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 +1,117 @@
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#
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# test/unit/bio/db/embl/common.rb - Unit test for Bio::EMBL::COMMON module
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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__), ['..'] * 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/common'
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module Bio
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# TestClass EMBLDB Inherited
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class EMBL_API < EMBLDB
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include Bio::EMBLDB::Common
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end
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class TestEMBLCommon < Test::Unit::TestCase
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def setup
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@obj = Bio::EMBLDB::Common
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end
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def test_ac
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assert(@obj.instance_methods.find {|x| x.to_s == 'ac' })
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end
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def test_accessions
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assert(@obj.instance_methods.find {|x| x.to_s == 'accessions' })
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end
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def test_accession
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assert(@obj.instance_methods.find {|x| x.to_s == 'accession' })
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end
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def test_de
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assert(@obj.instance_methods.find {|x| x.to_s == 'de' })
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end
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def test_description
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assert(@obj.instance_methods.find {|x| x.to_s == 'description' })
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end
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def test_definition
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assert(@obj.instance_methods.find {|x| x.to_s == 'definition' })
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end
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def test_os
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assert(@obj.instance_methods.find {|x| x.to_s == 'os' })
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end
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def test_og
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assert(@obj.instance_methods.find {|x| x.to_s == 'og' })
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end
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def test_oc
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assert(@obj.instance_methods.find {|x| x.to_s == 'oc' })
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end
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def test_kw
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assert(@obj.instance_methods.find {|x| x.to_s == 'kw' })
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end
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def test_keywords
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assert(@obj.instance_methods.find {|x| x.to_s == 'keywords' })
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end
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def test_ref
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assert(@obj.instance_methods.find {|x| x.to_s == 'ref' })
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end
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def test_references
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assert(@obj.instance_methods.find {|x| x.to_s == 'references' })
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end
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def test_dr
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assert(@obj.instance_methods.find {|x| x.to_s == 'dr' })
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end
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end
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class TestEMBLAPI < Test::Unit::TestCase
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|
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def setup
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data =<<END
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AC A12345; B23456;
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DE Dummy data for Bio::EMBL::Common APIs.
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OS Ruby Class Library for Bioinformatics (BioRuby) (open-bio).
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OC
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OG
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KW
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R
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DR
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END
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@obj = Bio::EMBL_API.new(data)
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end
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def test_ac
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assert_equal(["A12345", "B23456"], @obj.ac)
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end
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109
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def test_accessions
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assert_equal(["A12345", "B23456"], @obj.accessions)
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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/embl/test_embl.rb - Unit test for Bio::EMBL
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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_embl.rb,v 1.5.2.1 2008/02/20 09:56:22 aerts 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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|
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|
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require 'test/unit'
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require 'bio/db/embl/embl'
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|
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module Bio
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class TestEMBL < Test::Unit::TestCase
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|
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def setup
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22
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bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
|
23
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output = File.open(File.join(bioruby_root, 'test', 'data', 'embl', 'AB090716.embl')).read
|
24
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@obj = Bio::EMBL.new(output)
|
25
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end
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26
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|
27
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def test_id_line
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28
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assert(@obj.id_line)
|
29
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end
|
30
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|
31
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def test_id_line_iterator
|
32
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assert(@obj.id_line {|key, value| })
|
33
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+
end
|
34
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+
|
35
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def test_id_line_entry_name
|
36
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assert_equal('AB090716', @obj.id_line('ENTRY_NAME'))
|
37
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+
end
|
38
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+
|
39
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def test_id_line_data_class
|
40
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assert_equal('standard', @obj.id_line('DATA_CLASS'))
|
41
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+
end
|
42
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+
|
43
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def test_id_line_molecule_type
|
44
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assert_equal('genomic DNA', @obj.id_line('MOLECULE_TYPE'))
|
45
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+
end
|
46
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+
|
47
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def test_id_line_division
|
48
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+
assert_equal('VRT', @obj.id_line('DIVISION'))
|
49
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+
end
|
50
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+
|
51
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def test_id_line_sequence_length
|
52
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assert_equal(166, @obj.id_line('SEQUENCE_LENGTH'))
|
53
|
+
end
|
54
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+
|
55
|
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def test_entry
|
56
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entry_id = 'AB090716'
|
57
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assert_equal(entry_id, @obj.entry)
|
58
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assert_equal(entry_id, @obj.entry_name)
|
59
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assert_equal(entry_id, @obj.entry_id)
|
60
|
+
end
|
61
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|
62
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def test_molecule
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63
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molecule = 'genomic DNA'
|
64
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assert_equal(molecule, @obj.molecule)
|
65
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assert_equal(molecule, @obj.molecule_type)
|
66
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+
end
|
67
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|
68
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def test_division
|
69
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assert_equal('VRT', @obj.division)
|
70
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+
end
|
71
|
+
|
72
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def test_sequence_length
|
73
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seqlen = 166
|
74
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assert_equal(seqlen, @obj.sequence_length)
|
75
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assert_equal(seqlen, @obj.seqlen)
|
76
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+
end
|
77
|
+
|
78
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+
# Bio::EMBLDB::COMMON#ac
|
79
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def test_ac
|
80
|
+
ac = ['AB090716']
|
81
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+
assert_equal(ac, @obj.ac)
|
82
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assert_equal(ac, @obj.accessions)
|
83
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+
end
|
84
|
+
|
85
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# Bio::EMBLDB::COMMON#accession
|
86
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+
def test_accession
|
87
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+
assert_equal('AB090716', @obj.accession)
|
88
|
+
end
|
89
|
+
|
90
|
+
def test_sv
|
91
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+
assert_equal('AB090716.1', @obj.sv)
|
92
|
+
end
|
93
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+
|
94
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+
def test_version
|
95
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+
assert_equal(1, @obj.version)
|
96
|
+
end
|
97
|
+
|
98
|
+
def test_dt
|
99
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+
assert(@obj.dt)
|
100
|
+
end
|
101
|
+
|
102
|
+
def test_dt_iterator
|
103
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+
assert(@obj.dt {|key, value| })
|
104
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+
end
|
105
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+
|
106
|
+
def test_dt_created
|
107
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+
assert_equal('25-OCT-2002 (Rel. 73, Created)', @obj.dt('created'))
|
108
|
+
end
|
109
|
+
|
110
|
+
def test_dt_updated
|
111
|
+
assert_equal('29-NOV-2002 (Rel. 73, Last updated, Version 2)', @obj.dt('updated'))
|
112
|
+
end
|
113
|
+
|
114
|
+
# Bio::EMBLDB::COMMON#de
|
115
|
+
def test_de
|
116
|
+
assert_equal("Haplochromis sp. 'muzu, rukwa' LWS gene for long wavelength-sensitive opsin, partial cds, specimen_voucher:specimen No. HT-9361.", @obj.de)
|
117
|
+
end
|
118
|
+
|
119
|
+
# Bio::EMBLDB::COMMON#kw
|
120
|
+
def test_kw
|
121
|
+
k = []
|
122
|
+
assert_equal([], @obj.kw)
|
123
|
+
assert_equal([], @obj.keywords)
|
124
|
+
end
|
125
|
+
|
126
|
+
def test_os
|
127
|
+
# assert_equal('', @obj.os)
|
128
|
+
assert_raises(RuntimeError) { @obj.os }
|
129
|
+
end
|
130
|
+
|
131
|
+
def test_os_valid
|
132
|
+
@obj.instance_eval { @data['OS'] = "Haplochromis sp. 'muzu rukwa'" }
|
133
|
+
assert_equal("Haplochromis sp. 'muzu rukwa'", @obj.os)
|
134
|
+
end
|
135
|
+
|
136
|
+
# Bio::EMBLDB::COMMON#oc
|
137
|
+
def test_oc
|
138
|
+
assert_equal('Eukaryota', @obj.oc.first)
|
139
|
+
end
|
140
|
+
|
141
|
+
# Bio::EMBLDB::COMMON#og
|
142
|
+
def test_og
|
143
|
+
assert_equal([], @obj.og)
|
144
|
+
end
|
145
|
+
|
146
|
+
# Bio::EMBLDB::COMMON#ref
|
147
|
+
def test_ref
|
148
|
+
assert_equal(2, @obj.ref.size)
|
149
|
+
end
|
150
|
+
|
151
|
+
# Bio::EMBLDB::COMMON#references
|
152
|
+
def test_references
|
153
|
+
assert_equal(Array, @obj.references.class)
|
154
|
+
end
|
155
|
+
|
156
|
+
# Bio::EMBLDB::COMMON#dr
|
157
|
+
def test_dr
|
158
|
+
assert_equal({}, @obj.dr)
|
159
|
+
end
|
160
|
+
|
161
|
+
def test_fh
|
162
|
+
assert_equal('Key Location/Qualifiers', @obj.fh)
|
163
|
+
end
|
164
|
+
|
165
|
+
def test_ft
|
166
|
+
assert_equal(Array, @obj.ft.class)
|
167
|
+
end
|
168
|
+
|
169
|
+
def test_ft_iterator
|
170
|
+
@obj.ft.each do |feature|
|
171
|
+
assert_equal(Bio::Feature, feature.class)
|
172
|
+
end
|
173
|
+
end
|
174
|
+
|
175
|
+
def test_ft_accessor
|
176
|
+
assert_equal('CDS', @obj.ft[1].feature)
|
177
|
+
end
|
178
|
+
|
179
|
+
def test_each_cds
|
180
|
+
@obj.each_cds do |x|
|
181
|
+
assert_equal('CDS', x.feature)
|
182
|
+
end
|
183
|
+
end
|
184
|
+
|
185
|
+
def test_each_gene
|
186
|
+
@obj.each_gene do |x|
|
187
|
+
assert_equal('gene', x.feature)
|
188
|
+
end
|
189
|
+
end
|
190
|
+
|
191
|
+
def test_cc
|
192
|
+
assert_equal('', @obj.cc)
|
193
|
+
end
|
194
|
+
|
195
|
+
# def test_xx
|
196
|
+
# end
|
197
|
+
|
198
|
+
def test_sq
|
199
|
+
data = {"a"=>29, "c"=>42, "ntlen"=>166, "g"=>41, "t"=>54, "other"=>0}
|
200
|
+
assert_equal(data, @obj.sq)
|
201
|
+
end
|
202
|
+
|
203
|
+
def test_sq_get
|
204
|
+
assert_equal(29, @obj.sq("a"))
|
205
|
+
end
|
206
|
+
|
207
|
+
def test_seq
|
208
|
+
seq = 'gttctggcctcatggactgaagacttcctgtggacctgatgtgttcagtggaagtgaagaccctggagtacagtcctacatgattgttctcatgattacttgctgtttcatccccctggctatcatcatcctgtgctaccttgctgtgtggatggccatccgtgct'
|
209
|
+
assert_equal(seq, @obj.seq)
|
210
|
+
assert_equal(seq, @obj.naseq)
|
211
|
+
assert_equal(seq, @obj.ntseq)
|
212
|
+
end
|
213
|
+
end
|
214
|
+
end
|
@@ -0,0 +1,219 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/db/embl/test_embl_rel89.rb - Unit test for Bio::EMBL
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2007 Mitsuteru Nakao <n@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id: test_embl_rel89.rb,v 1.2.2.1 2008/02/20 09:56:22 aerts Exp $
|
8
|
+
#
|
9
|
+
|
10
|
+
require 'pathname'
|
11
|
+
libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
|
12
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
13
|
+
|
14
|
+
|
15
|
+
require 'test/unit'
|
16
|
+
require 'bio/db/embl/embl'
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18
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module Bio
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class TestEMBL89 < 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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output = File.open(File.join(bioruby_root, 'test', 'data', 'embl', 'AB090716.embl.rel89')).read
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@obj = Bio::EMBL.new(output)
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end
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# http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#s_3_4_1
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def test_id_line
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assert(@obj.id_line)
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end
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def test_id_line_iterator
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assert(@obj.id_line {|key, value| })
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end
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35
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def test_id_line_entry_name
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assert_equal('AB090716', @obj.id_line('ENTRY_NAME'))
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end
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40
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def test_id_line_data_class
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assert_equal('STD', @obj.id_line('DATA_CLASS'))
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end
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def test_id_line_sequence_version
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assert_equal('1', @obj.id_line('SEQUENCE_VERSION'))
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end
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48
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def test_id_line_molecule_type
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assert_equal('genomic DNA', @obj.id_line('MOLECULE_TYPE'))
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50
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end
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51
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+
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52
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def test_id_line_division
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assert_equal('VRT', @obj.id_line('DIVISION'))
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end
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55
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+
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56
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def test_id_line_sequence_length
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assert_equal(166, @obj.id_line('SEQUENCE_LENGTH'))
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end
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59
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60
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def test_entry
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entry_id = 'AB090716'
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assert_equal(entry_id, @obj.entry)
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assert_equal(entry_id, @obj.entry_name)
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assert_equal(entry_id, @obj.entry_id)
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end
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66
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+
|
67
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def test_molecule
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molecule = 'genomic DNA'
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assert_equal(molecule, @obj.molecule)
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assert_equal(molecule, @obj.molecule_type)
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end
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+
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73
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def test_division
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assert_equal('VRT', @obj.division)
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75
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+
end
|
76
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+
|
77
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def test_sequence_length
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seqlen = 166
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assert_equal(seqlen, @obj.sequence_length)
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assert_equal(seqlen, @obj.seqlen)
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81
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+
end
|
82
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+
|
83
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# Bio::EMBLDB::COMMON#ac
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84
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def test_ac
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85
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ac = ['AB090716']
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86
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assert_equal(ac, @obj.ac)
|
87
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assert_equal(ac, @obj.accessions)
|
88
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+
end
|
89
|
+
|
90
|
+
# Bio::EMBLDB::COMMON#accession
|
91
|
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def test_accession
|
92
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assert_equal('AB090716', @obj.accession)
|
93
|
+
end
|
94
|
+
|
95
|
+
def test_sv
|
96
|
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assert_equal('AB090716.1', @obj.sv)
|
97
|
+
end
|
98
|
+
|
99
|
+
def test_version
|
100
|
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assert_equal(1, @obj.version)
|
101
|
+
end
|
102
|
+
|
103
|
+
def test_dt
|
104
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assert(@obj.dt)
|
105
|
+
end
|
106
|
+
|
107
|
+
def test_dt_iterator
|
108
|
+
assert(@obj.dt {|key, value| })
|
109
|
+
end
|
110
|
+
|
111
|
+
def test_dt_created
|
112
|
+
assert_equal('25-OCT-2002 (Rel. 73, Created)', @obj.dt('created'))
|
113
|
+
end
|
114
|
+
|
115
|
+
def test_dt_updated
|
116
|
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assert_equal('14-NOV-2006 (Rel. 89, Last updated, Version 3)', @obj.dt('updated'))
|
117
|
+
end
|
118
|
+
|
119
|
+
# Bio::EMBLDB::COMMON#de
|
120
|
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def test_de
|
121
|
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assert_equal("Haplochromis sp. 'muzu, rukwa' LWS gene for long wavelength-sensitive opsin, partial cds, specimen_voucher:specimen No. HT-9361.", @obj.de)
|
122
|
+
end
|
123
|
+
|
124
|
+
# Bio::EMBLDB::COMMON#kw
|
125
|
+
def test_kw
|
126
|
+
k = []
|
127
|
+
assert_equal([], @obj.kw)
|
128
|
+
assert_equal([], @obj.keywords)
|
129
|
+
end
|
130
|
+
|
131
|
+
def test_os
|
132
|
+
# assert_equal('', @obj.os)
|
133
|
+
assert_raises(RuntimeError) { @obj.os }
|
134
|
+
end
|
135
|
+
|
136
|
+
def test_os_valid
|
137
|
+
@obj.instance_eval { @data['OS'] = "Haplochromis sp. 'muzu rukwa'" }
|
138
|
+
assert_equal("Haplochromis sp. 'muzu rukwa'", @obj.os)
|
139
|
+
end
|
140
|
+
|
141
|
+
# Bio::EMBLDB::COMMON#oc
|
142
|
+
def test_oc
|
143
|
+
assert_equal('Eukaryota', @obj.oc.first)
|
144
|
+
end
|
145
|
+
|
146
|
+
# Bio::EMBLDB::COMMON#og
|
147
|
+
def test_og
|
148
|
+
assert_equal([], @obj.og)
|
149
|
+
end
|
150
|
+
|
151
|
+
# Bio::EMBLDB::COMMON#ref
|
152
|
+
def test_ref
|
153
|
+
assert_equal(2, @obj.ref.size)
|
154
|
+
end
|
155
|
+
|
156
|
+
# Bio::EMBLDB::COMMON#references
|
157
|
+
def test_references
|
158
|
+
assert_equal(Array, @obj.references.class)
|
159
|
+
end
|
160
|
+
|
161
|
+
# Bio::EMBLDB::COMMON#dr
|
162
|
+
def test_dr
|
163
|
+
assert_equal({}, @obj.dr)
|
164
|
+
end
|
165
|
+
|
166
|
+
def test_fh
|
167
|
+
assert_equal('Key Location/Qualifiers', @obj.fh)
|
168
|
+
end
|
169
|
+
|
170
|
+
def test_ft
|
171
|
+
assert_equal(Array, @obj.ft.class)
|
172
|
+
end
|
173
|
+
|
174
|
+
def test_ft_iterator
|
175
|
+
@obj.ft.each do |feature|
|
176
|
+
assert_equal(Bio::Feature, feature.class)
|
177
|
+
end
|
178
|
+
end
|
179
|
+
|
180
|
+
def test_ft_accessor
|
181
|
+
assert_equal('CDS', @obj.ft[1].feature)
|
182
|
+
end
|
183
|
+
|
184
|
+
def test_each_cds
|
185
|
+
@obj.each_cds do |x|
|
186
|
+
assert_equal('CDS', x.feature)
|
187
|
+
end
|
188
|
+
end
|
189
|
+
|
190
|
+
def test_each_gene
|
191
|
+
@obj.each_gene do |x|
|
192
|
+
assert_equal('gene', x.feature)
|
193
|
+
end
|
194
|
+
end
|
195
|
+
|
196
|
+
def test_cc
|
197
|
+
assert_equal('', @obj.cc)
|
198
|
+
end
|
199
|
+
|
200
|
+
# def test_xx
|
201
|
+
# end
|
202
|
+
|
203
|
+
def test_sq
|
204
|
+
data = {"a"=>29, "c"=>42, "ntlen"=>166, "g"=>41, "t"=>54, "other"=>0}
|
205
|
+
assert_equal(data, @obj.sq)
|
206
|
+
end
|
207
|
+
|
208
|
+
def test_sq_get
|
209
|
+
assert_equal(29, @obj.sq("a"))
|
210
|
+
end
|
211
|
+
|
212
|
+
def test_seq
|
213
|
+
seq = 'gttctggcctcatggactgaagacttcctgtggacctgatgtgttcagtggaagtgaagaccctggagtacagtcctacatgattgttctcatgattacttgctgtttcatccccctggctatcatcatcctgtgctaccttgctgtgtggatggccatccgtgct'
|
214
|
+
assert_equal(seq, @obj.seq)
|
215
|
+
assert_equal(seq, @obj.naseq)
|
216
|
+
assert_equal(seq, @obj.ntseq)
|
217
|
+
end
|
218
|
+
end
|
219
|
+
end
|