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
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# test/unit/bio/db/test_gff.rb - Unit test for Bio::GFF
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#
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# Copyright:: Copyright (C) 2005, 2008
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# Mitsuteru Nakao <n@bioruby.org>
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# Naohisa Goto <ng@bioruby.org>
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# License:: The Ruby License
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#
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# $Id:$
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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 'digest/sha1'
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require 'bio/db/gff'
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module Bio
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class TestGFF < Test::Unit::TestCase
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def setup
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data = <<END_OF_DATA
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I sgd CEN 151453 151591 . + . CEN "CEN1" ; Note "CEN1\; Chromosome I Centromere"
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I sgd gene 147591 151163 . - . Gene "TFC3" ; Note "transcription factor tau (TFIIIC) subunit 138"
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I sgd gene 147591 151163 . - . Gene "FUN24" ; Note "transcription factor tau (TFIIIC) subunit 138"
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I sgd gene 147591 151163 . - . Gene "TSV115" ; Note "transcription factor tau (TFIIIC) subunit 138"
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I sgd ORF 147591 151163 . - . ORF "YAL001C" ; Note "TFC3\; transcription factor tau (TFIIIC) subunit 138"
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I sgd gene 143998 147528 . + . Gene "VPS8" ; Note "Vps8p is a membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif."
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I sgd gene 143998 147528 . + . Gene "FUN15" ; Note "Vps8p is a membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif."
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I sgd gene 143998 147528 . + . Gene "VPT8" ; Note "Vps8p is a membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif."
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END_OF_DATA
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@obj = Bio::GFF.new(data)
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end
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def test_records
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assert_equal(8, @obj.records.size)
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end
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def test_record_class
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assert_equal(Bio::GFF::Record, @obj.records[0].class)
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end
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end # class TestGFF
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class TestGFFRecord < Test::Unit::TestCase
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def setup
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data =<<END_OF_DATA
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I sgd gene 151453 151591 . + . Gene "CEN1" ; Note "Chromosome I Centromere"
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END_OF_DATA
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@obj = Bio::GFF::Record.new(data)
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end
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def test_seqname
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assert_equal('I', @obj.seqname)
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end
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def test_source
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assert_equal('sgd', @obj.source)
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end
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def test_feature
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assert_equal('gene', @obj.feature)
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end
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def test_start
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assert_equal('151453', @obj.start)
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end
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def test_end
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assert_equal('151591', @obj.end)
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end
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def test_score
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assert_equal('.', @obj.score)
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end
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def test_strand
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assert_equal('+', @obj.strand)
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end
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def test_frame
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assert_equal('.', @obj.frame)
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end
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def test_attributes
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at = {"Note"=>'"Chromosome I Centromere"', "Gene"=>'"CEN1"'}
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assert_equal(at, @obj.attributes)
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end
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def test_comment
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assert_equal(nil, @obj.comment)
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end
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end # class TestGFFRecord
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class TestGFFRecordConstruct < Test::Unit::TestCase
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def setup
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@obj = Bio::GFF.new
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end
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def test_add_seqname
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name = "test"
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record = Bio::GFF::Record.new("")
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record.seqname = name
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@obj.records << record
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assert_equal(name, @obj.records[0].seqname)
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end
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end # class TestGFFRecordConstruct
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class TestGFF2 < Test::Unit::TestCase
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def setup
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data = <<END_OF_DATA
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##gff-version 2
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##date 2008-09-22
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I sgd CEN 151453 151591 . + . CEN "CEN1" ; Note "CEN1; Chromosome I Centromere"
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I sgd gene 147591 151163 . - . Gene "TFC3" ; Note "transcription factor tau (TFIIIC) subunit 138"
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I sgd gene 147591 151163 . - . Gene "FUN24" ; Note "transcription factor tau (TFIIIC) subunit 138"
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I sgd gene 147591 151163 . - . Gene "TSV115" ; Note "transcription factor tau (TFIIIC) subunit 138"
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I sgd ORF 147591 151163 . - . ORF "YAL001C" ; Note "TFC3; transcription factor tau (TFIIIC) subunit 138"
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I sgd gene 143998 147528 . + . Gene "VPS8" ; Note "Vps8p is a membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif."
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I sgd gene 143998 147528 . + . Gene "FUN15" ; Note "Vps8p is a membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif."
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I sgd gene 143998 147528 . + . Gene "VPT8" ; Note "Vps8p is a membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif."
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END_OF_DATA
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@obj = Bio::GFF::GFF2.new(data)
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end
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def test_const_version
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assert_equal(2, Bio::GFF::GFF2::VERSION)
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end
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def test_gff_version
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assert_equal('2', @obj.gff_version)
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end
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def test_metadata_size
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assert_equal(1, @obj.metadata.size)
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end
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def test_metadata
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assert_equal(Bio::GFF::GFF2::MetaData.new('date', '2008-09-22'),
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@obj.metadata[0])
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end
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def test_records_size
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assert_equal(8, @obj.records.size)
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end
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def test_to_s
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str = <<END_OF_DATA
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##gff-version 2
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##date 2008-09-22
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I sgd CEN 151453 151591 . + . CEN CEN1 ; Note "CEN1; Chromosome I Centromere"
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I sgd gene 147591 151163 . - . Gene TFC3 ; Note "transcription factor tau (TFIIIC) subunit 138"
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I sgd gene 147591 151163 . - . Gene FUN24 ; Note "transcription factor tau (TFIIIC) subunit 138"
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I sgd gene 147591 151163 . - . Gene TSV115 ; Note "transcription factor tau (TFIIIC) subunit 138"
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I sgd ORF 147591 151163 . - . ORF YAL001C ; Note "TFC3; transcription factor tau (TFIIIC) subunit 138"
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I sgd gene 143998 147528 . + . Gene VPS8 ; Note "Vps8p is a membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif."
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I sgd gene 143998 147528 . + . Gene FUN15 ; Note "Vps8p is a membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif."
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I sgd gene 143998 147528 . + . Gene VPT8 ; Note "Vps8p is a membrane-associated hydrophilic protein which contains a C-terminal cysteine-rich region that conforms to the H2 variant of the RING finger Zn2+ binding motif."
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END_OF_DATA
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assert_equal(str, @obj.to_s)
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end
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end #class TestGFF2
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class TestGFF2Record < Test::Unit::TestCase
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def setup
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str = "seq1\tBLASTX\tsimilarity\t101\t235\t87.1\t+\t0\tTarget \"HBA_HUMAN\" 11 55 ; E_value 0.0003 ; Align 101 11 ; Align 179 36 ; Comment \"Please ignore this \\\"Comment\\\" attribute; Escape \\x1a\\037 and \\\\\\t\\r\\n\\f\\b\\a\\e\\v; This is test.\" 123 4.56e-34 \"Test for freetext\" ; Note \"\"; Misc IdString; Misc \"free text\"; Misc 5678 "
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@obj = Bio::GFF::GFF2::Record.new(str)
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end
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def test_to_s
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str = "seq1\tBLASTX\tsimilarity\t101\t235\t87.1\t+\t0\tTarget HBA_HUMAN 11 55 ; E_value 0.0003 ; Align 101 11 ; Align 179 36 ; Comment \"Please ignore this \\\"Comment\\\" attribute; Escape \\032\\037 and \\\\\\t\\r\\n\\f\\b\\a\\e\\v; This is test.\" 123 4.56e-34 \"Test for freetext\" ; Note \"\" ; Misc IdString ; Misc \"free text\" ; Misc 5678\n"
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assert_equal(str, @obj.to_s)
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end
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def test_eqeq
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obj2 = Bio::GFF::GFF2::Record.new(@obj.to_s)
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assert_equal(true, @obj == obj2)
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end
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def test_eqeq_false
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obj2 = Bio::GFF::GFF2::Record.new(@obj.to_s)
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obj2.seqname = 'seq2'
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assert_equal(false, @obj == obj2)
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end
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def test_comment_only?
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assert_equal(false, @obj.comment_only?)
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end
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def test_seqname
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assert_equal('seq1', @obj.seqname)
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end
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def test_source
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assert_equal('BLASTX', @obj.source)
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end
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def test_feature
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assert_equal('similarity', @obj.feature)
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end
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def test_start
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assert_equal(101, @obj.start)
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end
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def test_end
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assert_equal(235, @obj.end)
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end
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def test_score
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assert_equal(87.1, @obj.score)
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end
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def test_strand
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assert_equal('+', @obj.strand)
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end
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def test_frame
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assert_equal(0, @obj.frame)
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end
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def test_attributes_to_hash
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hash = {
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'Target' =>
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Bio::GFF::GFF2::Record::Value.new(['HBA_HUMAN', '11', '55']),
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'E_value' => '0.0003',
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'Align' =>
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Bio::GFF::GFF2::Record::Value.new(['101', '11']),
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'Comment' =>
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Bio::GFF::GFF2::Record::Value.new(["Please ignore this \"Comment\" attribute; Escape \x1a\037 and \\\t\r\n\f\b\a\e\v; This is test.", "123", "4.56e-34", "Test for freetext"]),
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'Note' => '',
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'Misc' => 'IdString'
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}
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assert_equal(hash, @obj.attributes_to_hash)
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end
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def test_attributes
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attributes =
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[ [ 'Target',
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Bio::GFF::GFF2::Record::Value.new(['HBA_HUMAN', '11', '55']) ],
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[ 'E_value', '0.0003' ],
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[ 'Align',
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Bio::GFF::GFF2::Record::Value.new(['101', '11']) ],
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[ 'Align',
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Bio::GFF::GFF2::Record::Value.new(['179', '36']) ],
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[ 'Comment',
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Bio::GFF::GFF2::Record::Value.new(["Please ignore this \"Comment\" attribute; Escape \x1a\037 and \\\t\r\n\f\b\a\e\v; This is test.", "123", "4.56e-34", "Test for freetext"]) ],
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[ 'Note', '' ],
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[ 'Misc', 'IdString' ],
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[ 'Misc', 'free text' ],
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[ 'Misc', '5678' ]
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]
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assert_equal(attributes, @obj.attributes)
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end
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def test_attribute
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val_Target = Bio::GFF::GFF2::Record::Value.new(['HBA_HUMAN', '11', '55'])
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assert_equal(val_Target, @obj.attribute('Target'))
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assert_equal('0.0003', @obj.attribute('E_value'))
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val_Align0 = Bio::GFF::GFF2::Record::Value.new(['101', '11'])
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val_Align1 = Bio::GFF::GFF2::Record::Value.new(['179', '36'])
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assert_equal(val_Align0, @obj.attribute('Align'))
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val_Comment = Bio::GFF::GFF2::Record::Value.new(["Please ignore this \"Comment\" attribute; Escape \x1a\037 and \\\t\r\n\f\b\a\e\v; This is test.", "123", "4.56e-34", "Test for freetext"])
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assert_equal(val_Comment, @obj.attribute('Comment'))
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assert_equal('', @obj.attribute('Note'))
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assert_equal('IdString', @obj.attribute('Misc'))
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end
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def test_attribute_nonexistent
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assert_equal(nil, @obj.attribute('NonExistent'))
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end
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def test_get_attribute
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val_Target = Bio::GFF::GFF2::Record::Value.new(['HBA_HUMAN', '11', '55'])
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assert_equal(val_Target, @obj.get_attribute('Target'))
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assert_equal('0.0003', @obj.get_attribute('E_value'))
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val_Align0 = Bio::GFF::GFF2::Record::Value.new(['101', '11'])
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+
val_Align1 = Bio::GFF::GFF2::Record::Value.new(['179', '36'])
|
287
|
+
assert_equal(val_Align0, @obj.get_attribute('Align'))
|
288
|
+
val_Comment = Bio::GFF::GFF2::Record::Value.new(["Please ignore this \"Comment\" attribute; Escape \x1a\037 and \\\t\r\n\f\b\a\e\v; This is test.", "123", "4.56e-34", "Test for freetext"])
|
289
|
+
assert_equal(val_Comment, @obj.get_attribute('Comment'))
|
290
|
+
assert_equal('', @obj.get_attribute('Note'))
|
291
|
+
assert_equal('IdString', @obj.get_attribute('Misc'))
|
292
|
+
end
|
293
|
+
|
294
|
+
def test_get_attribute_nonexistent
|
295
|
+
assert_equal(nil, @obj.get_attribute('NonExistent'))
|
296
|
+
end
|
297
|
+
|
298
|
+
def test_get_attributes
|
299
|
+
val_Target = Bio::GFF::GFF2::Record::Value.new(['HBA_HUMAN', '11', '55'])
|
300
|
+
assert_equal([ val_Target ], @obj.get_attributes('Target'))
|
301
|
+
assert_equal([ '0.0003' ], @obj.get_attributes('E_value'))
|
302
|
+
val_Align0 = Bio::GFF::GFF2::Record::Value.new(['101', '11'])
|
303
|
+
val_Align1 = Bio::GFF::GFF2::Record::Value.new(['179', '36'])
|
304
|
+
assert_equal([ val_Align0, val_Align1 ],
|
305
|
+
@obj.get_attributes('Align'))
|
306
|
+
val_Comment = Bio::GFF::GFF2::Record::Value.new(["Please ignore this \"Comment\" attribute; Escape \x1a\037 and \\\t\r\n\f\b\a\e\v; This is test.", "123", "4.56e-34", "Test for freetext"])
|
307
|
+
assert_equal([ val_Comment ], @obj.get_attributes('Comment'))
|
308
|
+
assert_equal([ '' ], @obj.get_attributes('Note'))
|
309
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
310
|
+
@obj.get_attributes('Misc'))
|
311
|
+
end
|
312
|
+
|
313
|
+
def test_get_attributes_nonexistent
|
314
|
+
assert_equal([], @obj.get_attributes('NonExistent'))
|
315
|
+
end
|
316
|
+
|
317
|
+
def test_set_attribute
|
318
|
+
assert_equal('0.0003', @obj.attribute('E_value'))
|
319
|
+
assert_equal('1e-10', @obj.set_attribute('E_value', '1e-10'))
|
320
|
+
assert_equal('1e-10', @obj.attribute('E_value'))
|
321
|
+
end
|
322
|
+
|
323
|
+
def test_set_attribute_multiple
|
324
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
325
|
+
@obj.get_attributes('Misc'))
|
326
|
+
assert_equal('Replaced',
|
327
|
+
@obj.set_attribute('Misc', 'Replaced'))
|
328
|
+
assert_equal([ 'Replaced', 'free text', '5678' ],
|
329
|
+
@obj.get_attributes('Misc'))
|
330
|
+
end
|
331
|
+
|
332
|
+
def test_set_attribute_nonexistent
|
333
|
+
assert_equal(nil, @obj.attribute('NonExistent'))
|
334
|
+
assert_equal('test', @obj.set_attribute('NonExistent', 'test'))
|
335
|
+
assert_equal('test', @obj.attribute('NonExistent'))
|
336
|
+
end
|
337
|
+
|
338
|
+
def test_replace_attributes
|
339
|
+
assert_equal([ '0.0003' ], @obj.get_attributes('E_value'))
|
340
|
+
assert_equal(@obj, @obj.replace_attributes('E_value', '1e-10'))
|
341
|
+
assert_equal([ '1e-10' ], @obj.get_attributes('E_value'))
|
342
|
+
end
|
343
|
+
|
344
|
+
def test_replace_attributes_single_multiple
|
345
|
+
assert_equal([ '0.0003' ], @obj.get_attributes('E_value'))
|
346
|
+
assert_equal(@obj, @obj.replace_attributes('E_value',
|
347
|
+
'1e-10', '3.14', '2.718'))
|
348
|
+
assert_equal([ '1e-10', '3.14', '2.718' ],
|
349
|
+
@obj.get_attributes('E_value'))
|
350
|
+
end
|
351
|
+
|
352
|
+
def test_replace_attributes_multiple_single
|
353
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
354
|
+
@obj.get_attributes('Misc'))
|
355
|
+
assert_equal(@obj,
|
356
|
+
@obj.replace_attributes('Misc', 'Replaced_All'))
|
357
|
+
assert_equal([ 'Replaced_All' ],
|
358
|
+
@obj.get_attributes('Misc'))
|
359
|
+
end
|
360
|
+
|
361
|
+
def test_replace_attributes_multiple_multiple_two
|
362
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
363
|
+
@obj.get_attributes('Misc'))
|
364
|
+
assert_equal(@obj,
|
365
|
+
@obj.replace_attributes('Misc',
|
366
|
+
'Replaced', 'test2'))
|
367
|
+
assert_equal([ 'Replaced', 'test2' ],
|
368
|
+
@obj.get_attributes('Misc'))
|
369
|
+
end
|
370
|
+
|
371
|
+
def test_replace_attributes_multiple_multiple_same
|
372
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
373
|
+
@obj.get_attributes('Misc'))
|
374
|
+
assert_equal(@obj,
|
375
|
+
@obj.replace_attributes('Misc',
|
376
|
+
'Replaced', 'test2', 'test3'))
|
377
|
+
assert_equal([ 'Replaced', 'test2', 'test3' ],
|
378
|
+
@obj.get_attributes('Misc'))
|
379
|
+
end
|
380
|
+
|
381
|
+
def test_replace_attributes_multiple_multiple_over
|
382
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
383
|
+
@obj.get_attributes('Misc'))
|
384
|
+
assert_equal(@obj,
|
385
|
+
@obj.replace_attributes('Misc',
|
386
|
+
'Replaced', 'test2', 'test3', '4'))
|
387
|
+
assert_equal([ 'Replaced', 'test2', 'test3', '4' ],
|
388
|
+
@obj.get_attributes('Misc'))
|
389
|
+
end
|
390
|
+
|
391
|
+
def test_replace_attributes_nonexistent
|
392
|
+
assert_equal(nil, @obj.attribute('NonExistent'))
|
393
|
+
assert_equal(@obj, @obj.replace_attributes('NonExistent', 'test'))
|
394
|
+
assert_equal([ 'test' ], @obj.get_attributes('NonExistent'))
|
395
|
+
end
|
396
|
+
|
397
|
+
def test_replace_attributes_nonexistent_multiple
|
398
|
+
assert_equal(nil, @obj.attribute('NonExistent'))
|
399
|
+
assert_equal(@obj,
|
400
|
+
@obj.replace_attributes('NonExistent',
|
401
|
+
'test', 'gff2', 'attr'))
|
402
|
+
assert_equal([ 'test', 'gff2', 'attr' ],
|
403
|
+
@obj.get_attributes('NonExistent'))
|
404
|
+
end
|
405
|
+
|
406
|
+
def test_delete_attribute
|
407
|
+
assert_equal('0.0003', @obj.attribute('E_value'))
|
408
|
+
assert_equal('0.0003', @obj.delete_attribute('E_value', '0.0003'))
|
409
|
+
assert_equal(nil, @obj.attribute('E_value'))
|
410
|
+
end
|
411
|
+
|
412
|
+
def test_delete_attribute_nil
|
413
|
+
assert_equal('0.0003', @obj.attribute('E_value'))
|
414
|
+
assert_equal(nil, @obj.delete_attribute('E_value', '3'))
|
415
|
+
assert_equal('0.0003', @obj.attribute('E_value'))
|
416
|
+
end
|
417
|
+
|
418
|
+
def test_delete_attribute_multiple
|
419
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
420
|
+
@obj.get_attributes('Misc'))
|
421
|
+
assert_equal('free text',
|
422
|
+
@obj.delete_attribute('Misc', 'free text'))
|
423
|
+
assert_equal([ 'IdString', '5678' ],
|
424
|
+
@obj.get_attributes('Misc'))
|
425
|
+
end
|
426
|
+
|
427
|
+
def test_delete_attribute_multiple2
|
428
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
429
|
+
@obj.get_attributes('Misc'))
|
430
|
+
assert_equal('IdString',
|
431
|
+
@obj.delete_attribute('Misc', 'IdString'))
|
432
|
+
assert_equal([ 'free text', '5678' ],
|
433
|
+
@obj.get_attributes('Misc'))
|
434
|
+
assert_equal('5678',
|
435
|
+
@obj.delete_attribute('Misc', '5678'))
|
436
|
+
assert_equal([ 'free text' ],
|
437
|
+
@obj.get_attributes('Misc'))
|
438
|
+
end
|
439
|
+
|
440
|
+
def test_delete_attribute_multiple_nil
|
441
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
442
|
+
@obj.get_attributes('Misc'))
|
443
|
+
assert_equal(nil,
|
444
|
+
@obj.delete_attribute('Misc', 'test'))
|
445
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
446
|
+
@obj.get_attributes('Misc'))
|
447
|
+
end
|
448
|
+
|
449
|
+
def test_delete_attribute_nonexistent
|
450
|
+
assert_equal(nil, @obj.attribute('NonExistent'))
|
451
|
+
assert_equal(nil, @obj.delete_attribute('NonExistent', 'test'))
|
452
|
+
assert_equal([], @obj.get_attributes('NonExistent'))
|
453
|
+
end
|
454
|
+
|
455
|
+
def test_delete_attributes
|
456
|
+
assert_equal('0.0003', @obj.attribute('E_value'))
|
457
|
+
assert_equal(@obj, @obj.delete_attributes('E_value'))
|
458
|
+
assert_equal(nil, @obj.attribute('E_value'))
|
459
|
+
end
|
460
|
+
|
461
|
+
def test_delete_attributes_multiple
|
462
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
463
|
+
@obj.get_attributes('Misc'))
|
464
|
+
assert_equal(@obj, @obj.delete_attributes('Misc'))
|
465
|
+
assert_equal([], @obj.get_attributes('Misc'))
|
466
|
+
end
|
467
|
+
|
468
|
+
def test_delete_attributes_nonexistent
|
469
|
+
assert_equal(nil, @obj.attribute('NonExistent'))
|
470
|
+
assert_equal(nil, @obj.delete_attributes('NonExistent'))
|
471
|
+
assert_equal([], @obj.get_attributes('NonExistent'))
|
472
|
+
end
|
473
|
+
|
474
|
+
def test_sort_attributes_by_tag!
|
475
|
+
tags = %w( Comment Align E_value Note )
|
476
|
+
assert_equal(@obj, @obj.sort_attributes_by_tag!(tags))
|
477
|
+
assert_equal(%w( Comment Align Align E_value Note Target
|
478
|
+
Misc Misc Misc ),
|
479
|
+
@obj.attributes.collect { |x| x[0] })
|
480
|
+
# check if the order of 'Misc' is not changed
|
481
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
482
|
+
@obj.get_attributes('Misc'))
|
483
|
+
end
|
484
|
+
|
485
|
+
def test_sort_attributes_by_tag_bang_test2
|
486
|
+
tags = %w( E_value Misc Note Target )
|
487
|
+
assert_equal(@obj, @obj.sort_attributes_by_tag!(tags))
|
488
|
+
assert_equal(%w( E_value Misc Misc Misc Note Target
|
489
|
+
Align Align Comment ),
|
490
|
+
@obj.attributes.collect { |x| x[0] })
|
491
|
+
# check if the order of 'Misc' is not changed
|
492
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
493
|
+
@obj.get_attributes('Misc'))
|
494
|
+
end
|
495
|
+
|
496
|
+
def test_sort_attributes_by_tag_bang_with_block
|
497
|
+
assert_equal(@obj,
|
498
|
+
@obj.sort_attributes_by_tag! { |x, y|
|
499
|
+
x <=> y
|
500
|
+
})
|
501
|
+
assert_equal(%w( Align Align Comment E_value Misc Misc Misc
|
502
|
+
Note Target ),
|
503
|
+
@obj.attributes.collect { |x| x[0] })
|
504
|
+
# check if the order of 'Misc' is not changed
|
505
|
+
assert_equal([ 'IdString', 'free text', '5678' ],
|
506
|
+
@obj.get_attributes('Misc'))
|
507
|
+
end
|
508
|
+
end #class TestGFF2Record
|
509
|
+
|
510
|
+
class TestGFF2RecordEmpty < Test::Unit::TestCase
|
511
|
+
def setup
|
512
|
+
@obj = Bio::GFF::GFF2::Record.new('# test comment')
|
513
|
+
end
|
514
|
+
|
515
|
+
def test_comment_only?
|
516
|
+
assert_equal(true, @obj.comment_only?)
|
517
|
+
end
|
518
|
+
|
519
|
+
def test_comment_only_false
|
520
|
+
@obj.seqname = 'test'
|
521
|
+
assert_equal(false, @obj.comment_only?)
|
522
|
+
end
|
523
|
+
|
524
|
+
def test_to_s
|
525
|
+
assert_equal("# test comment\n", @obj.to_s)
|
526
|
+
end
|
527
|
+
|
528
|
+
def test_to_s_not_empty
|
529
|
+
@obj.seqname = 'test'
|
530
|
+
@obj.feature = 'region'
|
531
|
+
@obj.start = 1
|
532
|
+
@obj.end = 100
|
533
|
+
assert_equal("test\t.\tregion\t1\t100\t.\t.\t.\t\t# test comment\n",
|
534
|
+
@obj.to_s)
|
535
|
+
@obj.add_attribute('Gene', 'unknown')
|
536
|
+
assert_equal("test\t.\tregion\t1\t100\t.\t.\t.\tGene unknown\t# test comment\n",
|
537
|
+
@obj.to_s)
|
538
|
+
end
|
539
|
+
|
540
|
+
def test_comment
|
541
|
+
assert_equal(' test comment', @obj.comment)
|
542
|
+
end
|
543
|
+
|
544
|
+
def test_comment_eq
|
545
|
+
assert_equal('changed the comment',
|
546
|
+
@obj.comment = 'changed the comment')
|
547
|
+
end
|
548
|
+
end #class TestGFF2RecordEmpty
|
549
|
+
|
550
|
+
class TestGFF2ComplexAttributes < Test::Unit::TestCase
|
551
|
+
|
552
|
+
# The test string comes from the Popular genome annotation from the JGI.
|
553
|
+
# ftp://ftp.jgi-psf.org/pub/JGI_data/Poplar/annotation/v1.1/Poptr1_1.JamboreeModels.gff.gz
|
554
|
+
# Thanks to Tomoaki NISHIYAMA who picks up the example line.
|
555
|
+
def test_attributes_case1
|
556
|
+
str = "LG_I\tJGI\tCDS\t11052\t11064\t.\t-\t0\tname \"grail3.0116000101\"; proteinId 639579; exonNumber 3\n"
|
557
|
+
|
558
|
+
attributes = [
|
559
|
+
[ "name", "grail3.0116000101" ],
|
560
|
+
[ "proteinId", "639579" ],
|
561
|
+
[ "exonNumber", "3" ]
|
562
|
+
]
|
563
|
+
record = Bio::GFF::GFF2::Record.new(str)
|
564
|
+
assert_equal(attributes, record.attributes)
|
565
|
+
end
|
566
|
+
|
567
|
+
# The test string is modified from that of test_attributes_case1.
|
568
|
+
def test_attributes_case2
|
569
|
+
str = "LG_I\tJGI\tCDS\t11052\t11064\t.\t-\t0\tname \"grail3.0116000101\"; proteinId 639579; exonNumber 3; Note \"Semicolons ; and \;, and quote \\\" can be OK\"; Comment \"This is the \\\"comment\\\"\"\n"
|
570
|
+
|
571
|
+
attributes = [
|
572
|
+
[ "name", "grail3.0116000101" ],
|
573
|
+
[ "proteinId", "639579" ],
|
574
|
+
[ "exonNumber", "3" ],
|
575
|
+
[ "Note", "Semicolons ; and ;, and quote \" can be OK" ],
|
576
|
+
[ "Comment", "This is the \"comment\"" ]
|
577
|
+
]
|
578
|
+
record = Bio::GFF::GFF2::Record.new(str)
|
579
|
+
assert_equal(attributes, record.attributes)
|
580
|
+
end
|
581
|
+
|
582
|
+
def test_attributes_incompatible_backslash_semicolon
|
583
|
+
# No special treatments for backslash-semicolon outside the free text.
|
584
|
+
str =<<END_OF_DATA
|
585
|
+
I sgd gene 151453 151591 . + . Gene "CEN1" ; Note "Chromosome I Centromere"; Semicolon a "b;c" d "e;f;g" h; Illegal a\\;b c d; Comment "a ; b"
|
586
|
+
END_OF_DATA
|
587
|
+
|
588
|
+
attributes = [
|
589
|
+
[ 'Gene', 'CEN1' ],
|
590
|
+
[ 'Note', 'Chromosome I Centromere' ],
|
591
|
+
[ 'Semicolon',
|
592
|
+
Bio::GFF::GFF2::Record::Value.new(['a', 'b;c', 'd', 'e;f;g', 'h']) ],
|
593
|
+
[ 'Illegal', "a\\" ],
|
594
|
+
[ 'b', Bio::GFF::GFF2::Record::Value.new(['c', 'd']) ],
|
595
|
+
[ 'Comment', 'a ; b' ]
|
596
|
+
]
|
597
|
+
record = Bio::GFF::GFF2::Record.new(str)
|
598
|
+
assert_equal(attributes, record.attributes)
|
599
|
+
end
|
600
|
+
|
601
|
+
end #class TestGFF2ComplexAttributes
|
602
|
+
|
603
|
+
class TestGFF2MetaData < Test::Unit::TestCase
|
604
|
+
def setup
|
605
|
+
@data =
|
606
|
+
Bio::GFF::GFF2::MetaData.new('date', '2008-09-22')
|
607
|
+
end
|
608
|
+
|
609
|
+
def test_parse
|
610
|
+
assert_equal(@data,
|
611
|
+
Bio::GFF::GFF2::MetaData.parse('##date 2008-09-22'))
|
612
|
+
end
|
613
|
+
|
614
|
+
def test_directive
|
615
|
+
assert_equal('date', @data.directive)
|
616
|
+
end
|
617
|
+
|
618
|
+
def test_data
|
619
|
+
assert_equal('2008-09-22', @data.data)
|
620
|
+
end
|
621
|
+
end #class TestGFF2MetaData
|
622
|
+
|
623
|
+
class TestGFF3 < Test::Unit::TestCase
|
624
|
+
def setup
|
625
|
+
@data =<<END_OF_DATA
|
626
|
+
##gff-version 3
|
627
|
+
##sequence-region test01 1 400
|
628
|
+
test01 RANDOM contig 1 400 . + . ID=test01;Note=this is test
|
629
|
+
test01 . mRNA 101 230 . + . ID=mrna01;Name=testmRNA;Note=this is test mRNA
|
630
|
+
test01 . mRNA 101 280 . + . ID=mrna01a;Name=testmRNAalterative;Note=test of alternative splicing variant
|
631
|
+
test01 . exon 101 160 . + . ID=exon01;Name=exon01;Alias=exon 1;Parent=mrna01,mrna01a
|
632
|
+
test01 . exon 201 230 . + . ID=exon02;Name=exon02;Alias=exon 2;Parent=mrna01
|
633
|
+
test01 . exon 251 280 . + . ID=exon02a;Name=exon02a;Alias=exon 2a;Parent=mrna01a
|
634
|
+
test01 . Match 101 123 . . . ID=match01;Name=match01;Target=EST101 1 21;Gap=M8 D3 M6 I1 M6
|
635
|
+
##FASTA
|
636
|
+
>test01
|
637
|
+
ACGAAGATTTGTATGACTGATTTATCCTGGACAGGCATTGGTCAGATGTCTCCTTCCGTATCGTCGTTTA
|
638
|
+
GTTGCAAATCCGAGTGTTCGGGGGTATTGCTATTTGCCACCTAGAAGCGCAACATGCCCAGCTTCACACA
|
639
|
+
CCATAGCGAACACGCCGCCCCGGTGGCGACTATCGGTCGAAGTTAAGACAATTCATGGGCGAAACGAGAT
|
640
|
+
AATGGGTACTGCACCCCTCGTCCTGTAGAGACGTCACAGCCAACGTGCCTTCTTATCTTGATACATTAGT
|
641
|
+
GCCCAAGAATGCGATCCCAGAAGTCTTGGTTCTAAAGTCGTCGGAAAGATTTGAGGAACTGCCATACAGC
|
642
|
+
CCGTGGGTGAAACTGTCGACATCCATTGTGCGAATAGGCCTGCTAGTGAC
|
643
|
+
END_OF_DATA
|
644
|
+
@gff3 = Bio::GFF::GFF3.new(@data)
|
645
|
+
end
|
646
|
+
|
647
|
+
def test_const_version
|
648
|
+
assert_equal(3, Bio::GFF::GFF3::VERSION)
|
649
|
+
end
|
650
|
+
|
651
|
+
def test_sequence_regions
|
652
|
+
region = Bio::GFF::GFF3::SequenceRegion.new('test01', 1, 400)
|
653
|
+
assert_equal([ region ], @gff3.sequence_regions)
|
654
|
+
end
|
655
|
+
|
656
|
+
def test_gff_version
|
657
|
+
assert_equal('3', @gff3.gff_version)
|
658
|
+
end
|
659
|
+
|
660
|
+
def test_records
|
661
|
+
assert_equal(7, @gff3.records.size)
|
662
|
+
r_test01 = Bio::GFF::GFF3::Record.new('test01',
|
663
|
+
'RANDOM',
|
664
|
+
'contig',
|
665
|
+
1, 400, nil, '+', nil,
|
666
|
+
[ ['ID', 'test01'],
|
667
|
+
['Note', 'this is test'] ])
|
668
|
+
r_mrna01 = Bio::GFF::GFF3::Record.new('test01',
|
669
|
+
nil,
|
670
|
+
'mRNA',
|
671
|
+
101, 230, nil, '+', nil,
|
672
|
+
[ ['ID', 'mrna01'],
|
673
|
+
['Name', 'testmRNA'],
|
674
|
+
['Note', 'this is test mRNA'] ])
|
675
|
+
r_exon01 = Bio::GFF::GFF3::Record.new('test01',
|
676
|
+
nil,
|
677
|
+
'exon',
|
678
|
+
101, 160, nil, '+', nil,
|
679
|
+
[ ['ID', 'exon01'],
|
680
|
+
['Name', 'exon01'],
|
681
|
+
['Alias', 'exon 1'],
|
682
|
+
['Parent', 'mrna01'],
|
683
|
+
['Parent', 'mrna01a'] ])
|
684
|
+
|
685
|
+
target = Bio::GFF::GFF3::Record::Target.new('EST101', 1, 21)
|
686
|
+
gap = Bio::GFF::GFF3::Record::Gap.new('M8 D3 M6 I1 M6')
|
687
|
+
r_match01 =Bio::GFF::GFF3::Record.new('test01',
|
688
|
+
nil,
|
689
|
+
'Match',
|
690
|
+
101, 123, nil, nil, nil,
|
691
|
+
[ ['ID', 'match01'],
|
692
|
+
['Name', 'match01'],
|
693
|
+
['Target', target],
|
694
|
+
['Gap', gap] ])
|
695
|
+
assert_equal(r_test01, @gff3.records[0])
|
696
|
+
assert_equal(r_mrna01, @gff3.records[1])
|
697
|
+
assert_equal(r_exon01, @gff3.records[3])
|
698
|
+
assert_equal(r_match01, @gff3.records[6])
|
699
|
+
end
|
700
|
+
|
701
|
+
def test_sequences
|
702
|
+
assert_equal(1, @gff3.sequences.size)
|
703
|
+
assert_equal('test01', @gff3.sequences[0].entry_id)
|
704
|
+
assert_equal('3510a3c4f66f9c2ab8d4d97446490aced7ed1fa4',
|
705
|
+
Digest::SHA1.hexdigest(@gff3.sequences[0].seq.to_s))
|
706
|
+
end
|
707
|
+
|
708
|
+
def test_to_s
|
709
|
+
assert_equal(@data, @gff3.to_s)
|
710
|
+
end
|
711
|
+
|
712
|
+
end #class TestGFF3
|
713
|
+
|
714
|
+
class TestGFF3Record < Test::Unit::TestCase
|
715
|
+
|
716
|
+
def setup
|
717
|
+
data =<<END_OF_DATA
|
718
|
+
chrI SGD centromere 151467 151584 . + . ID=CEN1;Name=CEN1;gene=CEN1;Alias=CEN1,test%3B0001;Note=Chromosome%20I%20centromere;dbxref=SGD:S000006463;Target=test%2002 123 456 -,test%2C03 159 314;memo%3Dtest%3Battr=99.9%25%09match
|
719
|
+
END_OF_DATA
|
720
|
+
@obj = Bio::GFF::GFF3::Record.new(data)
|
721
|
+
end
|
722
|
+
|
723
|
+
def test_seqname
|
724
|
+
assert_equal('chrI', @obj.seqname)
|
725
|
+
end
|
726
|
+
|
727
|
+
def test_source
|
728
|
+
assert_equal('SGD', @obj.source)
|
729
|
+
end
|
730
|
+
|
731
|
+
def test_feature
|
732
|
+
assert_equal('centromere', @obj.feature)
|
733
|
+
end
|
734
|
+
|
735
|
+
def test_start
|
736
|
+
assert_equal(151467, @obj.start)
|
737
|
+
end
|
738
|
+
|
739
|
+
def test_end
|
740
|
+
assert_equal(151584, @obj.end)
|
741
|
+
end
|
742
|
+
|
743
|
+
def test_score
|
744
|
+
assert_equal(nil, @obj.score)
|
745
|
+
end
|
746
|
+
|
747
|
+
def test_strand
|
748
|
+
assert_equal('+', @obj.strand)
|
749
|
+
end
|
750
|
+
|
751
|
+
def test_frame
|
752
|
+
assert_equal(nil, @obj.frame)
|
753
|
+
end
|
754
|
+
|
755
|
+
def test_attributes
|
756
|
+
attr = [
|
757
|
+
['ID', 'CEN1'],
|
758
|
+
['Name', 'CEN1'],
|
759
|
+
['gene', 'CEN1'],
|
760
|
+
['Alias', 'CEN1'],
|
761
|
+
['Alias', 'test;0001'],
|
762
|
+
['Note', 'Chromosome I centromere'],
|
763
|
+
['dbxref', 'SGD:S000006463'],
|
764
|
+
['Target',
|
765
|
+
Bio::GFF::GFF3::Record::Target.new('test 02', 123, 456, '-')],
|
766
|
+
['Target',
|
767
|
+
Bio::GFF::GFF3::Record::Target.new('test,03', 159, 314)],
|
768
|
+
['memo=test;attr', "99.9%\tmatch"]
|
769
|
+
]
|
770
|
+
assert_equal(attr, @obj.attributes)
|
771
|
+
end
|
772
|
+
|
773
|
+
def test_to_s
|
774
|
+
str =<<END_OF_DATA
|
775
|
+
chrI SGD centromere 151467 151584 . + . ID=CEN1;Name=CEN1;gene=CEN1;Alias=CEN1,test%3B0001;Note=Chromosome I centromere;dbxref=SGD:S000006463;Target=test%2002 123 456 -,test%2C03 159 314;memo%3Dtest%3Battr=99.9%25%09match
|
776
|
+
END_OF_DATA
|
777
|
+
assert_equal(str, @obj.to_s)
|
778
|
+
end
|
779
|
+
|
780
|
+
def test_to_s_attr_order_changed
|
781
|
+
str = <<END_OF_STR
|
782
|
+
chrI SGD centromere 151467 151584 . + . ID=CEN1;Name=CEN1;Alias=CEN1,test%3B0001;Target=test%2002 123 456 -,test%2C03 159 314;Note=Chromosome I centromere;dbxref=SGD:S000006463;gene=CEN1;memo%3Dtest%3Battr=99.9%25%09match
|
783
|
+
END_OF_STR
|
784
|
+
|
785
|
+
keys = [ 'ID', 'Name', 'Alias', 'Target', 'Note', 'dbxref', 'gene' ]
|
786
|
+
@obj.sort_attributes_by_tag!(keys)
|
787
|
+
assert_equal(str, @obj.to_s)
|
788
|
+
end
|
789
|
+
end #class TestGFF3Record
|
790
|
+
|
791
|
+
class TestGFF3RecordMisc < Test::Unit::TestCase
|
792
|
+
def test_attributes_none
|
793
|
+
# test blank with tab
|
794
|
+
data =<<END_OF_DATA
|
795
|
+
I sgd gene 151453 151591 . + .
|
796
|
+
END_OF_DATA
|
797
|
+
obj = Bio::GFF::GFF3::Record.new(data)
|
798
|
+
assert_equal([], obj.attributes)
|
799
|
+
|
800
|
+
# test blank with no tab at end
|
801
|
+
data =<<END_OF_DATA
|
802
|
+
I sgd gene 151453 151591 . + .
|
803
|
+
END_OF_DATA
|
804
|
+
obj = Bio::GFF::GFF3::Record.new(data)
|
805
|
+
assert_equal([], obj.attributes)
|
806
|
+
end
|
807
|
+
|
808
|
+
def test_attributes_one
|
809
|
+
data =<<END_OF_DATA
|
810
|
+
I sgd gene 151453 151591 . + . ID=CEN1
|
811
|
+
END_OF_DATA
|
812
|
+
obj = Bio::GFF::GFF3::Record.new(data)
|
813
|
+
at = [ ["ID", 'CEN1'] ]
|
814
|
+
assert_equal(at, obj.attributes)
|
815
|
+
end
|
816
|
+
|
817
|
+
def test_attributes_with_escaping
|
818
|
+
data =<<END_OF_DATA
|
819
|
+
I sgd gene 151453 151591 . + . ID=CEN1;gene=CEN1%3Boh;Note=Chromosome I Centromere
|
820
|
+
END_OF_DATA
|
821
|
+
obj = Bio::GFF::GFF3::Record.new(data)
|
822
|
+
at = [ ['ID', 'CEN1'],
|
823
|
+
["gene", 'CEN1;oh'],
|
824
|
+
["Note", 'Chromosome I Centromere']
|
825
|
+
]
|
826
|
+
assert_equal(at, obj.attributes)
|
827
|
+
end
|
828
|
+
|
829
|
+
def test_score
|
830
|
+
data =<<END_OF_DATA
|
831
|
+
ctg123 src match 456 788 1e-10 - . ID=test01
|
832
|
+
END_OF_DATA
|
833
|
+
obj = Bio::GFF::GFF3::Record.new(data)
|
834
|
+
assert_equal(1e-10, obj.score)
|
835
|
+
obj.score = 0.5
|
836
|
+
assert_equal(0.5, obj.score)
|
837
|
+
end
|
838
|
+
|
839
|
+
def test_phase
|
840
|
+
data =<<END_OF_DATA
|
841
|
+
ctg123 src CDS 456 788 . - 2 ID=test02
|
842
|
+
END_OF_DATA
|
843
|
+
obj = Bio::GFF::GFF3::Record.new(data)
|
844
|
+
assert_equal(2, obj.phase)
|
845
|
+
assert_equal(2, obj.frame)
|
846
|
+
obj.phase = 1
|
847
|
+
assert_equal(1, obj.phase)
|
848
|
+
assert_equal(1, obj.frame)
|
849
|
+
end
|
850
|
+
|
851
|
+
def test_initialize_9
|
852
|
+
obj = Bio::GFF::GFF3::Record.new('test01',
|
853
|
+
'testsrc',
|
854
|
+
'exon',
|
855
|
+
1, 400, nil, '+', nil,
|
856
|
+
[ ['ID', 'test01'],
|
857
|
+
['Note', 'this is test'] ])
|
858
|
+
assert_equal('test01', obj.seqid)
|
859
|
+
end
|
860
|
+
|
861
|
+
def test_to_s_void
|
862
|
+
obj = Bio::GFF::GFF3::Record.new
|
863
|
+
assert_equal(".\t.\t.\t.\t.\t.\t.\t.\t.\n", obj.to_s)
|
864
|
+
end
|
865
|
+
|
866
|
+
end #class TestGFF3RecordMisc
|
867
|
+
|
868
|
+
class TestGFF3RecordEscape < Test::Unit::TestCase
|
869
|
+
def setup
|
870
|
+
@obj = Object.new.extend(Bio::GFF::GFF3::Escape)
|
871
|
+
@str = "A>B\tC=100%;d=e,f,g h"
|
872
|
+
end
|
873
|
+
|
874
|
+
def test_escape
|
875
|
+
str = @str
|
876
|
+
assert_equal('A>B%09C=100%25;d=e,f,g h',
|
877
|
+
@obj.instance_eval { escape(str) })
|
878
|
+
end
|
879
|
+
|
880
|
+
def test_escape_attribute
|
881
|
+
str = @str
|
882
|
+
assert_equal('A>B%09C%3D100%25%3Bd%3De%2Cf%2Cg h',
|
883
|
+
@obj.instance_eval { escape_attribute(str) })
|
884
|
+
end
|
885
|
+
|
886
|
+
def test_escape_seqid
|
887
|
+
str = @str
|
888
|
+
assert_equal('A%3EB%09C%3D100%25%3Bd%3De%2Cf%2Cg%20h',
|
889
|
+
@obj.instance_eval { escape_seqid(str) })
|
890
|
+
end
|
891
|
+
|
892
|
+
def test_unescape
|
893
|
+
escaped_str = 'A%3EB%09C%3D100%25%3Bd%3De%2Cf%2Cg%20h'
|
894
|
+
assert_equal(@str,
|
895
|
+
@obj.instance_eval {
|
896
|
+
unescape(escaped_str) })
|
897
|
+
end
|
898
|
+
end #class TestGFF3RecordEscape
|
899
|
+
|
900
|
+
class TestGFF3RecordTarget < Test::Unit::TestCase
|
901
|
+
|
902
|
+
def setup
|
903
|
+
@target =
|
904
|
+
[ Bio::GFF::GFF3::Record::Target.new('ABCD1234', 123, 456, '+'),
|
905
|
+
Bio::GFF::GFF3::Record::Target.new(">X Y=Z;P%,Q\tR", 78, 90),
|
906
|
+
Bio::GFF::GFF3::Record::Target.new(nil, nil, nil),
|
907
|
+
]
|
908
|
+
end
|
909
|
+
|
910
|
+
def test_parse
|
911
|
+
strings =
|
912
|
+
[ 'ABCD1234 123 456 +',
|
913
|
+
'%3EX%20Y%3DZ%3BP%25%2CQ%09R 78 90',
|
914
|
+
''
|
915
|
+
]
|
916
|
+
@target.each do |target|
|
917
|
+
str = strings.shift
|
918
|
+
assert_equal(target, Bio::GFF::GFF3::Record::Target.parse(str))
|
919
|
+
end
|
920
|
+
end
|
921
|
+
|
922
|
+
def test_target_id
|
923
|
+
assert_equal('ABCD1234', @target[0].target_id)
|
924
|
+
assert_equal(">X Y=Z;P%,Q\tR", @target[1].target_id)
|
925
|
+
assert_equal(nil, @target[2].target_id)
|
926
|
+
end
|
927
|
+
|
928
|
+
def test_start
|
929
|
+
assert_equal(123, @target[0].start)
|
930
|
+
assert_equal(78, @target[1].start)
|
931
|
+
assert_nil(@target[2].start)
|
932
|
+
end
|
933
|
+
|
934
|
+
def test_end
|
935
|
+
assert_equal(456, @target[0].end)
|
936
|
+
assert_equal(90, @target[1].end)
|
937
|
+
assert_nil(@target[2].end)
|
938
|
+
end
|
939
|
+
|
940
|
+
def test_strand
|
941
|
+
assert_equal('+', @target[0].strand)
|
942
|
+
assert_nil(@target[1].strand)
|
943
|
+
assert_nil(@target[2].strand)
|
944
|
+
end
|
945
|
+
|
946
|
+
def test_to_s
|
947
|
+
assert_equal('ABCD1234 123 456 +', @target[0].to_s)
|
948
|
+
assert_equal('%3EX%20Y%3DZ%3BP%25%2CQ%09R 78 90', @target[1].to_s)
|
949
|
+
assert_equal('. . .', @target[2].to_s)
|
950
|
+
end
|
951
|
+
|
952
|
+
end #class TestGFF3RecordTarget
|
953
|
+
|
954
|
+
class TestGFF3RecordGap < Test::Unit::TestCase
|
955
|
+
def setup
|
956
|
+
# examples taken from http://song.sourceforge.net/gff3.shtml
|
957
|
+
@gaps_src = [ 'M8 D3 M6 I1 M6',
|
958
|
+
'M3 I1 M2 F1 M4',
|
959
|
+
'M3 I1 M2 R1 M4' ]
|
960
|
+
@gaps = @gaps_src.collect { |x| Bio::GFF::GFF3::Record::Gap.new(x) }
|
961
|
+
end
|
962
|
+
|
963
|
+
def test_to_s
|
964
|
+
@gaps_src.each do |src|
|
965
|
+
assert_equal(src, @gaps.shift.to_s)
|
966
|
+
end
|
967
|
+
end
|
968
|
+
|
969
|
+
def test_eqeq
|
970
|
+
gap = Bio::GFF::GFF3::Record::Gap.new('M8 D3 M6 I1 M6')
|
971
|
+
assert(gap == @gaps[0])
|
972
|
+
assert_equal(false, gap == @gaps[1])
|
973
|
+
end
|
974
|
+
|
975
|
+
def test_process_sequences_na
|
976
|
+
ref = 'CAAGACCTAAACTGGATTCCAAT'
|
977
|
+
tgt = 'CAAGACCTCTGGATATCCAAT'
|
978
|
+
ref_aligned = 'CAAGACCTAAACTGGAT-TCCAAT'
|
979
|
+
tgt_aligned = 'CAAGACCT---CTGGATATCCAAT'
|
980
|
+
assert_equal([ ref_aligned, tgt_aligned ],
|
981
|
+
@gaps[0].process_sequences_na(ref, tgt))
|
982
|
+
end
|
983
|
+
|
984
|
+
def test_process_sequences_na_tooshort
|
985
|
+
ref = 'CAAGACCTAAACTGGATTCCAA'
|
986
|
+
tgt = 'CAAGACCTCTGGATATCCAA'
|
987
|
+
assert_raise(RuntimeError) { @gaps[0].process_sequences_na(ref, tgt) }
|
988
|
+
ref = 'c'
|
989
|
+
tgt = 'c'
|
990
|
+
assert_raise(RuntimeError) { @gaps[0].process_sequences_na(ref, tgt) }
|
991
|
+
end
|
992
|
+
|
993
|
+
def test_process_sequences_na_aa
|
994
|
+
ref1 = 'atgaaggaggttattgaatgtcggcggt'
|
995
|
+
tgt1 = 'MKEVVINVGG'
|
996
|
+
ref1_aligned = 'atgaaggag---gttattgaatgtcggcggt'
|
997
|
+
tgt1_aligned = 'M K E V V I >N V G G '
|
998
|
+
assert_equal([ ref1_aligned, tgt1_aligned ],
|
999
|
+
@gaps[1].process_sequences_na_aa(ref1, tgt1))
|
1000
|
+
end
|
1001
|
+
|
1002
|
+
def test_process_sequences_na_aa_reverse_frameshift
|
1003
|
+
ref2 = 'atgaaggaggttataatgtcggcggt'
|
1004
|
+
tgt2 = 'MKEVVINVGG'
|
1005
|
+
ref2_aligned = 'atgaaggag---gttat<aatgtcggcggt'
|
1006
|
+
tgt2_aligned = 'M K E V V I N V G G '
|
1007
|
+
assert_equal([ ref2_aligned, tgt2_aligned ],
|
1008
|
+
@gaps[2].process_sequences_na_aa(ref2, tgt2))
|
1009
|
+
end
|
1010
|
+
|
1011
|
+
def test_process_sequences_na_aa_reverse_frameshift_more
|
1012
|
+
gap = Bio::GFF::GFF3::Record::Gap.new("M3 R3 M3")
|
1013
|
+
ref = 'atgaagattaatgtc'
|
1014
|
+
tgt = 'MKIINV'
|
1015
|
+
ref_aligned = 'atgaag<<<attaatgtc'
|
1016
|
+
tgt_aligned = 'M K I I N V '
|
1017
|
+
assert_equal([ ref_aligned, tgt_aligned ],
|
1018
|
+
gap.process_sequences_na_aa(ref, tgt))
|
1019
|
+
end
|
1020
|
+
|
1021
|
+
def test_process_sequences_na_aa_tooshort
|
1022
|
+
ref2 = 'atgaaggaggttataatgtcggcgg'
|
1023
|
+
tgt2 = 'MKEVVINVG'
|
1024
|
+
assert_raise(RuntimeError) do
|
1025
|
+
@gaps[2].process_sequences_na_aa(ref2, tgt2)
|
1026
|
+
end
|
1027
|
+
|
1028
|
+
ref2 = 'atg'
|
1029
|
+
tgt2 = 'M'
|
1030
|
+
assert_raise(RuntimeError) do
|
1031
|
+
@gaps[2].process_sequences_na_aa(ref2, tgt2)
|
1032
|
+
end
|
1033
|
+
end
|
1034
|
+
|
1035
|
+
def test___scan_gap
|
1036
|
+
str1 = 'CAAGACCT---CTGGATATCCAAT'
|
1037
|
+
str2 = '-aaaaaaa-a-a---ggag--'
|
1038
|
+
c = Bio::GFF::GFF3::Record::Gap::Code
|
1039
|
+
data1 = [ c.new(:M, 8), c.new(:I, 3), c.new(:M, 13) ]
|
1040
|
+
data2 = [ c.new(:I, 1), c.new(:M, 7), c.new(:I, 1),
|
1041
|
+
c.new(:M, 1), c.new(:I, 1), c.new(:M, 1),
|
1042
|
+
c.new(:I, 3), c.new(:M, 4), c.new(:I, 2) ]
|
1043
|
+
|
1044
|
+
assert_equal(data1, @gaps[0].instance_eval { __scan_gap(str1) })
|
1045
|
+
assert_equal(data2, @gaps[0].instance_eval { __scan_gap(str2) })
|
1046
|
+
end
|
1047
|
+
|
1048
|
+
def test_new_from_sequences_na
|
1049
|
+
ref_aligned = 'CAAGACCTAAACTGGAT-TCCAAT'
|
1050
|
+
tgt_aligned = 'CAAGACCT---CTGGATATCCAAT'
|
1051
|
+
|
1052
|
+
assert_equal(@gaps[0], Bio::GFF::GFF3::Record::Gap.new_from_sequences_na(ref_aligned, tgt_aligned))
|
1053
|
+
end
|
1054
|
+
|
1055
|
+
def test_new_from_sequences_na_aa
|
1056
|
+
ref = 'atgaaggag---gttattgaatgtcggcggt'
|
1057
|
+
tgt = 'M K E V V I >N V G G '
|
1058
|
+
assert_equal(@gaps[1],
|
1059
|
+
Bio::GFF::GFF3::Record::Gap.new_from_sequences_na_aa(ref,
|
1060
|
+
tgt))
|
1061
|
+
end
|
1062
|
+
|
1063
|
+
def test_new_from_sequences_na_aa_reverse_frameshift
|
1064
|
+
ref = 'atgaaggag---gttat<aatgtcggcggt'
|
1065
|
+
tgt = 'M K E V V I N V G G '
|
1066
|
+
assert_equal(@gaps[2],
|
1067
|
+
Bio::GFF::GFF3::Record::Gap.new_from_sequences_na_aa(ref,
|
1068
|
+
tgt))
|
1069
|
+
end
|
1070
|
+
|
1071
|
+
def test_new_from_sequences_na_aa_reverse_frameshift_more
|
1072
|
+
gap = Bio::GFF::GFF3::Record::Gap.new("M3 R3 M3")
|
1073
|
+
ref = 'atgaag<<<attaatgtc'
|
1074
|
+
tgt = 'M K I I N V '
|
1075
|
+
assert_equal(gap,
|
1076
|
+
Bio::GFF::GFF3::Record::Gap.new_from_sequences_na_aa(ref,
|
1077
|
+
tgt))
|
1078
|
+
end
|
1079
|
+
|
1080
|
+
def test_new_from_sequences_na_aa_boundary_gap
|
1081
|
+
g = Bio::GFF::GFF3::Record::Gap
|
1082
|
+
|
1083
|
+
ref = '---atgatg'
|
1084
|
+
tgt = 'K M M '
|
1085
|
+
assert_equal(Bio::GFF::GFF3::Record::Gap.new('I1 M2'),
|
1086
|
+
g.new_from_sequences_na_aa(ref, tgt))
|
1087
|
+
|
1088
|
+
ref = 'atgatg---'
|
1089
|
+
tgt = 'M M K '
|
1090
|
+
assert_equal(Bio::GFF::GFF3::Record::Gap.new('M2 I1'),
|
1091
|
+
g.new_from_sequences_na_aa(ref, tgt))
|
1092
|
+
|
1093
|
+
ref = 'atgatgatg'
|
1094
|
+
tgt = '- M M '
|
1095
|
+
assert_equal(Bio::GFF::GFF3::Record::Gap.new('D1 M2'),
|
1096
|
+
g.new_from_sequences_na_aa(ref, tgt))
|
1097
|
+
|
1098
|
+
ref = 'atgatgatg'
|
1099
|
+
tgt = 'M M - '
|
1100
|
+
assert_equal(Bio::GFF::GFF3::Record::Gap.new('M2 D1'),
|
1101
|
+
g.new_from_sequences_na_aa(ref, tgt))
|
1102
|
+
end
|
1103
|
+
|
1104
|
+
def test_new_from_sequences_na_aa_example
|
1105
|
+
gap = Bio::GFF::GFF3::Record::Gap.new('M2 R1 M1 F2 M1')
|
1106
|
+
ref1 = 'atgg-taagac-att'
|
1107
|
+
tgt1 = 'M V K - I '
|
1108
|
+
ref2 = 'atggt<aagacatt'
|
1109
|
+
tgt2 = 'M V K >>I '
|
1110
|
+
gap1 = Bio::GFF::GFF3::Record::Gap.new_from_sequences_na_aa(ref1, tgt1)
|
1111
|
+
assert_equal(gap, gap1)
|
1112
|
+
gap2 = Bio::GFF::GFF3::Record::Gap.new_from_sequences_na_aa(ref2, tgt2)
|
1113
|
+
assert_equal(gap, gap2)
|
1114
|
+
end
|
1115
|
+
end #class TestGFF3RecordGap
|
1116
|
+
|
1117
|
+
class TestGFF3SequenceRegion < Test::Unit::TestCase
|
1118
|
+
|
1119
|
+
def setup
|
1120
|
+
@data =
|
1121
|
+
[ Bio::GFF::GFF3::SequenceRegion.new('ABCD1234', 123, 456),
|
1122
|
+
Bio::GFF::GFF3::SequenceRegion.new(">X Y=Z;P%,Q\tR", 78, 90),
|
1123
|
+
Bio::GFF::GFF3::SequenceRegion.new(nil, nil, nil),
|
1124
|
+
]
|
1125
|
+
end
|
1126
|
+
|
1127
|
+
def test_parse
|
1128
|
+
strings =
|
1129
|
+
[ '##sequence-region ABCD1234 123 456',
|
1130
|
+
'##sequence-region %3EX%20Y%3DZ%3BP%25%2CQ%09R 78 90',
|
1131
|
+
'##sequence-region'
|
1132
|
+
]
|
1133
|
+
@data.each do |reg|
|
1134
|
+
str = strings.shift
|
1135
|
+
assert_equal(reg, Bio::GFF::GFF3::SequenceRegion.parse(str))
|
1136
|
+
end
|
1137
|
+
end
|
1138
|
+
|
1139
|
+
def test_seqid
|
1140
|
+
assert_equal('ABCD1234', @data[0].seqid)
|
1141
|
+
assert_equal(">X Y=Z;P%,Q\tR", @data[1].seqid)
|
1142
|
+
assert_equal(nil, @data[2].seqid)
|
1143
|
+
end
|
1144
|
+
|
1145
|
+
def test_start
|
1146
|
+
assert_equal(123, @data[0].start)
|
1147
|
+
assert_equal(78, @data[1].start)
|
1148
|
+
assert_nil(@data[2].start)
|
1149
|
+
end
|
1150
|
+
|
1151
|
+
def test_end
|
1152
|
+
assert_equal(456, @data[0].end)
|
1153
|
+
assert_equal(90, @data[1].end)
|
1154
|
+
assert_nil(@data[2].end)
|
1155
|
+
end
|
1156
|
+
|
1157
|
+
def test_to_s
|
1158
|
+
assert_equal("##sequence-region ABCD1234 123 456\n", @data[0].to_s)
|
1159
|
+
assert_equal("##sequence-region %3EX%20Y%3DZ%3BP%25%2CQ%09R 78 90\n",
|
1160
|
+
@data[1].to_s)
|
1161
|
+
assert_equal("##sequence-region . . .\n", @data[2].to_s)
|
1162
|
+
end
|
1163
|
+
|
1164
|
+
end #class TestGFF3SequenceRegion
|
1165
|
+
|
1166
|
+
class TestGFF3MetaData < Test::Unit::TestCase
|
1167
|
+
|
1168
|
+
def setup
|
1169
|
+
@data =
|
1170
|
+
Bio::GFF::GFF3::MetaData.new('feature-ontology',
|
1171
|
+
'http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12')
|
1172
|
+
end
|
1173
|
+
|
1174
|
+
def test_parse
|
1175
|
+
assert_equal(@data,
|
1176
|
+
Bio::GFF::GFF3::MetaData.parse('##feature-ontology http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12'))
|
1177
|
+
end
|
1178
|
+
|
1179
|
+
def test_directive
|
1180
|
+
assert_equal('feature-ontology', @data.directive)
|
1181
|
+
end
|
1182
|
+
|
1183
|
+
def test_data
|
1184
|
+
assert_equal('http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12', @data.data)
|
1185
|
+
end
|
1186
|
+
end #class TestGFF3MetaData
|
1187
|
+
|
1188
|
+
end #module Bio
|
1189
|
+
|
1190
|
+
|