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 +1,95 @@
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#
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# test/unit/bio/db/test_rebase.rb - Unit test for Bio::Lasergene
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#
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# Author:: Trevor Wennblom <mailto:trevor@corevx.com>
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# Copyright:: Copyright (c) 2007 Center for Biomedical Research Informatics, University of Minnesota (http://cbri.umn.edu)
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# License:: The Ruby License
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#
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# $Id: test_lasergene.rb,v 1.2 2007/04/05 23:35:43 trevor Exp $
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio'
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require 'bio/db/lasergene'
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module Bio #:nodoc:
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class TestLasergene < Test::Unit::TestCase #:nodoc:
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def setup
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file_format_1 = <<END
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"Contig 1" (1,934)
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Contig Length: 934 bases
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Average Length/Sequence: 467 bases
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Total Sequence Length: 1869 bases
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Top Strand: 2 sequences
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Bottom Strand: 2 sequences
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Total: 4 sequences
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^^
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ATGACGTATCCAAAGAGGCGTTACCGGAGAAGAAGACACCGCCCCCGCAGTCCTCTTGGCCAGATCCTCCGCCGCCGCCCCTGGCTCGTCCACCCCCGCCACAGTTACCGCTGGAGAAGGAAAAATGGCATCTTCAWCACCCGCCTATCCCGCAYCTTCGGAWRTACTATCAAGCGAACCACAGTCAGAACGCCCTCCTGGGCGGTGGACATGATGAGATTCAATATTAATGACTTTCTTCCCCCAGGAGGGGGCTCAAACCCCCGCTCTGTGCCCTTTGAATACTACAGAATAAGAAAGGTTAAGGTTGAATTCTGGCCCTGCTCCCCGATCACCCAGGGTGACAGGGGAATGGGCTCCAGTGCTGWTATTCTAGMTGATRRCTTKGTAACAAAGRCCACAGCCCTCACCTATGACCCCTATGTAAACTTCTCCTCCCGCCATACCATAACCCAGCCCTTCTCCTACCRCTCCCGYTACTTTACCCCCAAACCTGTCCTWGATKCCACTATKGATKACTKCCAACCAAACAACAAAAGAAACCAGCTGTGGSTGAGACTACAWACTGCTGGAAATGTAGACCWCGTAGGCCTSGGCACTGCGTKCGAAAACAGTATATACGACCAGGAATACAATATCCGTGTMACCATGTATGTACAATTCAGAGAATTTAATCTTAAAGACCCCCCRCTTMACCCKTAATGAATAATAAMAACCATTACGAAGTGATAAAAWAGWCTCAGTAATTTATTYCATATGGAAATTCWSGGCATGGGGGGGAAAGGGTGACGAACKKGCCCCCTTCCTCCSTSGMYTKTTCYGTAGCATTCYTCCAMAAYACCWAGGCAGYAMTCCTCCSATCAAGAGcYTSYACAGCTGGGACAGCAGTTGAGGAGGACCATTCAAAGGGGGTCGGATTGCTGGTAATCAGA
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END
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file_format_2 = <<END
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^^: 350,935
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Contig 1 (1,935)
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Contig Length: 935 bases
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Average Length/Sequence: 580 bases
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Total Sequence Length: 2323 bases
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Top Strand: 2 sequences
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Bottom Strand: 2 sequences
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Total: 4 sequences
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^^
|
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ATGTCGGGGAAATGCTTGACCGCGGGCTACTGCTCATCATTGCTTTCTTTGTGGTATATCGTGCCGTTCTGTTTTGCTGTGCTCGTCAACGCCAGCGGCGACAGCAGCTCTCATTTTCAGTCGATTTATAACTTGACGTTATGTGAGCTGAATGGCACGAACTGGCTGGCAGACAACTTTAACTGGGCTGTGGAGACTTTTGTCATCTTCCCCGTGTTGACTCACATTGTTTCCTATGGTGCACTCACTACCAGTCATTTTCTTGACACAGTTGGTCTAGTTACTGTGTCTACCGCCGGGTTTTATCACGGGCGGTACGTCTTGAGTAGCATCTACGCGGTCTGTGCTCTGGCTGCGTTGATTTGCTTCGCCATCAGGTTTGCGAAGAACTGCATGTCCTGGCGCTACTCTTGCACTAGATACACCAACTTCCTCCTGGACACCAAGGGCAGACTCTATCGTTGGCGGTCGCCTGTCATCATAGAGAAAGGGGGTAAGGTTGAGGTCGAAGGTCATCTGATCGATCTCAAAAGAGTTGTGCTTGATGGCTCTGTGGCGACACCTTTAACCAGAGTTTCAGCGGAACAATGGGGTCGTCCCTAGACGACTTTTGCCATGATAGTACAGCCCCACAGAAGGTGCTCTTGGCGTTTTCCATCACCTACACGCCAGTGATGATATATGCCCTAAAGGTAAGCCGCGGCCGACTTTTGGGGCTTCTGCACCTTTTGATTTTTTTGAACTGTGCCTTTACTTTCGGGTACATGACATTCGTGCACTTTCGGAGCACGAACAAGGTCGCGCTCACTATGGGAGCAGTAGTCGCACTCCTTTGGGGGGTGTACTCAGCCATAGAAACCTGGAAATTCATCACCTCCAGATGCCGTTGTGCTTGCTAGGCCGCAAGTACATTCTGGCCCCTGCCCACCACGTTG
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END
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file_format_3 = <<END
|
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LOCUS PRU87392 15411 bp RNA linear VRL 17-NOV-2000
|
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DEFINITION Porcine reproductive and respiratory syndrome virus strain VR-2332,
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complete genome.
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ACCESSION U87392 AF030244 U00153
|
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VERSION U87392.3 GI:11192298
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[...cut...]
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3'UTR 15261..15411
|
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polyA_site 15409
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ORIGIN
|
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^^
|
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atgacgtataggtgttggctctatgccttggcatttgtattgtcaggagctgtgaccattggcacagcccaaaacttgctgcacagaaacacccttctgtgatagcctccttcaggggagcttagggtttgtccctagcaccttgcttccggagttgcactgctttacggtctctccacccctttaaccatgtctgggatacttgatcggtgcacgtgtacccccaatgccagggtgtttatggcggagggccaagtctactgcacacgatgcctcagtgcacggtctctccttcccctgaacctccaagtttctgagctcggggtgctaggcctattctacaggcccgaagagccactccggtggacgttgccacgtgcattccccactgttgagtgctcccccgccggggcctgctggctttctgcaatctttccaatcgcacgaatgaccagtggaaacctgaacttccaacaaagaatggtacgggtcgcagctgagctttacagagccggccagctcacccctgcagtcttgaaggctctacaagtttatgaacggggttgccgctggtaccccattgttggacctgtccctggagtggccgttttcgccaattccctacatgtgagtgataaacctttcccgggagcaactcacgtgttgaccaacctgccgctcccgcagagacccaagcctgaagacttttgcccctttgagtgtgctatggctactgtctatgacattggtcatgacgccgtcatgtatgtggccgaaaggaaagtctcctgggcccctcgtggcggggatgaagtgaaatttgaagctgtccccggggagttgaagttgattgcgaaccggctccgcacctccttcccgccccaccacacagtggacatgtctaagttcgccttcacagcccctgggtgtggtgtttctatgcgggtcgaacgccaacacggctgccttcccgctgacactgtccctgaaggcaactgctggtggagcttgtttgacttgcttccactggaagttcagaacaaagaaattcgccatgctaaccaatttggctaccagaccaagcatggtgtctctggcaagtacctacagcggaggctgca
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END
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@lc = Bio::Lasergene
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@obj1 = @lc.new(file_format_1)
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@obj2 = @lc.new(file_format_2)
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@obj3 = @lc.new(file_format_3)
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end
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def test_methods
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a1 = @obj1
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a1_seq = 'atgacgtatccaaagaggcgttaccggagaagaagacaccgcccccgcagtcctcttggccagatcctccgccgccgcccctggctcgtccacccccgccacagttaccgctggagaaggaaaaatggcatcttcawcacccgcctatcccgcaycttcggawrtactatcaagcgaaccacagtcagaacgccctcctgggcggtggacatgatgagattcaatattaatgactttcttcccccaggagggggctcaaacccccgctctgtgccctttgaatactacagaataagaaaggttaaggttgaattctggccctgctccccgatcacccagggtgacaggggaatgggctccagtgctgwtattctagmtgatrrcttkgtaacaaagrccacagccctcacctatgacccctatgtaaacttctcctcccgccataccataacccagcccttctcctaccrctcccgytactttacccccaaacctgtcctwgatkccactatkgatkactkccaaccaaacaacaaaagaaaccagctgtggstgagactacawactgctggaaatgtagaccwcgtaggcctsggcactgcgtkcgaaaacagtatatacgaccaggaatacaatatccgtgtmaccatgtatgtacaattcagagaatttaatcttaaagaccccccrcttmacccktaatgaataataamaaccattacgaagtgataaaawagwctcagtaatttattycatatggaaattcwsggcatgggggggaaagggtgacgaackkgcccccttcctccstsgmytkttcygtagcattcytccamaayaccwaggcagyamtcctccsatcaagagcytsyacagctgggacagcagttgaggaggaccattcaaagggggtcggattgctggtaatcaga'
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a2 = @obj2
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a2_seq = 'atgtcggggaaatgcttgaccgcgggctactgctcatcattgctttctttgtggtatatcgtgccgttctgttttgctgtgctcgtcaacgccagcggcgacagcagctctcattttcagtcgatttataacttgacgttatgtgagctgaatggcacgaactggctggcagacaactttaactgggctgtggagacttttgtcatcttccccgtgttgactcacattgtttcctatggtgcactcactaccagtcattttcttgacacagttggtctagttactgtgtctaccgccgggttttatcacgggcggtacgtcttgagtagcatctacgcggtctgtgctctggctgcgttgatttgcttcgccatcaggtttgcgaagaactgcatgtcctggcgctactcttgcactagatacaccaacttcctcctggacaccaagggcagactctatcgttggcggtcgcctgtcatcatagagaaagggggtaaggttgaggtcgaaggtcatctgatcgatctcaaaagagttgtgcttgatggctctgtggcgacacctttaaccagagtttcagcggaacaatggggtcgtccctagacgacttttgccatgatagtacagccccacagaaggtgctcttggcgttttccatcacctacacgccagtgatgatatatgccctaaaggtaagccgcggccgacttttggggcttctgcaccttttgatttttttgaactgtgcctttactttcgggtacatgacattcgtgcactttcggagcacgaacaaggtcgcgctcactatgggagcagtagtcgcactcctttggggggtgtactcagccatagaaacctggaaattcatcacctccagatgccgttgtgcttgctaggccgcaagtacattctggcccctgcccaccacgttg'
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a3 = @obj3
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a3_seq = 'atgacgtataggtgttggctctatgccttggcatttgtattgtcaggagctgtgaccattggcacagcccaaaacttgctgcacagaaacacccttctgtgatagcctccttcaggggagcttagggtttgtccctagcaccttgcttccggagttgcactgctttacggtctctccacccctttaaccatgtctgggatacttgatcggtgcacgtgtacccccaatgccagggtgtttatggcggagggccaagtctactgcacacgatgcctcagtgcacggtctctccttcccctgaacctccaagtttctgagctcggggtgctaggcctattctacaggcccgaagagccactccggtggacgttgccacgtgcattccccactgttgagtgctcccccgccggggcctgctggctttctgcaatctttccaatcgcacgaatgaccagtggaaacctgaacttccaacaaagaatggtacgggtcgcagctgagctttacagagccggccagctcacccctgcagtcttgaaggctctacaagtttatgaacggggttgccgctggtaccccattgttggacctgtccctggagtggccgttttcgccaattccctacatgtgagtgataaacctttcccgggagcaactcacgtgttgaccaacctgccgctcccgcagagacccaagcctgaagacttttgcccctttgagtgtgctatggctactgtctatgacattggtcatgacgccgtcatgtatgtggccgaaaggaaagtctcctgggcccctcgtggcggggatgaagtgaaatttgaagctgtccccggggagttgaagttgattgcgaaccggctccgcacctccttcccgccccaccacacagtggacatgtctaagttcgccttcacagcccctgggtgtggtgtttctatgcgggtcgaacgccaacacggctgccttcccgctgacactgtccctgaaggcaactgctggtggagcttgtttgacttgcttccactggaagttcagaacaaagaaattcgccatgctaaccaatttggctaccagaccaagcatggtgtctctggcaagtacctacagcggaggctgca'
|
75
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+
|
76
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assert_equal(a1_seq, a1.seq.seq)
|
77
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assert_equal(a2_seq, a2.seq.seq)
|
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assert_equal(a3_seq, a3.seq.seq)
|
79
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|
80
|
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assert_equal('"Contig 1"', a1.entry_id)
|
81
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assert_equal('Contig 1', a2.name)
|
82
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assert_equal(nil, a3.name)
|
83
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|
84
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assert_equal(4, a1.total_sequences)
|
85
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assert_equal(4, a2.total_sequences)
|
86
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assert_equal(nil, a3.total_sequences)
|
87
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+
|
88
|
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assert_equal(true, a1.standard_comment?)
|
89
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assert_equal(true, a2.standard_comment?)
|
90
|
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assert_equal(false, a3.standard_comment?)
|
91
|
+
end
|
92
|
+
|
93
|
+
end
|
94
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+
|
95
|
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end
|
@@ -0,0 +1,127 @@
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#
|
2
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# test/unit/bio/db/test_medline.rb - Unit test for Bio::MEDLINE
|
3
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#
|
4
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# Copyright:: Copyright (C) 2008 Collaborative Drug Discovery, Inc. <github@collaborativedrug.com>
|
5
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# License:: The Ruby License
|
6
|
+
#
|
7
|
+
|
8
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+
require 'pathname'
|
9
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
|
10
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
11
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+
|
12
|
+
require 'test/unit'
|
13
|
+
require 'bio/db/medline'
|
14
|
+
|
15
|
+
module Bio
|
16
|
+
class TestMEDLINE < Test::Unit::TestCase
|
17
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+
def test_authors
|
18
|
+
assert_equal(["Kane, D. W.",
|
19
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+
"Hohman, M. M.",
|
20
|
+
"Cerami, E. G.",
|
21
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+
"McCormick, M. W.",
|
22
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+
"Kuhlmann, K. F.",
|
23
|
+
"Byrd, J. A."], Bio::MEDLINE.new(AGILE).authors)
|
24
|
+
end
|
25
|
+
|
26
|
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def test_authors_with_suffix
|
27
|
+
assert_equal(["Jenkins, F. A. Jr"], Bio::MEDLINE.new("AU - Jenkins FA Jr").authors)
|
28
|
+
end
|
29
|
+
|
30
|
+
def test_authors_with_last_name_all_caps
|
31
|
+
assert_equal(["GARTLER, S. M."], Bio::MEDLINE.new("AU - GARTLER SM").authors)
|
32
|
+
end
|
33
|
+
|
34
|
+
AGILE = <<-EOMED
|
35
|
+
PMID- 16734914
|
36
|
+
OWN - NLM
|
37
|
+
STAT- MEDLINE
|
38
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+
DA - 20060811
|
39
|
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DCOM- 20060928
|
40
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+
LR - 20081120
|
41
|
+
IS - 1471-2105 (Electronic)
|
42
|
+
VI - 7
|
43
|
+
DP - 2006
|
44
|
+
TI - Agile methods in biomedical software development: a multi-site experience
|
45
|
+
report.
|
46
|
+
PG - 273
|
47
|
+
AB - BACKGROUND: Agile is an iterative approach to software development that
|
48
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+
relies on strong collaboration and automation to keep pace with dynamic
|
49
|
+
environments. We have successfully used agile development approaches to
|
50
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+
create and maintain biomedical software, including software for
|
51
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+
bioinformatics. This paper reports on a qualitative study of our
|
52
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+
experiences using these methods. RESULTS: We have found that agile methods
|
53
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+
are well suited to the exploratory and iterative nature of scientific
|
54
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+
inquiry. They provide a robust framework for reproducing scientific
|
55
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+
results and for developing clinical support systems. The agile development
|
56
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+
approach also provides a model for collaboration between software
|
57
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+
engineers and researchers. We present our experience using agile
|
58
|
+
methodologies in projects at six different biomedical software development
|
59
|
+
organizations. The organizations include academic, commercial and
|
60
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+
government development teams, and included both bioinformatics and
|
61
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+
clinical support applications. We found that agile practices were a match
|
62
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+
for the needs of our biomedical projects and contributed to the success of
|
63
|
+
our organizations. CONCLUSION: We found that the agile development
|
64
|
+
approach was a good fit for our organizations, and that these practices
|
65
|
+
should be applicable and valuable to other biomedical software development
|
66
|
+
efforts. Although we found differences in how agile methods were used, we
|
67
|
+
were also able to identify a set of core practices that were common to all
|
68
|
+
of the groups, and that could be a focus for others seeking to adopt these
|
69
|
+
methods.
|
70
|
+
AD - SRA International, 4300 Fair Lakes Court, Fairfax, VA 22033, USA.
|
71
|
+
david_kane@sra.com
|
72
|
+
FAU - Kane, David W
|
73
|
+
AU - Kane DW
|
74
|
+
FAU - Hohman, Moses M
|
75
|
+
AU - Hohman MM
|
76
|
+
FAU - Cerami, Ethan G
|
77
|
+
AU - Cerami EG
|
78
|
+
FAU - McCormick, Michael W
|
79
|
+
AU - McCormick MW
|
80
|
+
FAU - Kuhlmann, Karl F
|
81
|
+
AU - Kuhlmann KF
|
82
|
+
FAU - Byrd, Jeff A
|
83
|
+
AU - Byrd JA
|
84
|
+
LA - eng
|
85
|
+
GR - U01 MH061915-03/MH/NIMH NIH HHS/United States
|
86
|
+
GR - U01 MH061915-04/MH/NIMH NIH HHS/United States
|
87
|
+
GR - U01 MH61915/MH/NIMH NIH HHS/United States
|
88
|
+
PT - Journal Article
|
89
|
+
PT - Research Support, N.I.H., Extramural
|
90
|
+
PT - Research Support, Non-U.S. Gov't
|
91
|
+
DEP - 20060530
|
92
|
+
PL - England
|
93
|
+
TA - BMC Bioinformatics
|
94
|
+
JT - BMC bioinformatics
|
95
|
+
JID - 100965194
|
96
|
+
SB - IM
|
97
|
+
MH - Algorithms
|
98
|
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MH - Automation
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AID - 10.1186/1471-2105-7-273 [doi]
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#
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# = test/bio/db/newick.rb - Unit test for Bio::Newick
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#
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# Copyright:: Copyright (C) 2004-2006
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# Daniel Amelang <dan@amelang.net>
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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: test_newick.rb,v 1.6 2007/12/12 16:06:22 ngoto Exp $
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#
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require 'test/unit'
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), [".."] * 4, "lib")).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'bio'
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require 'bio/tree'
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require 'bio/db/newick'
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module Bio
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class TestNewick < Test::Unit::TestCase
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TREE_STRING = <<-END_OF_TREE_STRING
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(
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(
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HexLEZ35:0.00263,
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HexMCZ42:0.00788
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):0.00854,
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(
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HexFLZ48:0.00457,
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(
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HexFLZ83:0.00217,
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HexFLZ13:0.00574
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):0.00100
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):0.04692,
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HexLEZ73:0.00268
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)[0.1250];
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END_OF_TREE_STRING
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def test_string_tree
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newick = Bio::Newick.new(TREE_STRING)
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tree = newick.tree
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assert_equal(3, tree.children(tree.root).size)
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assert_equal(9, tree.descendents(tree.root).size)
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assert_equal(6, tree.leaves.size)
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leaf = tree.get_node_by_name('HexFLZ83')
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assert_equal(3, tree.ancestors(leaf).size)
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assert_equal(tree.path(tree.root, leaf)[1], tree.ancestors(leaf)[1])
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assert_equal(0.00217, tree.get_edge(leaf, tree.parent(leaf)).distance)
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assert_equal("HexFLZ83", leaf.name)
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end
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end #class TestNewick
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class TestNewick2 < Test::Unit::TestCase
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TREE_STRING = <<-END_OF_TREE_STRING
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(
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(
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'this is test':0.0625,
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'test2 (abc, def)':0.125
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) 'internal node''s name' : 0.25,
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(
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'''':0.03125,
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(
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'ABCAC_HUMAN [ABC superfamily]':0.015625,
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hypothetical_protein:0.5
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) ABC : 0.25 [99]
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) test3 :0.5
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)root;
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END_OF_TREE_STRING
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def test_string_tree
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newick = Bio::Newick.new(TREE_STRING)
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tree = newick.tree
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assert_equal('root', tree.root.name)
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assert_equal([
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"this is test",
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"test2 (abc, def)",
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"internal node\'s name",
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"\'",
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"ABCAC_HUMAN [ABC superfamily]",
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"hypothetical protein",
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"ABC",
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"test3",
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"root"
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].sort,
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tree.nodes.collect { |x| x.name }.sort)
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assert_equal(tree.children(tree.root).collect { |x| x.name }.sort,
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[ "internal node\'s name", "test3" ])
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node = tree.get_node_by_name('ABC')
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assert_equal(99, node.bootstrap)
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assert_equal(1.5625,
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tree.distance(tree.get_node_by_name('hypothetical protein'),
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tree.get_node_by_name('this is test')))
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end
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end #class TestNewick2
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class TestNewickPrivate < Test::Unit::TestCase
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def setup
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@newick = Bio::Newick.new('') # dummy data
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end
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def test_parse_newick_leaf
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leaf_tokens = [ "A:B _C(D,E)F\'s G[H]", :":", '0.5', :"[",
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"&&NHX", :":", "S=human", :":", "E=1.1.1.1", :"]" ]
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node = Bio::Tree::Node.new
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edge = Bio::Tree::Edge.new
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options = {}
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assert_equal(true,
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@newick.instance_eval do
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__parse_newick_leaf(leaf_tokens, node, edge, options)
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end)
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assert_equal(:nhx, @newick.options[:original_format])
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assert_equal("A:B _C(D,E)F\'s G[H]", node.name)
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assert_equal("human", node.scientific_name)
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assert_equal("1.1.1.1", node.ec_number)
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assert_equal(0.5, edge.distance)
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+
end
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def test_parse_newick_get_tokens_for_leaf
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input = [ "A:B _C(D,E)F\'s G[H]", :":", '0.5', :"[",
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"&&NHX", :":", "S=human", :":", "E=1.1.1.1", :"]",
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:",", :"(", "bbb", :":", "0.2", :")" ]
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leaf_should_be = [ "A:B _C(D,E)F\'s G[H]", :":", '0.5', :"[",
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"&&NHX", :":", "S=human", :":", "E=1.1.1.1", :"]" ]
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rest_should_be = [ :",", :"(", "bbb", :":", "0.2", :")" ]
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+
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assert_equal(leaf_should_be,
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@newick.instance_eval do
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__parse_newick_get_tokens_for_leaf(input)
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end)
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+
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assert_equal(rest_should_be, input)
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end
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+
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def test_parse_newick_tokenize
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examples =
|
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[
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+
[
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+
'(a,b);', # input
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[ :"(", 'a', :",", 'b', :")" ], # normal parser result
|
151
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[ :"(", 'a', :",", 'b', :")" ], # naive parser result
|
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],
|
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[
|
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+
# input
|
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"(\'A:B _C(D,E)F\'\'s G[H]\':0.5[&&NHX:S=human:E=1.1.1.1], \n(bbb:0.2, c_d_e[&&NHX:B=100]);",
|
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# normal parser result
|
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[ :"(", "A:B _C(D,E)F\'s G[H]", :":", '0.5', :"[",
|
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"&&NHX", :":", "S=human", :":", "E=1.1.1.1", :"]",
|
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:",", :"(", "bbb", :":", "0.2", :",",
|
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"c d e", :"[", "&&NHX", :":", "B=100", :"]", :")" ],
|
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# naive parser result
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[ :"(", "\'A", :":", "B _C", :"(", "D", :",", "E",
|
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+
:")", "F\'\'s G", :"[", "H", :"]", "\'", :":", '0.5', :"[",
|
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+
"&&NHX", :":", "S=human", :":", "E=1.1.1.1", :"]",
|
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+
:",", :"(", "bbb", :":", "0.2", :",",
|
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"c_d_e", :"[", "&&NHX", :":", "B=100", :"]", :")" ]
|
167
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+
]
|
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+
]
|
169
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+
|
170
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+
examples.each do |a|
|
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# normal parser
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+
assert_equal(a[1],
|
173
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+
@newick.instance_eval do
|
174
|
+
__parse_newick_tokenize(a[0], {})
|
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+
end)
|
176
|
+
|
177
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+
# naive parser
|
178
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+
assert_equal(a[2],
|
179
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+
@newick.instance_eval do
|
180
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+
__parse_newick_tokenize(a[0], { :parser => :naive })
|
181
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+
end)
|
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+
end
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+
end
|
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end #class TestNewickPrivate
|
185
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+
|
186
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+
class TestBioTreeOutputPrivate < Test::Unit::TestCase
|
187
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+
|
188
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+
def setup
|
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+
@tree = Bio::Tree.new
|
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+
end
|
191
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+
|
192
|
+
def test_to_newick_format_label
|
193
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+
# unquoted_label
|
194
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+
assert_equal('ABC', @tree.instance_eval do
|
195
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+
__to_newick_format_label('ABC', {})
|
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|
+
end)
|
197
|
+
|
198
|
+
# unquoted_label, replaces blank to underscore
|
199
|
+
assert_equal('A_B_C', @tree.instance_eval do
|
200
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+
__to_newick_format_label('A B C', {})
|
201
|
+
end)
|
202
|
+
|
203
|
+
# quoted_label example 1
|
204
|
+
assert_equal("\'A B_C\'", @tree.instance_eval do
|
205
|
+
__to_newick_format_label('A B_C', {})
|
206
|
+
end)
|
207
|
+
|
208
|
+
# quoted_label example 2
|
209
|
+
assert_equal("\'A(B),C\'", @tree.instance_eval do
|
210
|
+
__to_newick_format_label('A(B),C', {})
|
211
|
+
end)
|
212
|
+
|
213
|
+
# normal formatter
|
214
|
+
assert_equal("\'A_B_C\'", @tree.instance_eval do
|
215
|
+
__to_newick_format_label('A_B_C', {})
|
216
|
+
end)
|
217
|
+
# naive formatter
|
218
|
+
assert_equal("A_B_C", @tree.instance_eval do
|
219
|
+
__to_newick_format_label('A_B_C',
|
220
|
+
{ :parser => :naive })
|
221
|
+
end)
|
222
|
+
end
|
223
|
+
|
224
|
+
|
225
|
+
def test_to_newick_format_leaf
|
226
|
+
node = Bio::Tree::Node.new('ABC')
|
227
|
+
edge = Bio::Tree::Edge.new(0.5)
|
228
|
+
|
229
|
+
assert_equal('ABC:0.5', @tree.instance_eval do
|
230
|
+
__to_newick_format_leaf(node, edge, {})
|
231
|
+
end)
|
232
|
+
|
233
|
+
# disable branch length
|
234
|
+
assert_equal('ABC', @tree.instance_eval do
|
235
|
+
__to_newick_format_leaf(node, edge,
|
236
|
+
{ :branch_length_style =>
|
237
|
+
:disabled })
|
238
|
+
end)
|
239
|
+
|
240
|
+
node.bootstrap = 98
|
241
|
+
# default: molphy style bootstrap
|
242
|
+
assert_equal('ABC:0.5[98]', @tree.instance_eval do
|
243
|
+
__to_newick_format_leaf(node, edge, {})
|
244
|
+
end)
|
245
|
+
# force molphy style bootstrap
|
246
|
+
assert_equal('ABC:0.5[98]', @tree.instance_eval do
|
247
|
+
__to_newick_format_leaf(node, edge,
|
248
|
+
{ :bootstrap_style => :molphy })
|
249
|
+
end)
|
250
|
+
# disable bootstrap output
|
251
|
+
assert_equal('ABC:0.5', @tree.instance_eval do
|
252
|
+
__to_newick_format_leaf(node, edge,
|
253
|
+
{ :bootstrap_style =>
|
254
|
+
:disabled })
|
255
|
+
end)
|
256
|
+
|
257
|
+
# force traditional bootstrap style
|
258
|
+
assert_equal('ABC98:0.5', @tree.instance_eval do
|
259
|
+
__to_newick_format_leaf(node, edge,
|
260
|
+
{ :bootstrap_style =>
|
261
|
+
:traditional })
|
262
|
+
end)
|
263
|
+
# normally, when traditional style, no node name allowed for the node
|
264
|
+
node2 = Bio::Tree::Node.new
|
265
|
+
node2.bootstrap = 98
|
266
|
+
assert_equal('98:0.5', @tree.instance_eval do
|
267
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+
__to_newick_format_leaf(node2, edge,
|
268
|
+
{ :bootstrap_style =>
|
269
|
+
:traditional })
|
270
|
+
end)
|
271
|
+
|
272
|
+
end
|
273
|
+
|
274
|
+
def test_to_newick_format_leaf_NHX
|
275
|
+
node = Bio::Tree::Node.new('ADH')
|
276
|
+
edge = Bio::Tree::Edge.new(0.5)
|
277
|
+
node.bootstrap = 98
|
278
|
+
node.ec_number = '1.1.1.1'
|
279
|
+
node.scientific_name = 'human'
|
280
|
+
node.taxonomy_id = '9606'
|
281
|
+
node.events.push :gene_duplication
|
282
|
+
edge.log_likelihood = 1.5
|
283
|
+
edge.width = 3
|
284
|
+
|
285
|
+
str = 'ADH:0.5[&&NHX:B=98:D=Y:E=1.1.1.1:L=1.5:S=human:T=9606:W=3]'
|
286
|
+
assert_equal(str, @tree.instance_eval do
|
287
|
+
__to_newick_format_leaf_NHX(node, edge, {})
|
288
|
+
end)
|
289
|
+
end
|
290
|
+
|
291
|
+
end #class TestBioTreeOutputPrivate
|
292
|
+
|
293
|
+
end #module Bio
|