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84
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# Warning about PAML's behavior:
|
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# PAML writes supplemental output files in the current directory
|
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# with fixed file names which can not be changed with parameters
|
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# or command-line options, for example, rates, rst, and rub.
|
88
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+
# This behavior may ovarwrite existing files, especially
|
89
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+
# previous supplemental results.
|
90
|
+
#
|
91
|
+
# ---
|
92
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+
# *Arguments*:
|
93
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+
# * (optional) _control_file_: file name of control file (String)
|
94
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+
# *Returns*:: messages printed to the standard output (String)
|
95
|
+
def run(control_file)
|
96
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+
exec_local([ control_file ])
|
97
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+
end
|
98
|
+
|
99
|
+
|
100
|
+
# Runs the program on the internal parameters with the specified
|
101
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+
# sequence alignment and tree.
|
102
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+
#
|
103
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# Note that parameters[:seqfile] and parameters[:outfile]
|
104
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# are always modified, and parameters[:treefile] is modified
|
105
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# when tree is specified.
|
106
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+
#
|
107
|
+
# To prevent overwrite of existing files by PAML, this method
|
108
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# automatically creates a temporary directory and the program
|
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# is run inside the directory. After the end of the program,
|
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# the temporary directory is automatically removed.
|
111
|
+
#
|
112
|
+
# ---
|
113
|
+
# *Arguments*:
|
114
|
+
# * (required) _alignment_: Bio::Alignment object or similar object
|
115
|
+
# * (optional) _tree_: Bio::Tree object
|
116
|
+
# *Returns*:: Report object
|
117
|
+
def query(alignment, tree = nil)
|
118
|
+
astr = alignment.output(:phylipnon)
|
119
|
+
if tree then
|
120
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+
tstr = [ sprintf("%3d %2d\n", tree.leaves.size, 1), "\n",
|
121
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+
tree.output(:newick,
|
122
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+
{ :indent => false,
|
123
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+
:bootstrap_style => :disabled,
|
124
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+
:branch_length_style => :disabled })
|
125
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+
].join('')
|
126
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+
else
|
127
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tstr = nil
|
128
|
+
end
|
129
|
+
str = _query_by_string(astr, tstr)
|
130
|
+
@report = self.class::Report.new(str)
|
131
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+
@report
|
132
|
+
end
|
133
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+
|
134
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+
# Runs the program on the internal parameters with the specified
|
135
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+
# sequence alignment data string and tree data string.
|
136
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+
#
|
137
|
+
# Note that parameters[:outfile] is always modified, and
|
138
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+
# parameters[:seqfile] and parameters[:treefile] are modified when
|
139
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+
# alignment and tree are specified respectively.
|
140
|
+
#
|
141
|
+
# It raises RuntimeError if seqfile is not specified in the argument
|
142
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+
# or in the parameter.
|
143
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+
#
|
144
|
+
# For other information, see the document of query method.
|
145
|
+
#
|
146
|
+
# ---
|
147
|
+
# *Arguments*:
|
148
|
+
# * (optional) _alignment_: String
|
149
|
+
# * (optional) _tree_: String or nil
|
150
|
+
# *Returns*:: contents of output file (String)
|
151
|
+
def query_by_string(alignment = nil, tree = nil)
|
152
|
+
_query_by_string(alignment, tree)
|
153
|
+
end
|
154
|
+
|
155
|
+
# (private) implementation of query_by_string().
|
156
|
+
def _query_by_string(alignment = nil, tree = nil)
|
157
|
+
@parameters ||= {}
|
158
|
+
Bio::Command.mktmpdir('paml') do |path|
|
159
|
+
#$stderr.puts path.inspect
|
160
|
+
filenames = []
|
161
|
+
begin
|
162
|
+
# preparing outfile
|
163
|
+
outfile = Tempfile.new('out', path)
|
164
|
+
outfile.close(false)
|
165
|
+
outfn = File.basename(outfile.path)
|
166
|
+
self.parameters[:outfile] = outfn
|
167
|
+
filenames.push outfn
|
168
|
+
# preparing seqfile
|
169
|
+
if alignment then
|
170
|
+
seqfile = Tempfile.new('seq', path)
|
171
|
+
seqfile.print alignment
|
172
|
+
seqfile.close(false)
|
173
|
+
seqfn = File.basename(seqfile.path)
|
174
|
+
self.parameters[:seqfile] = seqfn
|
175
|
+
filenames.push seqfn
|
176
|
+
end
|
177
|
+
# preparing treefile
|
178
|
+
if tree then
|
179
|
+
treefile = Tempfile.new('tree', path)
|
180
|
+
treefile.print tree
|
181
|
+
treefile.close(false)
|
182
|
+
treefn = File.basename(treefile.path)
|
183
|
+
self.parameters[:treefile] = treefn
|
184
|
+
filenames.push treefn
|
185
|
+
end
|
186
|
+
# preparing control file
|
187
|
+
ctlfile = Tempfile.new('control', path)
|
188
|
+
ctlfile.print self.dump_parameters
|
189
|
+
ctlfile.close(false)
|
190
|
+
ctlfn = File.basename(ctlfile.path)
|
191
|
+
filenames.push ctlfn
|
192
|
+
# check parameters
|
193
|
+
if errors = check_parameters then
|
194
|
+
msg = errors.collect { |e| "error in parameter #{e[0]}: #{e[1]}" }
|
195
|
+
raise RuntimeError, msg.join("; ")
|
196
|
+
end
|
197
|
+
# exec command
|
198
|
+
stdout = exec_local([ ctlfn ], { :chdir => path })
|
199
|
+
# get main output
|
200
|
+
outfile.open
|
201
|
+
@output = outfile.read
|
202
|
+
# get supplemental result files
|
203
|
+
@supplemental_outputs = {}
|
204
|
+
(Dir.entries(path) - filenames).each do |name|
|
205
|
+
next unless /\A\w/ =~ name
|
206
|
+
fn = File.join(path, name)
|
207
|
+
if File.file?(fn) then
|
208
|
+
@supplemental_outputs[name] = File.read(fn)
|
209
|
+
end
|
210
|
+
end
|
211
|
+
ensure
|
212
|
+
outfile.close(true) if outfile
|
213
|
+
seqfile.close(true) if seqfile
|
214
|
+
treefile.close(true) if treefile
|
215
|
+
ctlfile.close(true) if ctlfile
|
216
|
+
end
|
217
|
+
end
|
218
|
+
@output
|
219
|
+
end
|
220
|
+
private :_query_by_string
|
221
|
+
|
222
|
+
# the last result of the program (String)
|
223
|
+
attr_reader :output
|
224
|
+
|
225
|
+
# Report object created from the last result
|
226
|
+
attr_reader :report
|
227
|
+
|
228
|
+
# the last exit status of the program
|
229
|
+
attr_reader :exit_status
|
230
|
+
|
231
|
+
# the last output to the stdout (String)
|
232
|
+
attr_reader :data_stdout
|
233
|
+
|
234
|
+
# the last executed command (Array of String)
|
235
|
+
attr_reader :command
|
236
|
+
|
237
|
+
# contents of supplemental output files (Hash).
|
238
|
+
# Each key is a file name and value is content of the file.
|
239
|
+
attr_reader :supplemental_outputs
|
240
|
+
|
241
|
+
# Loads parameters from the specified string.
|
242
|
+
# Note that all previous parameters are erased.
|
243
|
+
# Returns the parameters as a hash.
|
244
|
+
# ---
|
245
|
+
# *Arguments*:
|
246
|
+
# * (required) _str_: contents of a PAML control file (String)
|
247
|
+
# *Returns*:: parameters (Hash)
|
248
|
+
def load_parameters(str)
|
249
|
+
hash = {}
|
250
|
+
str.each_line do |line|
|
251
|
+
param, value = parse_parameter(line)
|
252
|
+
hash[param] = value if param
|
253
|
+
end
|
254
|
+
self.parameters = hash
|
255
|
+
end
|
256
|
+
|
257
|
+
# Loads system-wide default parameters.
|
258
|
+
# Note that all previous parameters are erased.
|
259
|
+
# Returns the parameters as a hash.
|
260
|
+
# ---
|
261
|
+
# *Returns*:: parameters (Hash)
|
262
|
+
def set_default_parameters
|
263
|
+
self.parameters = self.class::DEFAULT_PARAMETERS.merge(Hash.new)
|
264
|
+
end
|
265
|
+
|
266
|
+
# Shows parameters (content of control file) as a string.
|
267
|
+
# The string can be used for control file.
|
268
|
+
# ---
|
269
|
+
# *Returns*:: string representation of the parameters (String)
|
270
|
+
def dump_parameters
|
271
|
+
keyorder = DEFAULT_PARAMETERS_ORDER
|
272
|
+
keys = parameters.keys
|
273
|
+
str = ''
|
274
|
+
keys.sort do |x, y|
|
275
|
+
(keyorder.index(x) || (keyorder.size + keys.index(x))) <=>
|
276
|
+
(keyorder.index(y) || (keyorder.size + keys.index(y)))
|
277
|
+
end.each do |key|
|
278
|
+
value = parameters[key]
|
279
|
+
# Note: spaces are required in both side of the "=".
|
280
|
+
str.concat "#{key.to_s} = #{value.to_s}\n" if value
|
281
|
+
end
|
282
|
+
str
|
283
|
+
end
|
284
|
+
|
285
|
+
private
|
286
|
+
|
287
|
+
# (private) clear attributes except program and parameters
|
288
|
+
def reset
|
289
|
+
@command = nil
|
290
|
+
@output = nil
|
291
|
+
@report = nil
|
292
|
+
@exit_status = nil
|
293
|
+
@data_stdout = nil
|
294
|
+
@supplemental_outputs = nil
|
295
|
+
end
|
296
|
+
|
297
|
+
# (private) parses a parameter in a line
|
298
|
+
# ---
|
299
|
+
# *Arguments*:
|
300
|
+
# * (required) _line_: single line string (String)
|
301
|
+
# *Returns*:: parameter name (Symbol or nil), value (String or nil)
|
302
|
+
def parse_parameter(line)
|
303
|
+
# remove comment
|
304
|
+
line = line.sub(/\*.*/, '')
|
305
|
+
# Note: spaces are required in both side of the "=".
|
306
|
+
param, value = line.strip.split(/\s+=\s+/, 2)
|
307
|
+
if !param or param.empty? then
|
308
|
+
param = nil
|
309
|
+
else
|
310
|
+
param = param.to_sym
|
311
|
+
end
|
312
|
+
return param, value
|
313
|
+
end
|
314
|
+
|
315
|
+
# (private) Runs the program on the parameters in the passed control file.
|
316
|
+
# No parameter check are executed.
|
317
|
+
# ---
|
318
|
+
# *Arguments*:
|
319
|
+
# * (optional) _control_file_: file name of control file (String)
|
320
|
+
# *Returns*:: messages printed to the standard output (String)
|
321
|
+
def exec_local(arguments, options = {})
|
322
|
+
reset
|
323
|
+
cmd = [ @program, *arguments ]
|
324
|
+
@command = cmd
|
325
|
+
stdout = Bio::Command.query_command(cmd, nil, options)
|
326
|
+
@exit_status = $?
|
327
|
+
@data_stdout = stdout
|
328
|
+
stdout
|
329
|
+
end
|
330
|
+
|
331
|
+
# (private) Checks parameters.
|
332
|
+
# Returns nil if no errors found. Otherwise, returns an Array
|
333
|
+
# containing [ parameter, message ] pairs.
|
334
|
+
# ---
|
335
|
+
# *Arguments*:
|
336
|
+
# *Returns*:: nil or Array
|
337
|
+
def check_parameters
|
338
|
+
errors = []
|
339
|
+
param = self.parameters
|
340
|
+
if !param[:seqfile] or param[:seqfile].empty? then
|
341
|
+
errors.push([ :seqfile, 'seqfile not specified' ])
|
342
|
+
end
|
343
|
+
errors.empty? ? nil : errors
|
344
|
+
end
|
345
|
+
|
346
|
+
end #class Common
|
347
|
+
end #module PAML
|
348
|
+
end #module Bio
|