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 +1,31 @@
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#
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# test/unit/bio/db/embl/test_uniprot.rb - Unit test for Bio::UniProt
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#
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# Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: test_uniprot.rb,v 1.5 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__), ['..'] * 5, '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/db/embl/uniprot'
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module Bio
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class TestUniProt < Test::Unit::TestCase
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def setup
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bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
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data = File.open(File.join(bioruby_root, 'test', 'data', 'uniprot', 'p53_human.uniprot')).read
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@obj = Bio::UniProt.new(data)
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end
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def test_gene_name
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assert_equal('TP53', @obj.gene_name)
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end
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end
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end
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#
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# test/unit/bio/db/kegg/test_genes.rb - Unit test for Bio::KEGG::GENES
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#
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# Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: test_genes.rb,v 1.5 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__), ['..'] * 5, '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/db/kegg/genes'
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module Bio
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class TestGenesDblinks < Test::Unit::TestCase
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def setup
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entry =<<END
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DBLINKS TIGR: At3g05560
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NCBI-GI: 15230008 42572267
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END
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@obj = Bio::KEGG::GENES.new(entry)
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end
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def test_data
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str = "DBLINKS TIGR: At3g05560\n NCBI-GI: 15230008 42572267"
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assert_equal(str, @obj.instance_eval('get("DBLINKS")'))
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end
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def test_dblinks_0
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assert_equal(Hash, @obj.dblinks.class)
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end
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def test_dblinks_1
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assert_equal(['At3g05560'], @obj.dblinks['TIGR'])
|
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end
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def test_dblinks_2
|
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assert_equal(['15230008', '42572267'], @obj.dblinks['NCBI-GI'])
|
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end
|
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end
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end
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#
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# = test/unit/bio/db/pdb/test_pdb.rb - Unit test for Bio::PDB classes
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#
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# Copyright:: Copyright (C) 2006
|
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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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# $Id:$
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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|
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require 'test/unit'
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require 'bio'
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module Bio
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#class TestPDB < Test::Unit::TestCase
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#end #class TestPDB
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module TestPDBRecord
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# test of Bio::PDB::Record::ATOM
|
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class TestATOM < Test::Unit::TestCase
|
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def setup
|
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# the data is taken from
|
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# http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_62.html
|
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@str = 'ATOM 154 CG2BVAL A 25 29.909 16.996 55.922 0.72 13.25 A1 C '
|
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@atom = Bio::PDB::Record::ATOM.new.initialize_from_string(@str)
|
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end
|
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|
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def test_record_name
|
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assert_equal('ATOM', @atom.record_name)
|
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end
|
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|
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def test_serial
|
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assert_equal(154, @atom.serial)
|
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end
|
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|
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def test_name
|
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assert_equal('CG2', @atom.name)
|
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end
|
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|
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def test_altLoc
|
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assert_equal('B', @atom.altLoc)
|
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end
|
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|
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def test_resName
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assert_equal('VAL', @atom.resName)
|
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end
|
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def test_chainID
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assert_equal('A', @atom.chainID)
|
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end
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|
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def test_resSeq
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assert_equal(25, @atom.resSeq)
|
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end
|
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|
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def test_iCode
|
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assert_equal('', @atom.iCode)
|
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end
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|
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def test_x
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assert_in_delta(29.909, @atom.x, Float::EPSILON)
|
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+
end
|
69
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|
70
|
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def test_y
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assert_in_delta(16.996, @atom.y, Float::EPSILON)
|
72
|
+
end
|
73
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|
74
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def test_z
|
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assert_in_delta(55.922, @atom.z, Float::EPSILON)
|
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|
+
end
|
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|
78
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def test_occupancy
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assert_in_delta(0.72, @atom.occupancy, Float::EPSILON)
|
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+
end
|
81
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|
82
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def test_tempFactor
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assert_in_delta(13.25, @atom.tempFactor, Float::EPSILON)
|
84
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+
end
|
85
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|
86
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def test_segID
|
87
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assert_equal('A1', @atom.segID)
|
88
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end
|
89
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|
90
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def test_element
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assert_equal('C', @atom.element)
|
92
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end
|
93
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|
94
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def test_charge
|
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assert_equal('', @atom.charge)
|
96
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+
end
|
97
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|
98
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def test_xyz
|
99
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assert_equal(Bio::PDB::Coordinate[
|
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"29.909".to_f,
|
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"16.996".to_f,
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"55.922".to_f ], @atom.xyz)
|
103
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end
|
104
|
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|
105
|
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def test_to_a
|
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assert_equal([ "29.909".to_f,
|
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"16.996".to_f,
|
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"55.922".to_f ], @atom.to_a)
|
109
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+
end
|
110
|
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|
111
|
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def test_comparable
|
112
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a = Bio::PDB::Record::ATOM.new
|
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a.serial = 999
|
114
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assert_equal(-1, @atom <=> a)
|
115
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a.serial = 154
|
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assert_equal( 0, @atom <=> a)
|
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a.serial = 111
|
118
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assert_equal( 1, @atom <=> a)
|
119
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end
|
120
|
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|
121
|
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def test_to_s
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assert_equal(@str + "\n", @atom.to_s)
|
123
|
+
end
|
124
|
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|
125
|
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def test_original_data
|
126
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assert_equal([ @str ], @atom.original_data)
|
127
|
+
end
|
128
|
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|
129
|
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def test_do_parse
|
130
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assert_equal(@atom, @atom.do_parse)
|
131
|
+
end
|
132
|
+
|
133
|
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def test_residue
|
134
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assert_equal(nil, @atom.residue)
|
135
|
+
end
|
136
|
+
|
137
|
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def test_sigatm
|
138
|
+
assert_equal(nil, @atom.sigatm)
|
139
|
+
end
|
140
|
+
|
141
|
+
def test_anisou
|
142
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assert_equal(nil, @atom.anisou)
|
143
|
+
end
|
144
|
+
|
145
|
+
def test_ter
|
146
|
+
assert_equal(nil, @atom.ter)
|
147
|
+
end
|
148
|
+
end #class TestATOM
|
149
|
+
|
150
|
+
end #module TestPDBRecord
|
151
|
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|
152
|
+
end #module Bio
|
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#
|
2
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# test/unit/bio/db/test_aaindex.rb - Unit test for Bio::AAindex
|
3
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+
#
|
4
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# Copyright:: Copyright (C) 2006
|
5
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# Mitsuteru C. Nakao <n@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
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+
# $Id: test_aaindex.rb,v 1.4 2007/04/05 23:35:43 trevor Exp $
|
9
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+
#
|
10
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+
|
11
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+
require 'pathname'
|
12
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+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
|
13
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+
$:.unshift(libpath) unless $:.include?(libpath)
|
14
|
+
|
15
|
+
require 'test/unit'
|
16
|
+
require 'bio/io/fetch'
|
17
|
+
require 'bio/db/aaindex'
|
18
|
+
|
19
|
+
module Bio
|
20
|
+
class DataAAindex
|
21
|
+
bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
|
22
|
+
TestDataAAindex = Pathname.new(File.join(bioruby_root, 'test', 'data', 'aaindex')).cleanpath.to_s
|
23
|
+
|
24
|
+
def self.aax1
|
25
|
+
File.read(File.join(TestDataAAindex, "PRAM900102"))
|
26
|
+
end
|
27
|
+
|
28
|
+
def self.aax2
|
29
|
+
File.read(File.join(TestDataAAindex, "DAYM780301"))
|
30
|
+
end
|
31
|
+
end
|
32
|
+
|
33
|
+
# A super class for Bio::AAindex1 and Bio::AAindex2
|
34
|
+
class TestAAindexConstant < Test::Unit::TestCase
|
35
|
+
def test_delimiter
|
36
|
+
rs = "\n//\n"
|
37
|
+
assert_equal(rs, Bio::AAindex::DELIMITER)
|
38
|
+
assert_equal(rs, Bio::AAindex::RS)
|
39
|
+
end
|
40
|
+
|
41
|
+
def test_tagsize
|
42
|
+
assert_equal(2, Bio::AAindex::TAGSIZE)
|
43
|
+
end
|
44
|
+
end
|
45
|
+
|
46
|
+
class TestAAindex < Test::Unit::TestCase
|
47
|
+
def test_api
|
48
|
+
api_methods = ['entry_id', 'definition', 'dblinks', 'author',
|
49
|
+
'title', 'journal', 'comment']
|
50
|
+
api_methods.each do |m|
|
51
|
+
end
|
52
|
+
end
|
53
|
+
|
54
|
+
def test_auto_aax1
|
55
|
+
assert_equal(Bio::AAindex1, Bio::AAindex.auto(DataAAindex.aax1).class)
|
56
|
+
end
|
57
|
+
|
58
|
+
def test_auto_aax2
|
59
|
+
assert_equal(Bio::AAindex2, Bio::AAindex.auto(DataAAindex.aax2).class)
|
60
|
+
end
|
61
|
+
end
|
62
|
+
|
63
|
+
class TestAAindex1 < Test::Unit::TestCase
|
64
|
+
def setup
|
65
|
+
str = DataAAindex.aax1
|
66
|
+
@obj = Bio::AAindex1.new(str)
|
67
|
+
end
|
68
|
+
|
69
|
+
def test_entry_id
|
70
|
+
assert_equal('PRAM900102', @obj.entry_id)
|
71
|
+
end
|
72
|
+
|
73
|
+
def test_definition
|
74
|
+
assert_equal('Relative frequency in alpha-helix (Prabhakaran, 1990)', @obj.definition)
|
75
|
+
end
|
76
|
+
|
77
|
+
def test_dblinks
|
78
|
+
assert_equal(['LIT:1614053b', 'PMID:2390062'], @obj.dblinks)
|
79
|
+
end
|
80
|
+
|
81
|
+
def test_author
|
82
|
+
assert_equal('Prabhakaran, M.', @obj.author)
|
83
|
+
end
|
84
|
+
|
85
|
+
def test_title
|
86
|
+
assert_equal('The distribution of physical, chemical and conformational properties in signal and nascent peptides', @obj.title)
|
87
|
+
end
|
88
|
+
|
89
|
+
def test_journal
|
90
|
+
assert_equal('Biochem. J. 269, 691-696 (1990) Original reference of these three data: Creighton, T.E. In "Protein Structure and Melecular Properties", (Freeman, W.H., ed.), San Francisco P.235 (1983)', @obj.journal)
|
91
|
+
end
|
92
|
+
|
93
|
+
def test_comment
|
94
|
+
assert_equal("", @obj.comment)
|
95
|
+
end
|
96
|
+
|
97
|
+
def test_correlation_coefficient
|
98
|
+
# str = "LEVM780101 1.000 LEVM780104 0.964 PALJ810101 0.943 KANM800101 0.942 ISOY800101 0.929 MAXF760101 0.924 ROBB760101 0.916 GEIM800101 0.912 GEIM800104 0.907 RACS820108 0.904 PALJ810102 0.902 PALJ810109 0.898 NAGK730101 0.894 CRAJ730101 0.887 CHOP780201 0.873 TANS770101 0.854 KANM800103 0.850 QIAN880107 0.829 QIAN880106 0.827 BURA740101 0.805 NAGK730103 -0.809"
|
99
|
+
# assert_equal(str, @obj.correlation_coefficient)
|
100
|
+
# to be this ?
|
101
|
+
hash = {'LEVM780101' => 1.000, 'LEVM780104' => 0.964, 'PALJ810101' => 0.943, 'KANM800101' => 0.942, 'ISOY800101' => 0.929, 'MAXF760101' => 0.924, 'ROBB760101' => 0.916, 'GEIM800101' => 0.912, 'GEIM800104' => 0.907, 'RACS820108' => 0.904, 'PALJ810102' => 0.902, 'PALJ810109' => 0.898, 'NAGK730101' => 0.894, 'CRAJ730101' => 0.887, 'CHOP780201' => 0.873, 'TANS770101' => 0.854, 'KANM800103' => 0.850, 'QIAN880107' => 0.829, 'QIAN880106' => 0.827, 'BURA740101' => 0.805, 'NAGK730103' => -0.809}
|
102
|
+
assert_equal(hash, @obj.correlation_coefficient)
|
103
|
+
end
|
104
|
+
|
105
|
+
def test_index
|
106
|
+
hash = {"V"=>0.91, "K"=>1.23, "W"=>0.99, "L"=>1.3, "A"=>1.29, "M"=>1.47, "Y"=>0.72, "C"=>1.11, "N"=>0.9, "D"=>1.04, "P"=>0.52, "E"=>1.44, "F"=>1.07, "Q"=>1.27, "G"=>0.56, "R"=>0.96, "S"=>0.82, "H"=>1.22, "T"=>0.82, "I"=>0.97}
|
107
|
+
assert_equal(hash, @obj.index)
|
108
|
+
end
|
109
|
+
end
|
110
|
+
|
111
|
+
|
112
|
+
class TestAAindex2 < Test::Unit::TestCase
|
113
|
+
def setup
|
114
|
+
str = DataAAindex.aax2
|
115
|
+
@obj = Bio::AAindex2.new(str)
|
116
|
+
end
|
117
|
+
|
118
|
+
def test_entry_id
|
119
|
+
assert_equal('DAYM780301', @obj.entry_id)
|
120
|
+
end
|
121
|
+
|
122
|
+
def test_definition
|
123
|
+
assert_equal('Log odds matrix for 250 PAMs (Dayhoff et al., 1978)', @obj.definition)
|
124
|
+
end
|
125
|
+
|
126
|
+
def test_dblinks
|
127
|
+
assert_equal([], @obj.dblinks)
|
128
|
+
end
|
129
|
+
|
130
|
+
def test_author
|
131
|
+
assert_equal("Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C.", @obj.author)
|
132
|
+
end
|
133
|
+
|
134
|
+
def test_title
|
135
|
+
assert_equal("A model of evolutionary change in proteins", @obj.title)
|
136
|
+
end
|
137
|
+
|
138
|
+
def test_journal
|
139
|
+
assert_equal('In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff, M.O., ed.), National Biomedical Research Foundation, Washington, D.C., p.352 (1978)', @obj.journal)
|
140
|
+
end
|
141
|
+
|
142
|
+
def test_comment
|
143
|
+
assert_equal("", @obj.comment)
|
144
|
+
end
|
145
|
+
|
146
|
+
def test_rows
|
147
|
+
ary = ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V"]
|
148
|
+
assert_equal(ary, @obj.rows)
|
149
|
+
end
|
150
|
+
|
151
|
+
def test_cols
|
152
|
+
ary = ["A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", "P", "S", "T", "W", "Y", "V"]
|
153
|
+
assert_equal(ary, @obj.cols)
|
154
|
+
end
|
155
|
+
|
156
|
+
def test_matrix
|
157
|
+
assert_equal(Matrix, @obj.matrix.class)
|
158
|
+
end
|
159
|
+
|
160
|
+
def test_matrix_2_2
|
161
|
+
assert_equal(2.0, @obj.matrix[2, 2])
|
162
|
+
end
|
163
|
+
|
164
|
+
def test_matrix_1_2
|
165
|
+
assert_equal(nil, @obj.matrix[1, 2])
|
166
|
+
end
|
167
|
+
|
168
|
+
def test_access_A_R
|
169
|
+
assert_equal(nil, @obj['A', 'R'])
|
170
|
+
end
|
171
|
+
|
172
|
+
def test_access_R_A
|
173
|
+
assert_equal(-2.0, @obj['R', 'A'])
|
174
|
+
end
|
175
|
+
|
176
|
+
def test_matrix_A_R
|
177
|
+
assert_equal(nil, @obj.matrix('A', 'R'))
|
178
|
+
end
|
179
|
+
|
180
|
+
def test_matrix_R_A
|
181
|
+
assert_equal(-2.0, @obj.matrix('R', 'A'))
|
182
|
+
end
|
183
|
+
|
184
|
+
def test_matrix_determinant
|
185
|
+
assert_equal(0, @obj.matrix.determinant)
|
186
|
+
end
|
187
|
+
|
188
|
+
def test_matrix_rank
|
189
|
+
assert_equal(1, @obj.matrix.rank)
|
190
|
+
end
|
191
|
+
|
192
|
+
def test_matrix_transpose
|
193
|
+
ary = Matrix[[2.0, -2.0, 0.0, 0.0, -2.0, 0.0, 0.0, 1.0, -1.0, -1.0, -2.0, -1.0, -1.0, -4.0, 1.0, 1.0, 1.0, -6.0, -3.0, 0.0]]
|
194
|
+
assert_equal(ary, @obj.matrix.transpose)
|
195
|
+
end
|
196
|
+
end
|
197
|
+
end
|
@@ -0,0 +1,250 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/db/test_fasta.rb - Unit test for Bio::FastaFormat
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005 Mitsuteru Nakao <n@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id: test_fasta.rb,v 1.5 2007/04/05 23:35:43 trevor Exp $
|
8
|
+
#
|
9
|
+
|
10
|
+
require 'pathname'
|
11
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
|
12
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
13
|
+
|
14
|
+
require 'test/unit'
|
15
|
+
require 'bio/db/fasta'
|
16
|
+
|
17
|
+
module Bio
|
18
|
+
class TestFastaFormatConst < Test::Unit::TestCase
|
19
|
+
|
20
|
+
def test_delimiter
|
21
|
+
assert_equal("\n>", Bio::FastaFormat::DELIMITER)
|
22
|
+
assert_equal("\n>", Bio::FastaFormat::RS)
|
23
|
+
end
|
24
|
+
|
25
|
+
end # class TestFastaFormatConst
|
26
|
+
|
27
|
+
|
28
|
+
class TestFastaFormatSwissProt < Test::Unit::TestCase
|
29
|
+
def setup
|
30
|
+
text =<<END
|
31
|
+
>gi|1171674|sp|P42267|NDD_BPR69 NUCLEAR DISRUPTION PROTEIN
|
32
|
+
MKYMTVTDLNNAGATVIGTIKGGEWFLGTPHKDILSKPGFYFLVSKLDGRPFSNPCVSARFYVGNQRSKQGFSAVLSHIR
|
33
|
+
QRRSQLARTIANNNMVYTVFYLPASKMKPLTTGFGKGQLALAFTRNHHSEYQTLEEMNRMLADNFKFVLQAY
|
34
|
+
END
|
35
|
+
@obj = Bio::FastaFormat.new(text)
|
36
|
+
end
|
37
|
+
|
38
|
+
def test_locus
|
39
|
+
assert_equal(nil, @obj.locus)
|
40
|
+
end
|
41
|
+
end
|
42
|
+
|
43
|
+
class TestFastaFormatKeggGenesNT < Test::Unit::TestCase
|
44
|
+
def setup
|
45
|
+
text =<<END
|
46
|
+
>eco:b0001 thrL; thr operon leader peptide (N)
|
47
|
+
atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcg
|
48
|
+
ggctga
|
49
|
+
END
|
50
|
+
@obj = Bio::FastaFormat.new(text)
|
51
|
+
end
|
52
|
+
|
53
|
+
def test_naseq_class
|
54
|
+
assert_equal(Bio::Sequence::NA, @obj.naseq.class)
|
55
|
+
end
|
56
|
+
|
57
|
+
def test_naseq
|
58
|
+
seq = 'atgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcgggctga'
|
59
|
+
assert_equal(seq, @obj.naseq)
|
60
|
+
end
|
61
|
+
|
62
|
+
def test_nalen
|
63
|
+
assert_equal(66, @obj.nalen)
|
64
|
+
end
|
65
|
+
end
|
66
|
+
|
67
|
+
class TestFastaFormatKeggGenesAA < Test::Unit::TestCase
|
68
|
+
def setup
|
69
|
+
text =<<END
|
70
|
+
>sce:YBR160W CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]
|
71
|
+
MSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG
|
72
|
+
VPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME
|
73
|
+
GIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL
|
74
|
+
KLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC
|
75
|
+
IFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP
|
76
|
+
QWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES
|
77
|
+
>sce:YBR274W CHK1; probable serine/threonine-protein kinase [EC:2.7.1.-] [SP:KB9S_YEAST]
|
78
|
+
MSLSQVSPLPHIKDVVLGDTVGQGAFACVKNAHLQMDPSIILAVKFIHVP
|
79
|
+
TCKKMGLSDKDITKEVVLQSKCSKHPNVLRLIDCNVSKEYMWIILEMADG
|
80
|
+
GDLFDKIEPDVGVDSDVAQFYFQQLVSAINYLHVECGVAHRDIKPENILL
|
81
|
+
DKNGNLKLADFGLASQFRRKDGTLRVSMDQRGSPPYMAPEVLYSEEGYYA
|
82
|
+
DRTDIWSIGILLFVLLTGQTPWELPSLENEDFVFFIENDGNLNWGPWSKI
|
83
|
+
EFTHLNLLRKILQPDPNKRVTLKALKLHPWVLRRASFSGDDGLCNDPELL
|
84
|
+
AKKLFSHLKVSLSNENYLKFTQDTNSNNRYISTQPIGNELAELEHDSMHF
|
85
|
+
QTVSNTQRAFTSYDSNTNYNSGTGMTQEAKWTQFISYDIAALQFHSDEND
|
86
|
+
CNELVKRHLQFNPNKLTKFYTLQPMDVLLPILEKALNLSQIRVKPDLFAN
|
87
|
+
FERLCELLGYDNVFPLIINIKTKSNGGYQLCGSISIIKIEEELKSVGFER
|
88
|
+
KTGDPLEWRRLFKKISTICRDIILIPN
|
89
|
+
END
|
90
|
+
@obj = Bio::FastaFormat.new(text)
|
91
|
+
end
|
92
|
+
|
93
|
+
def test_entry_id
|
94
|
+
assert_equal('sce:YBR160W', @obj.entry_id)
|
95
|
+
end
|
96
|
+
|
97
|
+
def test_acc_version
|
98
|
+
assert_equal(nil, @obj.acc_version)
|
99
|
+
end
|
100
|
+
|
101
|
+
def test_entry
|
102
|
+
data = ">sce:YBR160W CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]\nMSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG\nVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME\nGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL\nKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC\nIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP\nQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES\n"
|
103
|
+
assert_equal(data, @obj.entry)
|
104
|
+
end
|
105
|
+
|
106
|
+
def test_definition
|
107
|
+
data = "sce:YBR160W CDC28, SRM5; cyclin-dependent protein kinase catalytic subunit [EC:2.7.1.-] [SP:CC28_YEAST]"
|
108
|
+
assert_equal(data, @obj.definition)
|
109
|
+
end
|
110
|
+
|
111
|
+
def test_data
|
112
|
+
data = "\nMSGELANYKRLEKVGEGTYGVVYKALDLRPGQGQRVVALKKIRLESEDEG\nVPSTAIREISLLKELKDDNIVRLYDIVHSDAHKLYLVFEFLDLDLKRYME\nGIPKDQPLGADIVKKFMMQLCKGIAYCHSHRILHRDLKPQNLLINKDGNL\nKLGDFGLARAFGVPLRAYTHEIVTLWYRAPEVLLGGKQYSTGVDTWSIGC\nIFAEMCNRKPIFSGDSEIDQIFKIFRVLGTPNEAIWPDIVYLPDFKPSFP\nQWRRKDLSQVVPSLDPRGIDLLDKLLAYDPINRISARRAAIHPYFQES\n"
|
113
|
+
assert_equal(data, @obj.data)
|
114
|
+
end
|
115
|
+
end
|
116
|
+
|
117
|
+
class TestFastaFormat < Test::Unit::TestCase
|
118
|
+
|
119
|
+
def setup
|
120
|
+
text =<<END
|
121
|
+
>gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]
|
122
|
+
MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT
|
123
|
+
IALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF
|
124
|
+
TLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI
|
125
|
+
LFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL
|
126
|
+
>gi|55416190|gb|AAV50057.1| NADH dehydrogenase subunit 2 [Dasyurus hallucatus]
|
127
|
+
MSPYVLMILTLSLFIGTCLTIFSNHWFTAWMGLEINTLAIIPLMTAPNNPRSTEAATKYFLTQATASMLMMFAIIYNAWS
|
128
|
+
TNQWALPQLSDDWISLLMTVALAIKLGLAPFHFWVPEVTQGIPLLTGMILLTWQKIAPTAILFQIAPYLNMKFLVILAIL
|
129
|
+
STLVGGWGGLNQTHLRKILAYSSIAHMGWMIIIVQINPTLSIFTLTIYVMATLTTFLTLNLSNSTKIKSLGNLWNKSATA
|
130
|
+
TIIIFLTLLSLGGLPPLTGFMPKWLILQELINNGNIITATMMALSALLNLFFYMRLIYASSLTMFPSINNSKMQWYNNSM
|
131
|
+
KTTTLIPTATVISSLLLPLTPLFVTLY
|
132
|
+
END
|
133
|
+
@obj = Bio::FastaFormat.new(text)
|
134
|
+
end
|
135
|
+
|
136
|
+
def test_entry
|
137
|
+
data = ">gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]\nMFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT\nIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF\nTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI\nLFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL\n"
|
138
|
+
assert_equal(data, @obj.entry)
|
139
|
+
end
|
140
|
+
|
141
|
+
def test_entry_id
|
142
|
+
assert_equal('gi|55416189', @obj.entry_id)
|
143
|
+
end
|
144
|
+
|
145
|
+
def test_definition
|
146
|
+
data = "gi|55416189|gb|AAV50056.1| NADH dehydrogenase subunit 1 [Dasyurus hallucatus]"
|
147
|
+
assert_equal(data, @obj.definition)
|
148
|
+
end
|
149
|
+
|
150
|
+
def test_data
|
151
|
+
data = "\nMFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALT\nIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSF\nTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTI\nLFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL\n"
|
152
|
+
assert_equal(data, @obj.data)
|
153
|
+
end
|
154
|
+
|
155
|
+
def test_seq
|
156
|
+
seq = 'MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALTIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSFTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTILFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL'
|
157
|
+
assert_equal(seq, @obj.seq)
|
158
|
+
end
|
159
|
+
|
160
|
+
def test_length
|
161
|
+
assert_equal(318, @obj.length)
|
162
|
+
end
|
163
|
+
|
164
|
+
def test_aaseq
|
165
|
+
seq = "MFTINLLIYIIPILLAVAFLTLIERKMLGYMQFRKGPNIVGPYGLLQPFADAVKLFTKEPLRPLTSSISIFIIAPILALTIALTIWTPLPMPNTLLDLNLGLIFILSLSGLSVYSILWSGWASNSKYALIGALRAVAQTISYEVSLAIILLSIMLINGSFTLKTLSITQENLWLIITTWPLAMMWYISTLAETNRAPFDLTEGESELVSGFNVEYAAGPFAMFFLAEYANIIAMNAITTILFLGPSLTPNLSHLNTLSFMLKTLLLTMVFLWVRASYPRFRYDQLMHLLWKNFLPMTLAMCLWFISLPIALSCIPPQL"
|
166
|
+
assert_equal(seq, @obj.aaseq)
|
167
|
+
end
|
168
|
+
|
169
|
+
def test_aalen
|
170
|
+
assert_equal(318, @obj.aalen)
|
171
|
+
end
|
172
|
+
|
173
|
+
def test_identifiers
|
174
|
+
assert_equal(Bio::FastaDefline, @obj.identifiers.class)
|
175
|
+
end
|
176
|
+
|
177
|
+
def test_gi
|
178
|
+
assert_equal('55416189', @obj.gi)
|
179
|
+
end
|
180
|
+
|
181
|
+
def test_accession
|
182
|
+
assert_equal('AAV50056', @obj.accession)
|
183
|
+
end
|
184
|
+
|
185
|
+
def test_accessions
|
186
|
+
assert_equal(['AAV50056'], @obj.accessions)
|
187
|
+
end
|
188
|
+
|
189
|
+
def test_acc_version
|
190
|
+
assert_equal('AAV50056.1', @obj.acc_version)
|
191
|
+
end
|
192
|
+
|
193
|
+
end # class TestFastaFormat
|
194
|
+
|
195
|
+
|
196
|
+
class TestFastaNumericFormat < Test::Unit::TestCase
|
197
|
+
|
198
|
+
def setup
|
199
|
+
text =<<END
|
200
|
+
>CRA3575282.F
|
201
|
+
24 15 23 29 20 13 20 21 21 23 22 25 13 22 17 15 25 27 32 26
|
202
|
+
32 29 29 25
|
203
|
+
END
|
204
|
+
@obj = Bio::FastaNumericFormat.new(text)
|
205
|
+
end
|
206
|
+
|
207
|
+
def test_entry
|
208
|
+
assert_equal(">CRA3575282.F\n24 15 23 29 20 13 20 21 21 23 22 25 13 22 17 15 25 27 32 26 \n32 29 29 25\n", @obj.entry)
|
209
|
+
end
|
210
|
+
|
211
|
+
def test_entry_id
|
212
|
+
assert_equal('CRA3575282.F', @obj.entry_id)
|
213
|
+
end
|
214
|
+
|
215
|
+
def test_definition
|
216
|
+
assert_equal('CRA3575282.F', @obj.definition)
|
217
|
+
end
|
218
|
+
|
219
|
+
def test_data
|
220
|
+
data = [24, 15, 23, 29, 20, 13, 20, 21, 21, 23, 22, 25, 13, 22, 17, 15, 25, 27, 32, 26, 32, 29, 29, 25]
|
221
|
+
assert_equal(data, @obj.data)
|
222
|
+
end
|
223
|
+
|
224
|
+
def test_length
|
225
|
+
assert_equal(24, @obj.length)
|
226
|
+
end
|
227
|
+
|
228
|
+
def test_each
|
229
|
+
assert(@obj.each {|x| })
|
230
|
+
end
|
231
|
+
|
232
|
+
def test_arg
|
233
|
+
assert(@obj[0], '')
|
234
|
+
assert(@obj[-1], '')
|
235
|
+
end
|
236
|
+
|
237
|
+
|
238
|
+
end # class TestFastaFormatNumeric
|
239
|
+
|
240
|
+
|
241
|
+
class TestFastaDefinition < Test::Unit::TestCase
|
242
|
+
|
243
|
+
def setup
|
244
|
+
end
|
245
|
+
|
246
|
+
def test_defline
|
247
|
+
end
|
248
|
+
end # class TestFastaDefinition
|
249
|
+
|
250
|
+
end
|