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 +1,80 @@
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#
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# test/unit/bio/io/test_ddbjxml.rb - Unit test for DDBJ XML.
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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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# $Id:$
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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/io/ddbjxml'
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module Bio
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class TestDDBJXMLConstants < Test::Unit::TestCase
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def test_constants
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constants = ["DDBJ", "TxSearch", "ClustalW", "PML", "Gib", "Fasta",
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"BASE_URI", "SRS", "SERVER_URI", "Gtop", "GetEntry",
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"Blast", "RequestManager"].sort
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assert_equal(constants, Bio::DDBJ::XML.constants.sort.collect{|x| x.to_s})
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end
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def test_base_url
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assert_equal("http://xml.nig.ac.jp/wsdl/", Bio::DDBJ::XML::BASE_URI)
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end
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def test_blast_server_rul
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assert_equal("http://xml.nig.ac.jp/wsdl/Blast.wsdl", Bio::DDBJ::XML::Blast::SERVER_URI)
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end
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def test_clustalw_server_url
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assert_equal("http://xml.nig.ac.jp/wsdl/ClustalW.wsdl", Bio::DDBJ::XML::ClustalW::SERVER_URI)
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end
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def test_ddbj_server_url
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assert_equal("http://xml.nig.ac.jp/wsdl/DDBJ.wsdl", Bio::DDBJ::XML::DDBJ::SERVER_URI)
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end
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def test_fasta_server_url
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assert_equal("http://xml.nig.ac.jp/wsdl/Fasta.wsdl", Bio::DDBJ::XML::Fasta::SERVER_URI)
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end
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def test_getentry_server_url
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assert_equal("http://xml.nig.ac.jp/wsdl/GetEntry.wsdl", Bio::DDBJ::XML::GetEntry::SERVER_URI)
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end
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def test_gib_server_url
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assert_equal("http://xml.nig.ac.jp/wsdl/Gib.wsdl", Bio::DDBJ::XML::Gib::SERVER_URI)
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end
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def test_gtop_server_url
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assert_equal("http://xml.nig.ac.jp/wsdl/Gtop.wsdl", Bio::DDBJ::XML::Gtop::SERVER_URI)
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end
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def test_pml_server_url
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assert_equal("http://xml.nig.ac.jp/wsdl/PML.wsdl", Bio::DDBJ::XML::PML::SERVER_URI)
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end
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def test_srs_server_url
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assert_equal("http://xml.nig.ac.jp/wsdl/SRS.wsdl", Bio::DDBJ::XML::SRS::SERVER_URI)
|
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end
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def test_txsearch_server_url
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assert_equal("http://xml.nig.ac.jp/wsdl/TxSearch.wsdl", Bio::DDBJ::XML::TxSearch::SERVER_URI)
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end
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def test_requestmanager_server_url
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assert_equal("http://xml.nig.ac.jp/wsdl/RequestManager.wsdl", Bio::DDBJ::XML::RequestManager::SERVER_URI)
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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/io/test_ensembl.rb - Unit test for Bio::Ensembl.
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#
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# Copyright:: Copyright (C) 2006, 2007
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# Mitsuteru C. Nakao <n@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: test_ensembl.rb,v 1.6 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/io/ensembl'
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# tests for ensembl.rb,v 1.4
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class TestEnsembl_v14 < Test::Unit::TestCase
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def test_ensembl_url
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assert_equal('http://www.ensembl.org', Bio::Ensembl::ENSEMBL_URL)
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end
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def test_server
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obj = Bio::Ensembl.new('Homo_sapiens')
|
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assert_equal('http://www.ensembl.org', obj.server)
|
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end
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def test_organism
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organism = 'Homo_sapiens'
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obj = Bio::Ensembl.new(organism)
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assert_equal(organism, obj.organism)
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end
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def test_self_human
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organism = 'Homo_sapiens'
|
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obj = Bio::Ensembl.human
|
38
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assert_equal(organism, obj.organism)
|
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end
|
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|
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def test_self_mouse
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organism = 'Mus_musculus'
|
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obj = Bio::Ensembl.mouse
|
44
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assert_equal(organism, obj.organism)
|
45
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+
end
|
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|
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def test_new_with_2_args
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organism = 'Oryza_sativa'
|
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server_url = 'http://www.gramene.org'
|
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obj = Bio::Ensembl.new(organism, server_url)
|
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assert_equal(organism, obj.organism)
|
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assert_equal(server_url, obj.server)
|
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+
end
|
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end
|
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|
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|
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class TestEnsembl < Test::Unit::TestCase
|
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def test_server_name
|
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assert_equal('http://www.ensembl.org', Bio::Ensembl::EBIServerURI)
|
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+
end
|
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|
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def test_server_uri
|
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assert_equal('http://www.ensembl.org', Bio::Ensembl.server_uri)
|
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+
end
|
65
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|
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def test_set_server_uri
|
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host = 'http://localhost'
|
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Bio::Ensembl.server_uri(host)
|
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assert_equal(host, Bio::Ensembl.server_uri)
|
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+
end
|
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end
|
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|
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|
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class TestEnsemblBase < Test::Unit::TestCase
|
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def test_exportview
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|
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end
|
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end
|
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|
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class TestEnsemblBaseClient < Test::Unit::TestCase
|
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def test_class
|
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|
83
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end
|
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end
|
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|
86
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|
87
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class TestEnsemblHuman < Test::Unit::TestCase
|
88
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def test_organism
|
89
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assert_equal("Homo_sapiens", Bio::Ensembl::Human::Organism)
|
90
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+
end
|
91
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+
end
|
92
|
+
|
93
|
+
class TestEnsemblMouse < Test::Unit::TestCase
|
94
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def test_organism
|
95
|
+
assert_equal("Mus_musculus", Bio::Ensembl::Mouse::Organism)
|
96
|
+
end
|
97
|
+
end
|
98
|
+
|
99
|
+
|
100
|
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class TestEnsemblOldStyleClient < Test::Unit::TestCase
|
101
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class Rice < Bio::Ensembl::Base
|
102
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Organism = 'Oryza_sativa'
|
103
|
+
end
|
104
|
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|
105
|
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def test_organism
|
106
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assert_equal('Oryza_sativa', Rice::Organism)
|
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end
|
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end
|
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|
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|
@@ -0,0 +1,42 @@
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#
|
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# test/unit/bio/io/test_fastacmd.rb - Unit test for Bio::Blast::Fastacmd.
|
3
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#
|
4
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# Copyright:: Copyright (C) 2006 Mitsuteru Nakao <n@bioruby.org>
|
5
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# License:: The Ruby License
|
6
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#
|
7
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# $Id:$
|
8
|
+
#
|
9
|
+
|
10
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require 'pathname'
|
11
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+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
|
12
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+
$:.unshift(libpath) unless $:.include?(libpath)
|
13
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+
|
14
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+
|
15
|
+
require 'test/unit'
|
16
|
+
require 'bio/io/fastacmd'
|
17
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+
|
18
|
+
module Bio
|
19
|
+
|
20
|
+
class TestFastacmd < Test::Unit::TestCase
|
21
|
+
|
22
|
+
def setup
|
23
|
+
@obj = Bio::Blast::Fastacmd.new('/dev/null')
|
24
|
+
end
|
25
|
+
|
26
|
+
def test_database
|
27
|
+
assert_equal('/dev/null', @obj.database)
|
28
|
+
end
|
29
|
+
|
30
|
+
def test_fastacmd
|
31
|
+
assert_equal("fastacmd", @obj.fastacmd)
|
32
|
+
end
|
33
|
+
|
34
|
+
def test_methods
|
35
|
+
method_list = [ :get_by_id, :fetch, :each_entry, :each ]
|
36
|
+
method_list.each do |method|
|
37
|
+
assert(@obj.respond_to?(method))
|
38
|
+
end
|
39
|
+
end
|
40
|
+
|
41
|
+
end
|
42
|
+
end
|
@@ -0,0 +1,505 @@
|
|
1
|
+
#
|
2
|
+
# = test/unit/bio/io/test_flatfile.rb - unit test for Bio::FlatFile
|
3
|
+
#
|
4
|
+
# Copyright (C) 2006 Naohisa Goto <ng@bioruby.org>
|
5
|
+
#
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: test_flatfile.rb,v 1.2 2007/04/05 23:35:43 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'pathname'
|
12
|
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
|
13
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
14
|
+
|
15
|
+
require 'test/unit'
|
16
|
+
require 'bio'
|
17
|
+
require 'stringio'
|
18
|
+
|
19
|
+
|
20
|
+
module Bio
|
21
|
+
|
22
|
+
module TestFlatFile
|
23
|
+
|
24
|
+
bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4)).cleanpath.to_s
|
25
|
+
TestDataPath = Pathname.new(File.join(bioruby_root, 'test', 'data')).cleanpath.to_s
|
26
|
+
TestData01 = File.join(TestDataPath, 'fasta', 'example1.txt')
|
27
|
+
|
28
|
+
TestData01Ent1def =
|
29
|
+
"At1g02580 mRNA (2291 bp) UTR's and CDS"
|
30
|
+
TestData01Ent4def =
|
31
|
+
'At1g65300: mRNA 837bp (shortened from start)'
|
32
|
+
TestData01Ent4naseq = Bio::Sequence::NA.new <<__END_OF_SEQ__
|
33
|
+
ttcatctttacctcttcctattgttgcgaatgcagctgcaccagtcg
|
34
|
+
gatttgatggtcctatgtttcaatatcataatcaaaatcagcaaaagccggttcaattccaatatcaggctcttta
|
35
|
+
tgatttttatgatcagattccaaagaaaattcatggttttaatatgaatatgaataaggattcgaatcaaagtatg
|
36
|
+
gttttggatttgaatcaaaatcttaatgatggagaggacgagggcattccttgcatggacaacaacaactaccacc
|
37
|
+
ccgaaatcgattgtctcgctaccgtcaccactgcccccactgatgtttgtgctcctaacatcaccaatgatctcta
|
38
|
+
g
|
39
|
+
__END_OF_SEQ__
|
40
|
+
|
41
|
+
# test Bio::FlatFile class method
|
42
|
+
# class TestFlatFileClassMethod < Test::Unit::TestCase
|
43
|
+
#
|
44
|
+
# def setup
|
45
|
+
# @filename = TestData01
|
46
|
+
# @klass = Bio::FastaFormat
|
47
|
+
# end
|
48
|
+
#
|
49
|
+
# # test template for Bio::FlatFile.open
|
50
|
+
# def open_TestData01(*arg)
|
51
|
+
# assert_instance_of(Bio::FlatFile,
|
52
|
+
# ff = Bio::FlatFile.open(*arg))
|
53
|
+
# assert_equal(@klass, ff.dbclass)
|
54
|
+
# assert_nil(ff.close)
|
55
|
+
# end
|
56
|
+
# private :open_TestData01
|
57
|
+
#
|
58
|
+
# # test template for Bio::FlatFile.open with block
|
59
|
+
# def open_with_block_TestData01(*arg)
|
60
|
+
# ret = Bio::FlatFile.open(*arg) do |ff|
|
61
|
+
# assert_instance_of(Bio::FlatFile, ff)
|
62
|
+
# assert_equal(@klass, ff.dbclass)
|
63
|
+
# ff.each do |e|
|
64
|
+
# assert_instance_of(@klass, e)
|
65
|
+
# assert_instance_of(String, ff.entry_raw)
|
66
|
+
# end
|
67
|
+
# 'test return value'
|
68
|
+
# end
|
69
|
+
# assert_equal('test return value', ret)
|
70
|
+
# end
|
71
|
+
# private :open_with_block_TestData01
|
72
|
+
#
|
73
|
+
# def test_open_0arg
|
74
|
+
# assert_raise(ArgumentError) { Bio::FlatFile.open }
|
75
|
+
# end
|
76
|
+
#
|
77
|
+
# def test_open_1arg_nil
|
78
|
+
# assert_raise(ArgumentError) { Bio::FlatFile.open(nil) }
|
79
|
+
# end
|
80
|
+
#
|
81
|
+
# def test_open_1arg_class
|
82
|
+
# assert_raise(ArgumentError) { Bio::FlatFile.open(Bio::GenBank) }
|
83
|
+
# end
|
84
|
+
#
|
85
|
+
# def test_open_1arg_filename
|
86
|
+
# open_TestData01(@filename)
|
87
|
+
# end
|
88
|
+
#
|
89
|
+
# def test_open_1arg_io
|
90
|
+
# io = File.open(@filename)
|
91
|
+
# open_TestData01(io)
|
92
|
+
# assert(io.closed?)
|
93
|
+
# end
|
94
|
+
#
|
95
|
+
# def test_open_1arg_with_block
|
96
|
+
# open_with_block_TestData01(@filename)
|
97
|
+
# end
|
98
|
+
#
|
99
|
+
# def test_open_1arg_io_with_block
|
100
|
+
# io = File.open(@filename)
|
101
|
+
# open_with_block_TestData01(io)
|
102
|
+
# # When IO object is given, the IO is NOT automatically closed.
|
103
|
+
# assert_equal(false, io.closed?)
|
104
|
+
# assert_nothing_raised { io.close }
|
105
|
+
# end
|
106
|
+
#
|
107
|
+
# def test_open_2arg_autodetect
|
108
|
+
# open_TestData01(nil, @filename)
|
109
|
+
# end
|
110
|
+
#
|
111
|
+
# def test_open_2arg_autodetect_with_block
|
112
|
+
# open_with_block_TestData01(nil, @filename)
|
113
|
+
# end
|
114
|
+
#
|
115
|
+
# def test_open_2arg_autodetect_io
|
116
|
+
# io = File.open(@filename)
|
117
|
+
# open_TestData01(nil, io)
|
118
|
+
# assert(io.closed?)
|
119
|
+
# end
|
120
|
+
#
|
121
|
+
# def test_open_2arg_autodetect_io_with_block
|
122
|
+
# io = File.open(@filename)
|
123
|
+
# open_with_block_TestData01(nil, io)
|
124
|
+
# # When IO object is given, the IO is NOT automatically closed.
|
125
|
+
# assert_equal(false, io.closed?)
|
126
|
+
# assert_nothing_raised { io.close }
|
127
|
+
# end
|
128
|
+
#
|
129
|
+
# def test_open_2arg_class
|
130
|
+
# open_TestData01(@klass, @filename)
|
131
|
+
# end
|
132
|
+
#
|
133
|
+
# def test_open_2arg_class_with_block
|
134
|
+
# open_with_block_TestData01(@klass, @filename)
|
135
|
+
# end
|
136
|
+
#
|
137
|
+
# def test_open_2arg_class_io
|
138
|
+
# io = File.open(@filename)
|
139
|
+
# open_TestData01(@klass, io)
|
140
|
+
# assert(io.closed?)
|
141
|
+
# end
|
142
|
+
#
|
143
|
+
# def test_open_2arg_class_io_with_block
|
144
|
+
# io = File.open(@filename)
|
145
|
+
# open_with_block_TestData01(@klass, io)
|
146
|
+
# # When IO object is given, the IO is NOT automatically closed.
|
147
|
+
# assert_equal(false, io.closed?)
|
148
|
+
# assert_nothing_raised { io.close }
|
149
|
+
# end
|
150
|
+
#
|
151
|
+
# def test_open_2arg_filename_mode
|
152
|
+
# open_TestData01(@filename, 'r')
|
153
|
+
# end
|
154
|
+
#
|
155
|
+
# def test_open_2arg_filename_mode_with_block
|
156
|
+
# open_with_block_TestData01(@filename, 'r')
|
157
|
+
# end
|
158
|
+
#
|
159
|
+
# def test_open_3arg
|
160
|
+
# open_TestData01(nil, @filename, 'r')
|
161
|
+
# open_TestData01(@klass, @filename, 'r')
|
162
|
+
# open_TestData01(@filename, File::RDONLY, 0)
|
163
|
+
# end
|
164
|
+
#
|
165
|
+
# def test_open_3arg_with_block
|
166
|
+
# open_with_block_TestData01(nil, @filename, 'r')
|
167
|
+
# open_with_block_TestData01(@klass, @filename, 'r')
|
168
|
+
# open_with_block_TestData01(@filename, File::RDONLY, 0)
|
169
|
+
# end
|
170
|
+
#
|
171
|
+
# def test_open_4arg
|
172
|
+
# open_TestData01(nil, @filename, File::RDONLY, 0)
|
173
|
+
# open_TestData01(Bio::FastaFormat,
|
174
|
+
# @filename, File::RDONLY, 0)
|
175
|
+
#
|
176
|
+
# open_with_block_TestData01(nil, @filename, File::RDONLY, 0)
|
177
|
+
# open_with_block_TestData01(Bio::FastaFormat,
|
178
|
+
# @filename, File::RDONLY, 0)
|
179
|
+
# end
|
180
|
+
#
|
181
|
+
# # test template for Bio::FlatFile.auto
|
182
|
+
# def auto_TestData01(*arg)
|
183
|
+
# assert_instance_of(Bio::FlatFile,
|
184
|
+
# ff = Bio::FlatFile.auto(*arg))
|
185
|
+
# assert_equal(@klass, ff.dbclass)
|
186
|
+
# assert_nil(ff.close)
|
187
|
+
# end
|
188
|
+
# private :auto_TestData01
|
189
|
+
#
|
190
|
+
# # test template for Bio::FlatFile.auto with block
|
191
|
+
# def auto_with_block_TestData01(*arg)
|
192
|
+
# ret = Bio::FlatFile.auto(*arg) do |ff|
|
193
|
+
# assert_instance_of(Bio::FlatFile, ff)
|
194
|
+
# assert_equal(@klass, ff.dbclass)
|
195
|
+
# ff.each do |e|
|
196
|
+
# assert_instance_of(@klass, e)
|
197
|
+
# assert_instance_of(String, ff.entry_raw)
|
198
|
+
# end
|
199
|
+
# 'test return value'
|
200
|
+
# end
|
201
|
+
# assert_equal('test return value', ret)
|
202
|
+
# end
|
203
|
+
# private :auto_with_block_TestData01
|
204
|
+
#
|
205
|
+
# def test_auto_0arg
|
206
|
+
# assert_raise(ArgumentError) { Bio::FlatFile.auto }
|
207
|
+
# end
|
208
|
+
#
|
209
|
+
# def test_auto_1arg_filename
|
210
|
+
# auto_TestData01(@filename)
|
211
|
+
# end
|
212
|
+
#
|
213
|
+
# def test_auto_1arg_io
|
214
|
+
# io = File.open(@filename)
|
215
|
+
# auto_TestData01(io)
|
216
|
+
# assert(io.closed?)
|
217
|
+
# end
|
218
|
+
#
|
219
|
+
# def test_auto_1arg_with_block
|
220
|
+
# auto_with_block_TestData01(@filename)
|
221
|
+
# end
|
222
|
+
#
|
223
|
+
# def test_auto_1arg_io_with_block
|
224
|
+
# io = File.open(@filename)
|
225
|
+
# auto_with_block_TestData01(io)
|
226
|
+
# # When IO object is given, the IO is NOT automatically closed.
|
227
|
+
# assert_equal(false, io.closed?)
|
228
|
+
# assert_nothing_raised { io.close }
|
229
|
+
# end
|
230
|
+
#
|
231
|
+
# def test_auto_2arg_filename_mode
|
232
|
+
# auto_TestData01(@filename, 'r')
|
233
|
+
# end
|
234
|
+
#
|
235
|
+
# def test_auto_2arg_filename_mode_with_block
|
236
|
+
# auto_with_block_TestData01(@filename, 'r')
|
237
|
+
# end
|
238
|
+
#
|
239
|
+
# def test_auto_3arg
|
240
|
+
# auto_TestData01(@filename, File::RDONLY, 0)
|
241
|
+
# end
|
242
|
+
#
|
243
|
+
# def test_auto_3arg_with_block
|
244
|
+
# auto_with_block_TestData01(@filename, File::RDONLY, 0)
|
245
|
+
# end
|
246
|
+
#
|
247
|
+
# def test_to_a
|
248
|
+
# assert_instance_of(Array,
|
249
|
+
# a = Bio::FlatFile.to_a(@filename))
|
250
|
+
# assert_equal(5, a.size)
|
251
|
+
# assert_instance_of(Bio::FastaFormat, a[3])
|
252
|
+
# assert_equal(TestData01Ent4def,
|
253
|
+
# a[3].definition)
|
254
|
+
#
|
255
|
+
# assert_equal(TestData01Ent4naseq, a[3].naseq)
|
256
|
+
# end
|
257
|
+
#
|
258
|
+
# def test_foreach
|
259
|
+
# Bio::FlatFile.foreach(@filename) do |ent|
|
260
|
+
# assert_instance_of(Bio::FastaFormat, ent)
|
261
|
+
# end
|
262
|
+
# end
|
263
|
+
#
|
264
|
+
# def test_new_2arg_nil
|
265
|
+
# io = File.open(@filename)
|
266
|
+
# assert_instance_of(Bio::FlatFile,
|
267
|
+
# ff = Bio::FlatFile.new(nil, io))
|
268
|
+
# assert_equal(@klass, ff.dbclass)
|
269
|
+
# assert_nil(ff.close)
|
270
|
+
# end
|
271
|
+
#
|
272
|
+
# def test_new_2arg_class
|
273
|
+
# io = File.open(@filename)
|
274
|
+
# assert_instance_of(Bio::FlatFile,
|
275
|
+
# ff = Bio::FlatFile.new(@klass, io))
|
276
|
+
# assert_equal(@klass, ff.dbclass)
|
277
|
+
# assert_nil(ff.close)
|
278
|
+
# end
|
279
|
+
#
|
280
|
+
# end #class TestFlatFileClassMethod
|
281
|
+
#
|
282
|
+
# # test Bio::FlatFile instance methods
|
283
|
+
# class TestFlatFileFastaFormat < Test::Unit::TestCase
|
284
|
+
# def setup
|
285
|
+
# @klass = Bio::FastaFormat
|
286
|
+
# @filename = TestData01
|
287
|
+
# @ff = Bio::FlatFile.open(@klass, @filename)
|
288
|
+
# end
|
289
|
+
#
|
290
|
+
# def test_to_io
|
291
|
+
# assert_instance_of(File, @ff.to_io)
|
292
|
+
# end
|
293
|
+
#
|
294
|
+
# def test_path
|
295
|
+
# assert_equal(@filename, @ff.path)
|
296
|
+
# end
|
297
|
+
#
|
298
|
+
# def test_next_entry
|
299
|
+
# assert_instance_of(@klass, ent = @ff.next_entry)
|
300
|
+
# assert_equal(TestData01Ent1def, ent.definition)
|
301
|
+
# assert_instance_of(@klass, ent = @ff.next_entry)
|
302
|
+
# assert_instance_of(@klass, ent = @ff.next_entry)
|
303
|
+
# assert_instance_of(@klass, ent = @ff.next_entry)
|
304
|
+
# assert_equal(TestData01Ent4def, ent.definition)
|
305
|
+
# assert_equal(TestData01Ent4naseq, ent.naseq)
|
306
|
+
# end
|
307
|
+
#
|
308
|
+
# def test_entry_raw
|
309
|
+
# 4.times { @ff.next_entry }
|
310
|
+
# assert_instance_of(String, str = @ff.entry_raw)
|
311
|
+
# assert_equal(TestData01Ent4def, @klass.new(str).definition)
|
312
|
+
# assert_equal(TestData01Ent4naseq, @klass.new(str).naseq)
|
313
|
+
# end
|
314
|
+
#
|
315
|
+
# def test_entry_pos_flag
|
316
|
+
# # default is nil
|
317
|
+
# assert_equal(nil, @ff.entry_pos_flag)
|
318
|
+
# # set as true
|
319
|
+
# assert_equal(true, @ff.entry_pos_flag = true)
|
320
|
+
# assert_equal(true, @ff.entry_pos_flag)
|
321
|
+
# end
|
322
|
+
#
|
323
|
+
# def test_start_pos_ended_pos_not_recorded
|
324
|
+
# # default is nil
|
325
|
+
# assert_equal(nil, @ff.entry_start_pos)
|
326
|
+
# #
|
327
|
+
# @ff.entry_pos_flag = false
|
328
|
+
# @ff.next_entry
|
329
|
+
# # nil if not recorded
|
330
|
+
# assert_equal(nil, @ff.entry_start_pos)
|
331
|
+
# assert_equal(nil, @ff.entry_ended_pos)
|
332
|
+
# @ff.next_entry
|
333
|
+
# # nil if not recorded
|
334
|
+
# assert_equal(nil, @ff.entry_start_pos)
|
335
|
+
# assert_equal(nil, @ff.entry_ended_pos)
|
336
|
+
# end
|
337
|
+
#
|
338
|
+
# def test_start_pos
|
339
|
+
# @ff.entry_pos_flag = true
|
340
|
+
# @ff.next_entry
|
341
|
+
# assert_equal(0, @ff.entry_start_pos)
|
342
|
+
# @ff.next_entry
|
343
|
+
# # On Windows, the values might be different.
|
344
|
+
# assert_equal(2367, @ff.entry_start_pos)
|
345
|
+
# end
|
346
|
+
#
|
347
|
+
# def test_ended_pos
|
348
|
+
# @ff.entry_pos_flag = true
|
349
|
+
# @ff.next_entry
|
350
|
+
# # On Windows, the values might be different.
|
351
|
+
# assert_equal(2367, @ff.entry_ended_pos)
|
352
|
+
# @ff.next_entry
|
353
|
+
# # On Windows, the values might be different.
|
354
|
+
# assert_equal(3244, @ff.entry_ended_pos)
|
355
|
+
# end
|
356
|
+
#
|
357
|
+
# def test_each_entry
|
358
|
+
# i = 0
|
359
|
+
# @ff.each_entry do |ent|
|
360
|
+
# assert_instance_of(@klass, ent)
|
361
|
+
# i += 1
|
362
|
+
# if i == 4 then
|
363
|
+
# assert_equal(TestData01Ent4def, ent.definition)
|
364
|
+
# assert_equal(TestData01Ent4naseq, ent.naseq)
|
365
|
+
# end
|
366
|
+
# end
|
367
|
+
# end
|
368
|
+
#
|
369
|
+
# # each is an alias of each_entry
|
370
|
+
# def test_each
|
371
|
+
# assert_nothing_raised { @ff.each {} }
|
372
|
+
# end
|
373
|
+
#
|
374
|
+
# def test_rewind
|
375
|
+
# @ff.next_entry
|
376
|
+
# assert_not_equal(0, @ff.pos)
|
377
|
+
# assert_equal(0, @ff.rewind)
|
378
|
+
# assert_equal(0, @ff.pos)
|
379
|
+
# end
|
380
|
+
#
|
381
|
+
# def test_close
|
382
|
+
# assert_nil(@ff.close)
|
383
|
+
# end
|
384
|
+
#
|
385
|
+
# def test_pos
|
386
|
+
# assert_equal(0, @ff.pos)
|
387
|
+
# @ff.next_entry
|
388
|
+
# assert_not_equal(0, @ff.pos)
|
389
|
+
# end
|
390
|
+
#
|
391
|
+
# def test_eof?
|
392
|
+
# 5.times { @ff.next_entry }
|
393
|
+
# assert_equal(true, @ff.eof?)
|
394
|
+
# end
|
395
|
+
#
|
396
|
+
# def test_raw
|
397
|
+
# # default false
|
398
|
+
# assert_equal(false, @ff.raw)
|
399
|
+
# # changes to true
|
400
|
+
# assert_equal(true, @ff.raw = true)
|
401
|
+
# @ff.each do |ent|
|
402
|
+
# assert_instance_of(String, ent)
|
403
|
+
# end
|
404
|
+
# end
|
405
|
+
#
|
406
|
+
# def test_dbclass
|
407
|
+
# assert_equal(@klass, @ff.dbclass)
|
408
|
+
# end
|
409
|
+
#
|
410
|
+
# def test_dbclass_eq
|
411
|
+
# klass = Bio::FastaNumericFormat
|
412
|
+
# assert_equal(klass, @ff.dbclass = klass)
|
413
|
+
# assert_equal(klass, @ff.dbclass)
|
414
|
+
# end
|
415
|
+
#
|
416
|
+
# def test_dbclass_nil
|
417
|
+
# assert_equal(nil, @ff.dbclass = nil)
|
418
|
+
# assert_equal(nil, @ff.dbclass)
|
419
|
+
# assert_raise(Bio::FlatFile::UnknownDataFormatError) { @ff.next_entry }
|
420
|
+
# end
|
421
|
+
#
|
422
|
+
# def test_autodetect
|
423
|
+
# @ff.dbclass = nil
|
424
|
+
# assert_equal(@klass, @ff.autodetect)
|
425
|
+
# assert_equal(@klass, @ff.dbclass)
|
426
|
+
# end
|
427
|
+
#
|
428
|
+
# end #class TestFlatFileFastaFormat
|
429
|
+
#
|
430
|
+
#
|
431
|
+
# class TestFlatFileWithCustomClass < Test::Unit::TestCase
|
432
|
+
#
|
433
|
+
# # very simple parser for tab-separated data
|
434
|
+
# class SimpleFormat
|
435
|
+
# # delimiter needed for flatfile
|
436
|
+
# DELIMITER = RS = nil # nil means no delimiter and reading entire file
|
437
|
+
# def initialize(str)
|
438
|
+
# @data = str.split(/\n/).collect { |x| x.to_s.split(/\t/) }
|
439
|
+
# end
|
440
|
+
# attr_reader :data
|
441
|
+
# end
|
442
|
+
#
|
443
|
+
# def test_simpleformat
|
444
|
+
# testdata = "AAA\tBBB\tCCCCC\tDDDD\n123\t456\n"
|
445
|
+
# testio = StringIO.new(testdata)
|
446
|
+
# Bio::FlatFile.open(SimpleFormat, testio) do |ff|
|
447
|
+
# ff.each do |entry|
|
448
|
+
# assert_equal([ [ 'AAA', 'BBB', 'CCCCC', 'DDDD' ],
|
449
|
+
# [ '123', '456' ] ], entry.data)
|
450
|
+
# end
|
451
|
+
# end
|
452
|
+
# end
|
453
|
+
#
|
454
|
+
# # very simple parser for "//"-separated entries
|
455
|
+
# class SimpleFormat2
|
456
|
+
# # delimiter needed for flatfile
|
457
|
+
# DELIMITER = RS = "//\n" # the end of each entry is "//\n"
|
458
|
+
# def initialize(str)
|
459
|
+
# # very simple parser only to store a text data
|
460
|
+
# @data = str
|
461
|
+
# end
|
462
|
+
# attr_reader :data
|
463
|
+
# end
|
464
|
+
#
|
465
|
+
# def test_simpleformat2
|
466
|
+
# testdata = <<__END_OF_TESTDATA__
|
467
|
+
#test01
|
468
|
+
#This is a test.
|
469
|
+
#//
|
470
|
+
#test02
|
471
|
+
#This is an example.
|
472
|
+
#//
|
473
|
+
#__END_OF_TESTDATA__
|
474
|
+
# a = testdata.split(/(\/\/\n)/)
|
475
|
+
# results = [ a[0]+a[1], a[2]+a[3] ]
|
476
|
+
# testio = StringIO.new(testdata)
|
477
|
+
# Bio::FlatFile.open(SimpleFormat2, testio) do |ff|
|
478
|
+
# ff.each do |entry|
|
479
|
+
# assert_equal(results.shift, entry.data)
|
480
|
+
# end
|
481
|
+
# end
|
482
|
+
# end
|
483
|
+
#
|
484
|
+
# end #class TestFlatFileWithCustomClass
|
485
|
+
|
486
|
+
class TestFlatFileToHashClass < Test::Unit::TestCase
|
487
|
+
def test_default
|
488
|
+
testdata = <<__END_OF_TESTDATA__
|
489
|
+
>entry1
|
490
|
+
ABC
|
491
|
+
>entry2
|
492
|
+
AATA
|
493
|
+
__END_OF_TESTDATA__
|
494
|
+
|
495
|
+
testio = StringIO.new(testdata)
|
496
|
+
|
497
|
+
hash = Bio::FlatFile.open(testio).to_hash
|
498
|
+
|
499
|
+
assert_equal 'ABC', hash['entry1'].seq
|
500
|
+
assert_equal 'AATA', hash['entry2'].seq
|
501
|
+
end
|
502
|
+
end #class TestFlatFileToHashClass
|
503
|
+
end #module TestFlatFile
|
504
|
+
|
505
|
+
end #module Bio
|