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 +1,185 @@
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#
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# test/unit/bio/shell/plugin/test_seq.rb - Unit test for Bio::Shell plugin for biological sequence manipulations
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#
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# Copyright:: Copyright (C) 2005
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# Mitsuteru Nakao <n@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: test_seq.rb,v 1.9 2007/04/05 23:35:44 trevor Exp $
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio/shell'
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require 'bio/shell/plugin/seq'
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module Bio
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class TestShellPluginSeq < Test::Unit::TestCase
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include Bio::Shell
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Bio::Shell.config = {:color => false}
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def test_htmlseq
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str = 'ATGC'
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html =<<END
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<div style="font-family:monospace;">
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<span style="background:#64F73F;">a</span>
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<span style="background:#3C88EE;">t</span>
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<span style="background:#EB413C;">g</span>
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<span style="background:#FFB340;">c</span>
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<br>
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</div>
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END
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assert_equal(html, htmlseq(str))
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end
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def test_naseq
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str = 'ACGT'
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assert_equal(Bio::Sequence, getseq(str).class)
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assert_equal(Bio::Sequence::NA, getseq(str).moltype)
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assert_equal('acgt', getseq(str).seq)
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end
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def test_aaseq
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str = 'WD'
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assert_equal(Bio::Sequence, getseq(str).class)
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assert_equal(Bio::Sequence::AA, getseq(str).moltype)
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assert_equal('WD', getseq(str).seq)
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end
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def test_na_seqstat
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naseq = 'atgcatgcatgc'
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output =<<END
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* * * Sequence statistics * * *
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5'->3' sequence : atgcatgcatgc
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3'->5' sequence : gcatgcatgcat
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Translation 1 : MHAC
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Translation 2 : CMH
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Translation 3 : ACM
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Translation -1 : ACMH
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Translation -2 : HAC
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Translation -3 : MHA
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Length : 12 bp
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GC percent : 50 %
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Composition : a - 3 ( 25.00 %)
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c - 3 ( 25.00 %)
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g - 3 ( 25.00 %)
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t - 3 ( 25.00 %)
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Codon usage :
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*---------------------------------------------*
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| | 2nd | |
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| 1st |-------------------------------| 3rd |
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| | U | C | A | G | |
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|-------+-------+-------+-------+-------+-----|
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| U U |F 0.0%|S 0.0%|Y 0.0%|C 0.0%| u |
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| U U |F 0.0%|S 0.0%|Y 0.0%|C 25.0%| c |
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| U U |L 0.0%|S 0.0%|* 0.0%|* 0.0%| a |
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| UUU |L 0.0%|S 0.0%|* 0.0%|W 0.0%| g |
|
88
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|-------+-------+-------+-------+-------+-----|
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| CCCC |L 0.0%|P 0.0%|H 25.0%|R 0.0%| u |
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| C |L 0.0%|P 0.0%|H 0.0%|R 0.0%| c |
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| C |L 0.0%|P 0.0%|Q 0.0%|R 0.0%| a |
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| CCCC |L 0.0%|P 0.0%|Q 0.0%|R 0.0%| g |
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|-------+-------+-------+-------+-------+-----|
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| A |I 0.0%|T 0.0%|N 0.0%|S 0.0%| u |
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| A A |I 0.0%|T 0.0%|N 0.0%|S 0.0%| c |
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| AAAAA |I 0.0%|T 0.0%|K 0.0%|R 0.0%| a |
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97
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| A A |M 25.0%|T 0.0%|K 0.0%|R 0.0%| g |
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|-------+-------+-------+-------+-------+-----|
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| GGGG |V 0.0%|A 0.0%|D 0.0%|G 0.0%| u |
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| G |V 0.0%|A 0.0%|D 0.0%|G 0.0%| c |
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| G GGG |V 0.0%|A 25.0%|E 0.0%|G 0.0%| a |
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| GG G |V 0.0%|A 0.0%|E 0.0%|G 0.0%| g |
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*---------------------------------------------*
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Molecular weight : 3701.61444
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Protein weight : 460.565
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//
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END
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$str = ''
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alias puts_orig puts
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def puts(*args)
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args.each do |obj|
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$str << obj.to_s
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end
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end
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seqstat(naseq)
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undef puts
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alias puts puts_orig
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assert_equal(output, $str)
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end
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def test_aa_seqstat
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aaseq = 'WD'
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output =<<END
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* * * Sequence statistics * * *
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N->C sequence : WD
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Length : 2 aa
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Composition : D Asp - 1 ( 50.00 %) aspartic acid
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W Trp - 1 ( 50.00 %) tryptophan
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Protein weight : 319.315
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//
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END
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$str = ''
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alias puts_orig puts
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def puts(*args)
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args.each do |obj|
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$str << obj.to_s
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end
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end
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seqstat(aaseq)
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undef puts
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alias puts puts_orig
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assert_equal(output, $str)
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end
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def test_doublehelix
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seq = 'ACGTACGTACGTACGT'
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output = <<END
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at
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c--g
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g---c
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t----a
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a----t
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c---g
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g--c
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ta
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ta
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g--c
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c---g
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a----t
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t----a
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g---c
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c--g
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at
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END
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$str = ''
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alias puts_orig puts
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def puts(*args)
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args.each do |obj|
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$str << obj.to_s
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end
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end
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doublehelix(seq)
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undef puts
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alias puts puts_orig
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assert_equal(output, $str)
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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/test_alignment.rb - Unit test for Bio::Alignment
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#
|
4
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# Copyright:: Copyright (C) 2004
|
5
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# Moses Hohman <mmhohman@northwestern.edu>
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# 2005 Naohisa Goto <ng@bioruby.org>
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7
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# License:: The Ruby License
|
8
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#
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9
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# $Id: test_alignment.rb,v 1.12 2007/12/26 13:55:40 ngoto Exp $
|
10
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#
|
11
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|
12
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require 'pathname'
|
13
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 3, 'lib')).cleanpath.to_s
|
14
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$:.unshift(libpath) unless $:.include?(libpath)
|
15
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|
16
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require 'test/unit'
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17
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require 'bio/alignment'
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18
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|
19
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module Bio
|
20
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|
21
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class TestAlignmentPropertyMethods < Test::Unit::TestCase
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22
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+
|
23
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def setup
|
24
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@obj = Object.new
|
25
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@obj.extend(Alignment::PropertyMethods)
|
26
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end
|
27
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+
|
28
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def test_is_gap_default_false
|
29
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+
assert_equal(false, @obj.is_gap?('a'), "\"a\" isn't a gap")
|
30
|
+
end
|
31
|
+
|
32
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+
def test_is_gap_default_true
|
33
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+
assert_equal(true, @obj.is_gap?('-'), '"-" is a gap')
|
34
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+
end
|
35
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+
|
36
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+
def test_gap_regexp
|
37
|
+
assert_not_nil(@obj.gap_regexp)
|
38
|
+
end
|
39
|
+
|
40
|
+
def test_gap_regexp_never_nil
|
41
|
+
@obj.gap_regexp = nil
|
42
|
+
assert_not_nil(@obj.gap_regexp)
|
43
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+
end
|
44
|
+
|
45
|
+
def test_gap_regexp=()
|
46
|
+
@obj.gap_regexp = /[^a-zA-Z0-9]/
|
47
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+
assert_equal(/[^a-zA-Z0-9]/, @obj.gap_regexp)
|
48
|
+
end
|
49
|
+
|
50
|
+
def test_is_gap_nodefault_false
|
51
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@obj.gap_regexp = /[^a-zA-Z0-9]/
|
52
|
+
assert_equal(false, @obj.is_gap?('3'))
|
53
|
+
end
|
54
|
+
|
55
|
+
def test_is_gap_nodefault_true
|
56
|
+
@obj.gap_regexp = /[^atgc]/
|
57
|
+
assert_equal(true, @obj.is_gap?('z'))
|
58
|
+
end
|
59
|
+
|
60
|
+
def test_gap_char_default
|
61
|
+
assert_not_nil(@obj.gap_char)
|
62
|
+
end
|
63
|
+
|
64
|
+
def test_gap_char_never_nil
|
65
|
+
@obj.gap_char = nil
|
66
|
+
assert_not_nil(@obj.gap_char)
|
67
|
+
end
|
68
|
+
|
69
|
+
def test_gap_char=()
|
70
|
+
@obj.gap_char = '#'
|
71
|
+
assert_equal('#', @obj.gap_char)
|
72
|
+
end
|
73
|
+
|
74
|
+
def test_missing_char_default
|
75
|
+
assert_not_nil(@obj.missing_char)
|
76
|
+
end
|
77
|
+
|
78
|
+
def test_missing_char_never_nil
|
79
|
+
@obj.missing_char = nil
|
80
|
+
assert_not_nil(@obj.missing_char)
|
81
|
+
end
|
82
|
+
|
83
|
+
def test_missing_char=()
|
84
|
+
@obj.missing_char = '_'
|
85
|
+
assert_equal('_', @obj.missing_char)
|
86
|
+
end
|
87
|
+
|
88
|
+
def test_seqclass_default
|
89
|
+
assert_not_nil(@obj.seqclass)
|
90
|
+
end
|
91
|
+
|
92
|
+
def test_seqclass_never_nil
|
93
|
+
@obj.seqclass = nil
|
94
|
+
assert_not_nil(@obj.seqclass)
|
95
|
+
end
|
96
|
+
|
97
|
+
def test_seqclass=()
|
98
|
+
@obj.seqclass = Sequence::NA
|
99
|
+
assert_equal(Sequence::NA, @obj.seqclass)
|
100
|
+
end
|
101
|
+
|
102
|
+
def test_get_all_property_default
|
103
|
+
assert_equal({}, @obj.get_all_property)
|
104
|
+
end
|
105
|
+
|
106
|
+
def test_get_all_property_nodefault
|
107
|
+
@obj.gap_regexp = /[^acgt]/
|
108
|
+
@obj.gap_char = '#'
|
109
|
+
@obj.missing_char = '_'
|
110
|
+
@obj.seqclass = Sequence::NA
|
111
|
+
assert_equal({ :gap_regexp => /[^acgt]/,
|
112
|
+
:gap_char => '#',
|
113
|
+
:missing_char => '_',
|
114
|
+
:seqclass => Sequence::NA },
|
115
|
+
@obj.get_all_property)
|
116
|
+
end
|
117
|
+
|
118
|
+
def test_set_all_property
|
119
|
+
h = { :gap_regexp => /[^acgt]/,
|
120
|
+
:gap_char => '#',
|
121
|
+
:missing_char => '_',
|
122
|
+
:seqclass => Sequence::NA }
|
123
|
+
@obj.set_all_property(h)
|
124
|
+
assert_equal(h, @obj.get_all_property)
|
125
|
+
end
|
126
|
+
end #class TestAlignmentPropertyMethods
|
127
|
+
|
128
|
+
# This is a unit test of Bio::Alignment::Site class and
|
129
|
+
# Bio::Alignment::SiteMethods module.
|
130
|
+
# Since Bio::Alignment::Site includes Bio::Alignment::SiteMethods,
|
131
|
+
# we can test both at a time.
|
132
|
+
class TestAlignmentSite < Test::Unit::TestCase
|
133
|
+
|
134
|
+
def test_has_gap_true
|
135
|
+
site = Alignment::Site[ 'a', '-', 'c', 'g', 't' ]
|
136
|
+
assert_equal(true, site.has_gap?)
|
137
|
+
end
|
138
|
+
|
139
|
+
def test_has_gap_false
|
140
|
+
site = Alignment::Site[ 'a', 'c', 'g', 't' ]
|
141
|
+
assert_equal(false, site.has_gap?)
|
142
|
+
end
|
143
|
+
|
144
|
+
def test_remove_gaps!
|
145
|
+
site = Alignment::Site[ 'a', '-', 'c', '-' ]
|
146
|
+
assert_equal(Alignment::Site['a', 'c'], site.remove_gaps!)
|
147
|
+
end
|
148
|
+
|
149
|
+
def test_remove_gaps_bang_not_removed
|
150
|
+
site = Alignment::Site[ 'a', 'c']
|
151
|
+
assert_equal(nil, site.remove_gaps!)
|
152
|
+
end
|
153
|
+
|
154
|
+
def test_consensus_string_default
|
155
|
+
site = Alignment::Site[ 'a', 'a', 'a', 'a']
|
156
|
+
assert_equal('a', site.consensus_string)
|
157
|
+
end
|
158
|
+
|
159
|
+
def test_consensus_string_default_nil
|
160
|
+
site = Alignment::Site[ 'a', 'a', 'a', 'c']
|
161
|
+
assert_nil(site.consensus_string)
|
162
|
+
end
|
163
|
+
|
164
|
+
def test_consensus_string_50percent
|
165
|
+
site = Alignment::Site[ 'a', 'a', 'c', 'g']
|
166
|
+
assert_equal('a', site.consensus_string(0.5))
|
167
|
+
end
|
168
|
+
|
169
|
+
def test_consensus_string_50percent_nil
|
170
|
+
site = Alignment::Site[ 'a', 'c', 'g', 't']
|
171
|
+
assert_nil(site.consensus_string(0.5))
|
172
|
+
end
|
173
|
+
|
174
|
+
def test_consensus_iupac
|
175
|
+
data = {
|
176
|
+
'a' => [ 'a' ],
|
177
|
+
'c' => [ 'c' ],
|
178
|
+
'g' => [ 'g' ],
|
179
|
+
't' => [ 't' ],
|
180
|
+
't' => [ 't', 'u' ],
|
181
|
+
'm' => [ 'a', 'c' ],
|
182
|
+
'r' => [ 'a', 'g' ],
|
183
|
+
'w' => [ 'a', 't' ],
|
184
|
+
's' => [ 'c', 'g' ],
|
185
|
+
'y' => [ 'c', 't' ],
|
186
|
+
'k' => [ 'g', 't' ],
|
187
|
+
'v' => [ 'a', 'c', 'g' ],
|
188
|
+
'h' => [ 'a', 'c', 't' ],
|
189
|
+
'd' => [ 'a', 'g', 't' ],
|
190
|
+
'b' => [ 'c', 'g', 't' ],
|
191
|
+
'n' => [ 'a', 'c', 'g', 't' ],
|
192
|
+
nil => [ 'z', 'a' ]
|
193
|
+
}
|
194
|
+
data.each do |cons, testdata|
|
195
|
+
site = Alignment::Site[ *testdata ]
|
196
|
+
assert_equal(cons, site.consensus_iupac,
|
197
|
+
"IUPAC consensus of #{testdata.join(',')} is #{cons}")
|
198
|
+
end
|
199
|
+
end
|
200
|
+
|
201
|
+
def test_match_line_amino_missing
|
202
|
+
site = Alignment::Site[ 'P', 'Q', 'R', 'S' ]
|
203
|
+
assert_equal(' ', site.match_line_amino)
|
204
|
+
end
|
205
|
+
|
206
|
+
def test_match_line_amino_100percent
|
207
|
+
site = Alignment::Site[ 'M', 'M', 'M', 'M' ]
|
208
|
+
assert_equal('*', site.match_line_amino)
|
209
|
+
end
|
210
|
+
|
211
|
+
def test_match_line_amino_strong
|
212
|
+
site = Alignment::Site[ 'N', 'E', 'Q', 'K' ]
|
213
|
+
assert_equal(':', site.match_line_amino)
|
214
|
+
end
|
215
|
+
|
216
|
+
def test_match_line_amino_weak
|
217
|
+
site = Alignment::Site[ 'S', 'G', 'N', 'D' ]
|
218
|
+
assert_equal('.', site.match_line_amino)
|
219
|
+
end
|
220
|
+
|
221
|
+
def test_match_line_nuc_missing
|
222
|
+
site = Alignment::Site[ 'A', 'C', 'G', 'T' ]
|
223
|
+
assert_equal(' ', site.match_line_nuc)
|
224
|
+
end
|
225
|
+
|
226
|
+
def test_match_line_nuc_100percent
|
227
|
+
site = Alignment::Site[ 'G', 'G', 'G', 'G' ]
|
228
|
+
assert_equal('*', site.match_line_nuc)
|
229
|
+
end
|
230
|
+
end #class TestAlignmentSite
|
231
|
+
|
232
|
+
# This is sample class for testing Bio::Alignment::EnumerableExtension.
|
233
|
+
class A < Array
|
234
|
+
include Alignment::EnumerableExtension
|
235
|
+
end
|
236
|
+
|
237
|
+
class TestAlignmentEnumerableExtension < Test::Unit::TestCase
|
238
|
+
def test_each_seq
|
239
|
+
expected_results = [ 'atg', 'aag', 'acg' ]
|
240
|
+
a = A[ *expected_results ]
|
241
|
+
a.each_seq do |x|
|
242
|
+
assert_equal(expected_results.shift, x)
|
243
|
+
end
|
244
|
+
assert(expected_results.empty?)
|
245
|
+
end
|
246
|
+
|
247
|
+
def test_seqclass_default
|
248
|
+
a = A.new
|
249
|
+
assert_equal(String, a.seqclass)
|
250
|
+
end
|
251
|
+
|
252
|
+
def test_seqclass
|
253
|
+
a = A[ Bio::Sequence::NA.new('atg') ]
|
254
|
+
assert_equal(Bio::Sequence::NA, a.seqclass)
|
255
|
+
end
|
256
|
+
|
257
|
+
def test_seqclass=()
|
258
|
+
a = A.new
|
259
|
+
assert_equal(String, a.seqclass)
|
260
|
+
a << Bio::Sequence::NA.new('a')
|
261
|
+
assert_equal(Bio::Sequence::NA, a.seqclass)
|
262
|
+
a.seqclass = Bio::Sequence::AA
|
263
|
+
assert_equal(Bio::Sequence::AA, a.seqclass)
|
264
|
+
end
|
265
|
+
|
266
|
+
def test_alignment_length
|
267
|
+
a = A[ 'a', 'at', 'atgc', 'atg', '' ]
|
268
|
+
assert_equal(4, a.alignment_length)
|
269
|
+
end
|
270
|
+
|
271
|
+
def test_private_alignment_site
|
272
|
+
a = A[ 'a', 'at', 'atgc', 'atg', '' ]
|
273
|
+
assert_equal(Alignment::Site[ '-', 't', 't', 't', '-' ],
|
274
|
+
a.instance_eval { _alignment_site(1) })
|
275
|
+
end
|
276
|
+
|
277
|
+
def test_alignment_site
|
278
|
+
a = A[ 'a', 'at', 'atgc', 'atg', '' ]
|
279
|
+
assert_equal(Alignment::Site[ '-', 't', 't', 't', '-' ],
|
280
|
+
a.__send__(:_alignment_site, 1))
|
281
|
+
end
|
282
|
+
|
283
|
+
def test_each_site
|
284
|
+
expected_results = [
|
285
|
+
Alignment::Site[ 'a', 'a', 'a', 'a', '-' ],
|
286
|
+
Alignment::Site[ '-', 't', 't', 't', '-' ],
|
287
|
+
Alignment::Site[ '-', '-', 'g', 'g', '-' ],
|
288
|
+
Alignment::Site[ '-', '-', 'c', '-', '-' ]
|
289
|
+
]
|
290
|
+
a = A[ 'a', 'at', 'atgc', 'atg', '' ]
|
291
|
+
a.each_site do |site|
|
292
|
+
assert_equal(expected_results.shift, site)
|
293
|
+
end
|
294
|
+
assert(expected_results.empty?)
|
295
|
+
end
|
296
|
+
|
297
|
+
def test_each_site_step
|
298
|
+
expected_results = [
|
299
|
+
Alignment::Site[ '-', 't', 't', 't', '-' ], # site 1
|
300
|
+
Alignment::Site[ '-', 'a', 'g', 't', '-' ], # site 3
|
301
|
+
]
|
302
|
+
a = A[ 'a', 'atgatc', 'atggcc', 'atgtga', '' ]
|
303
|
+
a.each_site_step(1, 4, 2) do |site|
|
304
|
+
assert_equal(expected_results.shift, site)
|
305
|
+
end
|
306
|
+
assert(expected_results.empty?)
|
307
|
+
end
|
308
|
+
|
309
|
+
def test_alignment_collect
|
310
|
+
a = A[ 'a', 'at', 'atgc', 'atg', '' ]
|
311
|
+
assert_equal(Alignment::SequenceArray[ 'a', 'au', 'augc', 'aug', '' ],
|
312
|
+
a.alignment_collect { |x| x.gsub(/t/, 'u') })
|
313
|
+
end
|
314
|
+
|
315
|
+
def test_alignment_window
|
316
|
+
a = A[ 'a', 'at', 'atgca', 'atg', '' ]
|
317
|
+
assert_equal(Alignment::SequenceArray[ '', 't', 'tgc', 'tg', '' ],
|
318
|
+
a.alignment_window(1, 3))
|
319
|
+
end
|
320
|
+
|
321
|
+
def test_each_window
|
322
|
+
expected_results = [
|
323
|
+
Alignment::SequenceArray[ 'atg', 'tcg', '' ], # 0..2
|
324
|
+
Alignment::SequenceArray[ 'gca', 'gat', '' ], # 2..4
|
325
|
+
Alignment::SequenceArray[ 'atg', 'tgc', '' ], # 4..6
|
326
|
+
Alignment::SequenceArray[ 'c', 'a', '' ] # 7..7
|
327
|
+
]
|
328
|
+
a = A[ 'atgcatgc', 'tcgatgca', '' ]
|
329
|
+
r = a.each_window(3, 2) do |x|
|
330
|
+
assert_equal(expected_results.shift, x)
|
331
|
+
end
|
332
|
+
assert_equal(expected_results.shift, r)
|
333
|
+
assert(expected_results.empty?)
|
334
|
+
end
|
335
|
+
|
336
|
+
def test_collect_each_site
|
337
|
+
a = A[ 'a', 'at', 'atgc', 'atg', '' ]
|
338
|
+
assert_equal(["aaaa-", "-ttt-", "--gg-", "--c--" ],
|
339
|
+
a.collect_each_site { |x| x.join('') })
|
340
|
+
end
|
341
|
+
|
342
|
+
def test_consensus_each_site_default
|
343
|
+
expected_results = [
|
344
|
+
Alignment::Site[ 'a', 'a', 'a', 'a', 'a' ],
|
345
|
+
Alignment::Site[ 'a', 'c', 'g', 't', '-' ]
|
346
|
+
]
|
347
|
+
|
348
|
+
a = A[ 'aa', 'ac', 'ag', 'at', 'a-' ]
|
349
|
+
result = a.consensus_each_site do |site|
|
350
|
+
assert_equal(expected_results.shift, site)
|
351
|
+
'x'
|
352
|
+
end
|
353
|
+
assert_equal('xx', result)
|
354
|
+
assert(expected_results.empty?)
|
355
|
+
end
|
356
|
+
|
357
|
+
def test_consensus_each_site_gap_mode_1
|
358
|
+
expected_results = [
|
359
|
+
Alignment::Site[ 'a', 'a', 'a', 'a', 'a' ]
|
360
|
+
]
|
361
|
+
|
362
|
+
a = A[ 'aa', 'ac', 'ag', 'at', 'a-' ]
|
363
|
+
result = a.consensus_each_site(:gap_mode => 1) do |site|
|
364
|
+
assert_equal(expected_results.shift, site)
|
365
|
+
'x'
|
366
|
+
end
|
367
|
+
assert_equal('x-', result)
|
368
|
+
assert(expected_results.empty?)
|
369
|
+
end
|
370
|
+
|
371
|
+
def test_consensus_each_site_gap_mode_minus1
|
372
|
+
expected_results = [
|
373
|
+
Alignment::Site[ 'a', 'a', 'a', 'a', 'a' ],
|
374
|
+
Alignment::Site[ 'a', 'c', 'g', 't' ]
|
375
|
+
]
|
376
|
+
|
377
|
+
a = A[ 'aa', 'ac', 'ag', 'at', 'a-' ]
|
378
|
+
result = a.consensus_each_site(:gap_mode => -1) do |site|
|
379
|
+
assert_equal(expected_results.shift, site)
|
380
|
+
'x'
|
381
|
+
end
|
382
|
+
assert_equal('xx', result)
|
383
|
+
assert(expected_results.empty?)
|
384
|
+
end
|
385
|
+
|
386
|
+
def test_consensus_string_default
|
387
|
+
a = A[ 'ata', 'aac', 'aag', 'aat' ]
|
388
|
+
assert_equal('a??', a.consensus_string)
|
389
|
+
end
|
390
|
+
|
391
|
+
def test_consensus_string_half
|
392
|
+
a = A[ 'ata', 'aac', 'aag', 'aat' ]
|
393
|
+
assert_equal('aa?', a.consensus_string(0.5))
|
394
|
+
end
|
395
|
+
|
396
|
+
def test_consensus_iupac
|
397
|
+
a = A[
|
398
|
+
'acgtaaaccgaaacaz',
|
399
|
+
'acgtaaaccgccggcz',
|
400
|
+
'acgtcgtgttgtttgz',
|
401
|
+
'acgtcgtgttaaactz'
|
402
|
+
]
|
403
|
+
assert_equal('acgtmrwsykvhdbn?', a.consensus_iupac)
|
404
|
+
end
|
405
|
+
|
406
|
+
def test_match_line_amino
|
407
|
+
a = A[
|
408
|
+
'M-SNNNQMMHF-CASSSSSNNFH-AW',
|
409
|
+
'M-TEHDHIIYY-STATTGNDEVF-FW',
|
410
|
+
'M-AQQERLLHW-AVGNPNDEQLY-HW',
|
411
|
+
'M-SKKQKVFYF-CASKADEQHIH-LW',
|
412
|
+
'M-TNNNQMMHY-STASSSQHRMF-QW',
|
413
|
+
'M-AEHDHIIYW-AVGTTGKKKFY-YW'
|
414
|
+
#* ::::::::: ........... *
|
415
|
+
]
|
416
|
+
assert_equal('* ::::::::: ........... *', a.match_line_amino)
|
417
|
+
end
|
418
|
+
|
419
|
+
def test_match_line_nuc
|
420
|
+
a = A[ 'aaa', 'aa-','aac', 'at-' ]
|
421
|
+
assert_equal('* ', a.match_line_nuc)
|
422
|
+
end
|
423
|
+
|
424
|
+
def test_match_line
|
425
|
+
a = A[
|
426
|
+
Sequence::AA.new('MNSA'),
|
427
|
+
Sequence::AA.new('MHTL'),
|
428
|
+
Sequence::AA.new('MQNV'),
|
429
|
+
Sequence::AA.new('MKKW')
|
430
|
+
]
|
431
|
+
assert_equal('*:. ', a.match_line)
|
432
|
+
assert_equal('*:. ', a.match_line(:type => :aa))
|
433
|
+
assert_equal('* ', a.match_line(:type => :na))
|
434
|
+
end
|
435
|
+
|
436
|
+
def test_convert_match
|
437
|
+
a = A[
|
438
|
+
'aaaa',
|
439
|
+
'accc',
|
440
|
+
'acac',
|
441
|
+
'actc'
|
442
|
+
]
|
443
|
+
a.convert_match
|
444
|
+
assert_equal(A[ 'aaaa', '.ccc', '.c.c', '.ctc' ], a)
|
445
|
+
end
|
446
|
+
|
447
|
+
def test_convert_unmatch
|
448
|
+
a = A[ 'aaaa', '.ccc', '.c.c', '.ctc' ]
|
449
|
+
a.convert_unmatch
|
450
|
+
assert_equal(A[ 'aaaa', 'accc', 'acac', 'actc' ], a)
|
451
|
+
end
|
452
|
+
|
453
|
+
def test_alignment_normalize!
|
454
|
+
a = A[ 'a', 'atg', 'atgc', '' ]
|
455
|
+
a.alignment_normalize!
|
456
|
+
assert_equal(A[ 'a---', 'atg-', 'atgc', '----'], a)
|
457
|
+
end
|
458
|
+
|
459
|
+
def test_alignment_rstrip!
|
460
|
+
a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
|
461
|
+
assert(a.alignment_rstrip!)
|
462
|
+
assert_equal(A[ '--aaa', '--t-t', '---g-', '--t' ], a)
|
463
|
+
end
|
464
|
+
|
465
|
+
def test_alignment_rstrip_nil
|
466
|
+
a = A[ 'aa', '-a', 'a-' ]
|
467
|
+
assert_nil(a.alignment_rstrip!)
|
468
|
+
assert_equal(A[ 'aa', '-a', 'a-' ], a)
|
469
|
+
end
|
470
|
+
|
471
|
+
def test_alignment_lstrip!
|
472
|
+
a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
|
473
|
+
assert(a.alignment_lstrip!)
|
474
|
+
assert_equal(A[ 'aaa--', 't-t--', '-g---', 't' ], a)
|
475
|
+
end
|
476
|
+
|
477
|
+
def test_alignment_lstrip_nil
|
478
|
+
a = A[ 'aa', '-a', 'a-' ]
|
479
|
+
assert_nil(a.alignment_lstrip!)
|
480
|
+
assert_equal(A[ 'aa', '-a', 'a-' ], a)
|
481
|
+
end
|
482
|
+
|
483
|
+
def test_alignment_strip!
|
484
|
+
a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
|
485
|
+
assert(a.alignment_strip!)
|
486
|
+
assert_equal(A[ 'aaa', 't-t', '-g-', 't' ], a)
|
487
|
+
end
|
488
|
+
|
489
|
+
def test_alignment_strip_nil
|
490
|
+
a = A[ 'aa', '-a', 'a-' ]
|
491
|
+
assert_nil(a.alignment_strip!)
|
492
|
+
assert_equal(A[ 'aa', '-a', 'a-' ], a)
|
493
|
+
end
|
494
|
+
|
495
|
+
def test_remove_all_gaps!
|
496
|
+
a = A[ '--aaa--', '--t-t--', '---g---', '--t' ]
|
497
|
+
assert(a.remove_all_gaps!)
|
498
|
+
assert_equal(A[ 'aaa', 'tt', 'g', 't' ], a)
|
499
|
+
end
|
500
|
+
|
501
|
+
# test of alignment_slice.
|
502
|
+
# Please also refer alignment_window.
|
503
|
+
def test_alignment_slice
|
504
|
+
a = A[ 'a', 'at', 'atgca', 'atg', '' ]
|
505
|
+
assert_equal(Alignment::SequenceArray[ '', 't', 'tgc', 'tg', nil ],
|
506
|
+
a.alignment_slice(1, 3))
|
507
|
+
end
|
508
|
+
|
509
|
+
def test_alignment_subseq
|
510
|
+
a = A[
|
511
|
+
Sequence::NA.new('a'),
|
512
|
+
Sequence::NA.new('at'),
|
513
|
+
Sequence::NA.new('atgca'),
|
514
|
+
Sequence::NA.new('atg'),
|
515
|
+
Sequence::NA.new('')
|
516
|
+
]
|
517
|
+
assert_equal(Alignment::SequenceArray[
|
518
|
+
Sequence::NA.new(''),
|
519
|
+
Sequence::NA.new('t'),
|
520
|
+
Sequence::NA.new('tgc'),
|
521
|
+
Sequence::NA.new('tg'),
|
522
|
+
nil
|
523
|
+
], a.alignment_subseq(2,4))
|
524
|
+
end
|
525
|
+
|
526
|
+
def test_alignment_concat
|
527
|
+
a = A[ 'aaa', 'c', 'gg', 't' ]
|
528
|
+
a.alignment_concat(A[ 'ttt', 'gg', 'aa', 'cc', 'aa' ])
|
529
|
+
assert_equal(A[ 'aaattt', 'cgg', 'ggaa', 'tcc' ], a)
|
530
|
+
a.alignment_concat([ 'c', 't' ])
|
531
|
+
assert_equal(A[ 'aaatttc', 'cggt', 'ggaa', 'tcc' ], a)
|
532
|
+
end
|
533
|
+
end #class TestAlignmentEnumerableExtension
|
534
|
+
|
535
|
+
class TestAlignmentOutput < Test::Unit::TestCase
|
536
|
+
def setup
|
537
|
+
@obj = Object.new
|
538
|
+
@obj.extend(Alignment::Output)
|
539
|
+
end
|
540
|
+
|
541
|
+
def test_clustal_have_same_name_true
|
542
|
+
assert_equal([ 0, 1 ], @obj.instance_eval {
|
543
|
+
__clustal_have_same_name?([ 'ATP ATG', 'ATP ATA', 'BBB' ]) })
|
544
|
+
end
|
545
|
+
|
546
|
+
def test_have_same_name_false
|
547
|
+
assert_equal(false, @obj.instance_eval {
|
548
|
+
__clustal_have_same_name?([ 'GTP ATG', 'ATP ATA', 'BBB' ]) })
|
549
|
+
end
|
550
|
+
|
551
|
+
def test_avoid_same_name
|
552
|
+
assert_equal([ 'ATP_ATG', 'ATP_ATA', 'BBB' ],
|
553
|
+
@obj.instance_eval {
|
554
|
+
__clustal_avoid_same_name([ 'ATP ATG', 'ATP ATA', 'BBB' ]) })
|
555
|
+
end
|
556
|
+
|
557
|
+
def test_avoid_same_name_numbering
|
558
|
+
assert_equal([ '0_ATP', '1_ATP', '2_BBB' ],
|
559
|
+
@obj.instance_eval {
|
560
|
+
__clustal_avoid_same_name([ 'ATP', 'ATP', 'BBB' ]) })
|
561
|
+
end
|
562
|
+
|
563
|
+
end #class TestAlignmentOutput
|
564
|
+
|
565
|
+
|
566
|
+
class TestAlignment < Test::Unit::TestCase
|
567
|
+
|
568
|
+
# testing helper method
|
569
|
+
def build_na_alignment(*sequences)
|
570
|
+
sequences.inject(Alignment.new) { |alignment, sequence| alignment << Sequence::NA.new(sequence) }
|
571
|
+
end
|
572
|
+
private :build_na_alignment
|
573
|
+
|
574
|
+
def test_equals
|
575
|
+
alignment1 = Alignment.new([Sequence::NA.new("agct"), Sequence::NA.new("tagc")])
|
576
|
+
alignment2 = Alignment.new([Sequence::NA.new("agct"), Sequence::NA.new("tagc")])
|
577
|
+
assert_equal(alignment1, alignment2)
|
578
|
+
end
|
579
|
+
|
580
|
+
# Alignment#store
|
581
|
+
|
582
|
+
def test_store_cannot_override_key
|
583
|
+
alignment = Alignment.new
|
584
|
+
alignment.store("Cat DNA", Sequence::NA.new("cat"))
|
585
|
+
alignment.store("Cat DNA", Sequence::NA.new("gcat"))
|
586
|
+
assert_equal("cat", alignment["Cat DNA"])
|
587
|
+
end
|
588
|
+
|
589
|
+
def test_store_with_nil_key_uses_next_number_for_key
|
590
|
+
alignment = Alignment.new
|
591
|
+
alignment.store(nil, Sequence::NA.new("cat"))
|
592
|
+
alignment.store(nil, Sequence::NA.new("gat"))
|
593
|
+
alignment.store(nil, Sequence::NA.new("tat"))
|
594
|
+
assert_equal({0=>"cat",1=>"gat",2=>"tat"}, alignment.to_hash)
|
595
|
+
end
|
596
|
+
|
597
|
+
def test_store_with_default_keys_and_user_defined_keys
|
598
|
+
alignment = Alignment.new
|
599
|
+
alignment.store("cat key", Sequence::NA.new("cat"))
|
600
|
+
alignment.store(nil, Sequence::NA.new("cag"))
|
601
|
+
alignment.store("gat key", Sequence::NA.new("gat"))
|
602
|
+
alignment.store(nil, Sequence::NA.new("gag"))
|
603
|
+
assert_equal({"gat key"=>"gat",1=>"cag",3=>"gag","cat key"=>"cat"}, alignment.to_hash)
|
604
|
+
end
|
605
|
+
|
606
|
+
# Test append operator
|
607
|
+
|
608
|
+
def test_seqclass_when_sequence_used
|
609
|
+
alignment = Alignment.new
|
610
|
+
alignment << Sequence::NA.new("cat")
|
611
|
+
assert_equal({0=>"cat"}, alignment.to_hash)
|
612
|
+
end
|
613
|
+
|
614
|
+
# Test seqclass
|
615
|
+
|
616
|
+
def test_seqclass_when_sequence_used_no_seqclass_set
|
617
|
+
alignment = Alignment.new
|
618
|
+
alignment << Sequence::NA.new("cat")
|
619
|
+
assert_equal(Sequence::NA, alignment.seqclass)
|
620
|
+
end
|
621
|
+
|
622
|
+
def test_seqclass_String_seq_not_present_no_seqclass_set
|
623
|
+
alignment = Alignment.new
|
624
|
+
alignment << nil
|
625
|
+
assert_equal(String, alignment.seqclass)
|
626
|
+
end
|
627
|
+
|
628
|
+
def test_seqclass_when_seqclass_set
|
629
|
+
alignment = Alignment.new
|
630
|
+
alignment.seqclass = Fixnum
|
631
|
+
alignment << "this doesn't really make sense"
|
632
|
+
assert_equal(Fixnum, alignment.seqclass)
|
633
|
+
end
|
634
|
+
|
635
|
+
# Alignment#gap_char
|
636
|
+
|
637
|
+
def test_default_gap_char
|
638
|
+
alignment = Alignment.new
|
639
|
+
assert_equal("-", alignment.gap_char)
|
640
|
+
end
|
641
|
+
|
642
|
+
def test_set_and_get_gap_char
|
643
|
+
alignment = Alignment.new
|
644
|
+
alignment.gap_char = "+"
|
645
|
+
assert_equal("+", alignment.gap_char)
|
646
|
+
end
|
647
|
+
|
648
|
+
# Alignment#gap_regexp
|
649
|
+
|
650
|
+
def test_default_gap_regexp_matches_default_gap_char
|
651
|
+
alignment = Alignment.new
|
652
|
+
assert(alignment.gap_regexp.match(alignment.gap_char))
|
653
|
+
end
|
654
|
+
|
655
|
+
# Alignment#missing_char
|
656
|
+
|
657
|
+
def test_default_missing_char
|
658
|
+
alignment = Alignment.new
|
659
|
+
assert_equal("?", alignment.missing_char)
|
660
|
+
end
|
661
|
+
|
662
|
+
# Alignment#seq_length
|
663
|
+
|
664
|
+
def test_seq_length_when_one_sequence
|
665
|
+
alignment = build_na_alignment("agt")
|
666
|
+
assert_equal(3, alignment.seq_length)
|
667
|
+
end
|
668
|
+
|
669
|
+
def test_seq_length_is_max_seq_length
|
670
|
+
alignment = build_na_alignment("agt", "agtaa", "agta")
|
671
|
+
assert_equal(5, alignment.seq_length)
|
672
|
+
end
|
673
|
+
|
674
|
+
# Alignment#each_site
|
675
|
+
|
676
|
+
def test_each_site_equal_length
|
677
|
+
alignment = build_na_alignment("acg", "gta")
|
678
|
+
expected_sites = [["a", "g"], ["c", "t"], ["g", "a"]]
|
679
|
+
alignment.each_site do |site|
|
680
|
+
assert_equal expected_sites.shift, site, "site ##{3-expected_sites.size} wrong"
|
681
|
+
end
|
682
|
+
end
|
683
|
+
|
684
|
+
def test_each_site_unequal_length
|
685
|
+
alignment = build_na_alignment("ac", "gta")
|
686
|
+
expected_sites = [["a", "g"], ["c", "t"], ["-", "a"]]
|
687
|
+
alignment.each_site do |site|
|
688
|
+
assert_equal expected_sites.shift, site, "site ##{3-expected_sites.size} wrong"
|
689
|
+
end
|
690
|
+
end
|
691
|
+
|
692
|
+
#TODO: Lots of stuff needing tests here
|
693
|
+
|
694
|
+
# Alignment#add_seq
|
695
|
+
|
696
|
+
def test_add_seq_no_key
|
697
|
+
alignment = Alignment.new
|
698
|
+
alignment.add_seq("agct")
|
699
|
+
assert_equal(String, alignment.seqclass, "wrong class")
|
700
|
+
assert_equal({0=>"agct"}, alignment.to_hash, "wrong hash")
|
701
|
+
end
|
702
|
+
|
703
|
+
def test_add_seq_using_seq_with_seq_method
|
704
|
+
seq = "agtc"
|
705
|
+
class <<seq
|
706
|
+
def seq
|
707
|
+
Sequence::NA.new(self)
|
708
|
+
end
|
709
|
+
end
|
710
|
+
|
711
|
+
alignment = Alignment.new
|
712
|
+
alignment.add_seq(seq, "key")
|
713
|
+
assert_equal(Sequence::NA, alignment.seqclass, "wrong class")
|
714
|
+
assert_equal({"key"=>"agtc"}, alignment.to_hash, "wrong hash")
|
715
|
+
end
|
716
|
+
|
717
|
+
def test_add_seq_using_seq_with_naseq_method
|
718
|
+
seq = "agtc"
|
719
|
+
class <<seq
|
720
|
+
def naseq
|
721
|
+
Sequence::NA.new(self)
|
722
|
+
end
|
723
|
+
end
|
724
|
+
|
725
|
+
alignment = Alignment.new
|
726
|
+
alignment.add_seq(seq, "key")
|
727
|
+
assert_equal(Sequence::NA, alignment.seqclass, "wrong class")
|
728
|
+
assert_equal({"key"=>"agtc"}, alignment.to_hash, "wrong hash")
|
729
|
+
end
|
730
|
+
|
731
|
+
def test_add_seq_using_seq_with_aaseq_method
|
732
|
+
seq = "AVGR"
|
733
|
+
class <<seq
|
734
|
+
def aaseq
|
735
|
+
Sequence::AA.new(self)
|
736
|
+
end
|
737
|
+
end
|
738
|
+
|
739
|
+
alignment = Alignment.new
|
740
|
+
alignment.add_seq(seq, "key")
|
741
|
+
assert_equal(Sequence::AA, alignment.seqclass, "wrong class")
|
742
|
+
assert_equal({"key"=>"AVGR"}, alignment.to_hash, "wrong hash")
|
743
|
+
end
|
744
|
+
|
745
|
+
def test_add_seq_using_seq_with_definition_method
|
746
|
+
seq = "atgc"
|
747
|
+
class <<seq
|
748
|
+
def definition
|
749
|
+
"this is the key"
|
750
|
+
end
|
751
|
+
end
|
752
|
+
|
753
|
+
alignment = Alignment.new
|
754
|
+
alignment.add_seq(seq)
|
755
|
+
assert_equal({"this is the key"=>"atgc"}, alignment.to_hash, "wrong hash")
|
756
|
+
end
|
757
|
+
|
758
|
+
def test_add_seq_using_seq_with_entry_id_method
|
759
|
+
seq = "atgc"
|
760
|
+
class <<seq
|
761
|
+
def entry_id
|
762
|
+
271828
|
763
|
+
end
|
764
|
+
end
|
765
|
+
|
766
|
+
alignment = Alignment.new
|
767
|
+
alignment.add_seq(seq)
|
768
|
+
assert_equal({271828=>"atgc"}, alignment.to_hash, "wrong hash")
|
769
|
+
end
|
770
|
+
|
771
|
+
# Alignment#consensus_string
|
772
|
+
|
773
|
+
def test_consensus_string_no_gaps
|
774
|
+
alignment = build_na_alignment("agtcgattaa",
|
775
|
+
"tttcgatgcc")
|
776
|
+
assert_equal("??tcgat???", alignment.consensus_string)
|
777
|
+
end
|
778
|
+
|
779
|
+
def test_consensus_threshold_two_sequences
|
780
|
+
alignment = build_na_alignment("agtcgattaa",
|
781
|
+
"tttcgatgcc")
|
782
|
+
# the threshold is the fraction of sequences in which a symbol must
|
783
|
+
# occur at a given position to be considered the consensus symbol
|
784
|
+
assert_equal("agtcgattaa", alignment.consensus(0.5))
|
785
|
+
assert_equal("??tcgat???", alignment.consensus(0.500000001))
|
786
|
+
end
|
787
|
+
|
788
|
+
def test_consensus_threshold_four_sequences
|
789
|
+
alignment = build_na_alignment("agtg",
|
790
|
+
"ttag",
|
791
|
+
"actc",
|
792
|
+
"tatc")
|
793
|
+
# ties go to the symbol that occurs in the earliest sequence
|
794
|
+
assert_equal("agtg", alignment.consensus(0.25))
|
795
|
+
assert_equal("a?tg", alignment.consensus(0.26))
|
796
|
+
end
|
797
|
+
|
798
|
+
def test_consensus_opt_gap_mode
|
799
|
+
alignment = build_na_alignment("gt-gt-a",
|
800
|
+
"ttcggc-",
|
801
|
+
"ttcggc-")
|
802
|
+
# using threshold = 0.5, that is a symbol must occur >= half the time in order to be consensus
|
803
|
+
# gap_mode -1 means gaps are ignored
|
804
|
+
assert_equal("ttcggca", alignment.consensus(0.5, :gap_mode => -1), "gap mode -1")
|
805
|
+
# gap_mode 0 means gaps are treated like regular symbols, yielding a gap in the last position
|
806
|
+
assert_equal("ttcggc-", alignment.consensus(0.5, :gap_mode => 0), "gap mode 0")
|
807
|
+
# gap_mode 1 means gaps take precedence over any other symbol, yielding two more gaps
|
808
|
+
assert_equal("tt-gg--", alignment.consensus(0.5, :gap_mode => 1), "gap mode 1")
|
809
|
+
end
|
810
|
+
|
811
|
+
def test_consensus_opt_missing_char
|
812
|
+
alignment = build_na_alignment("agtcgattaa",
|
813
|
+
"tttcgatgcc")
|
814
|
+
assert_equal("**tcgat***", alignment.consensus(1, :missing_char => "*"))
|
815
|
+
end
|
816
|
+
|
817
|
+
# Alignment#consensus_iupac
|
818
|
+
|
819
|
+
def test_consensus_iupac_no_gaps
|
820
|
+
alignment = build_na_alignment("agtcgattaa", "tttcgatgcc")
|
821
|
+
assert_equal("wktcgatkmm", alignment.consensus_iupac)
|
822
|
+
end
|
823
|
+
|
824
|
+
def test_consensus_iupac_of_ambiguous_bases
|
825
|
+
alignment = build_na_alignment("tmrwsykvhdbnd", "uaaaccgaaacab")
|
826
|
+
assert_equal("tmrwsykvhdbnn", alignment.consensus_iupac)
|
827
|
+
end
|
828
|
+
|
829
|
+
def test_consensus_iupac_gap_modes
|
830
|
+
alignment = build_na_alignment("a-t", "acc")
|
831
|
+
# gap_mode -1 means gaps are ignored
|
832
|
+
assert_equal("acy", alignment.consensus_iupac(:gap_mode => -1))
|
833
|
+
# gap_mode 0 means gaps are treated as normal characters, yielding a missing symbol
|
834
|
+
assert_equal("a?y", alignment.consensus_iupac(:gap_mode => 0))
|
835
|
+
# gap_mode 1 means gaps take precedence over everything, yielding a gap
|
836
|
+
assert_equal("a-y", alignment.consensus_iupac(:gap_mode => 1))
|
837
|
+
end
|
838
|
+
|
839
|
+
def test_consensus_iupac_yields_correct_ambiguous_bases
|
840
|
+
assert_equal "t", build_na_alignment("t", "u").consensus_iupac # not really IUPAC
|
841
|
+
|
842
|
+
# m = a c
|
843
|
+
assert_equal "m", build_na_alignment("a", "c").consensus_iupac, "m #1"
|
844
|
+
assert_equal "m", build_na_alignment("m", "c").consensus_iupac, "m #2"
|
845
|
+
assert_equal "m", build_na_alignment("a", "m").consensus_iupac, "m #3"
|
846
|
+
assert_equal "m", build_na_alignment("m", "a", "c").consensus_iupac, "m #4"
|
847
|
+
|
848
|
+
# r = a g
|
849
|
+
assert_equal "r", build_na_alignment("a", "g").consensus_iupac, "r #1"
|
850
|
+
assert_equal "r", build_na_alignment("r", "g").consensus_iupac, "r #2"
|
851
|
+
assert_equal "r", build_na_alignment("a", "r").consensus_iupac, "r #3"
|
852
|
+
assert_equal "r", build_na_alignment("a", "r", "g").consensus_iupac, "r #4"
|
853
|
+
|
854
|
+
# w = a t/u
|
855
|
+
assert_equal "w", build_na_alignment("a", "t").consensus_iupac, "w #1"
|
856
|
+
assert_equal "w", build_na_alignment("a", "u").consensus_iupac, "w #2"
|
857
|
+
assert_equal "w", build_na_alignment("w", "a").consensus_iupac, "w #3"
|
858
|
+
assert_equal "w", build_na_alignment("t", "w").consensus_iupac, "w #4"
|
859
|
+
assert_equal "w", build_na_alignment("w", "u").consensus_iupac, "w #5"
|
860
|
+
assert_equal "w", build_na_alignment("u", "t", "a").consensus_iupac, "w #6"
|
861
|
+
assert_equal "w", build_na_alignment("w", "u", "t", "a").consensus_iupac, "w #7"
|
862
|
+
|
863
|
+
# s = c g
|
864
|
+
assert_equal "s", build_na_alignment("c", "g").consensus_iupac, "s #1"
|
865
|
+
assert_equal "s", build_na_alignment("s", "g").consensus_iupac, "s #2"
|
866
|
+
assert_equal "s", build_na_alignment("c", "s").consensus_iupac, "s #3"
|
867
|
+
assert_equal "s", build_na_alignment("c", "s", "g").consensus_iupac, "s #4"
|
868
|
+
|
869
|
+
# y = c t/u
|
870
|
+
assert_equal "y", build_na_alignment("c", "t").consensus_iupac, "y #1"
|
871
|
+
assert_equal "y", build_na_alignment("c", "u").consensus_iupac, "y #2"
|
872
|
+
assert_equal "y", build_na_alignment("y", "c").consensus_iupac, "y #3"
|
873
|
+
assert_equal "y", build_na_alignment("t", "y").consensus_iupac, "y #4"
|
874
|
+
assert_equal "y", build_na_alignment("y", "u").consensus_iupac, "y #5"
|
875
|
+
assert_equal "y", build_na_alignment("u", "t", "c").consensus_iupac, "y #6"
|
876
|
+
assert_equal "y", build_na_alignment("y", "u", "t", "c").consensus_iupac, "y #7"
|
877
|
+
|
878
|
+
# k = g t/u
|
879
|
+
assert_equal "k", build_na_alignment("g", "t").consensus_iupac, "k #1"
|
880
|
+
assert_equal "k", build_na_alignment("g", "u").consensus_iupac, "k #2"
|
881
|
+
assert_equal "k", build_na_alignment("k", "g").consensus_iupac, "k #3"
|
882
|
+
assert_equal "k", build_na_alignment("t", "k").consensus_iupac, "k #4"
|
883
|
+
assert_equal "k", build_na_alignment("k", "u").consensus_iupac, "k #5"
|
884
|
+
assert_equal "k", build_na_alignment("u", "t", "g").consensus_iupac, "k #6"
|
885
|
+
assert_equal "k", build_na_alignment("k", "u", "t", "g").consensus_iupac, "k #7"
|
886
|
+
|
887
|
+
# v = a c g m r s
|
888
|
+
assert_equal "v", build_na_alignment("a", "c", "g").consensus_iupac, "v #1"
|
889
|
+
assert_equal "v", build_na_alignment("g", "m").consensus_iupac, "v #2"
|
890
|
+
assert_equal "v", build_na_alignment("a", "s").consensus_iupac, "v #3"
|
891
|
+
assert_equal "v", build_na_alignment("c", "r").consensus_iupac, "v #4"
|
892
|
+
assert_equal "v", build_na_alignment("m", "s").consensus_iupac, "v #5"
|
893
|
+
assert_equal "v", build_na_alignment("m", "r").consensus_iupac, "v #6"
|
894
|
+
assert_equal "v", build_na_alignment("s", "r").consensus_iupac, "v #7"
|
895
|
+
assert_equal "v", build_na_alignment("s", "r", "m").consensus_iupac, "v #8"
|
896
|
+
assert_equal "v", build_na_alignment("s", "r", "m", "a", "c", "g").consensus_iupac, "v #9"
|
897
|
+
assert_equal "v", build_na_alignment("v", "g").consensus_iupac, "v #10" # alright, enough
|
898
|
+
|
899
|
+
# b = t/u c g s y k
|
900
|
+
assert_equal "b", build_na_alignment("t", "c", "g").consensus_iupac, "b #1"
|
901
|
+
assert_equal "b", build_na_alignment("g", "y").consensus_iupac, "b #2"
|
902
|
+
assert_equal "b", build_na_alignment("t", "s").consensus_iupac, "b #3"
|
903
|
+
assert_equal "b", build_na_alignment("c", "k").consensus_iupac, "b #4"
|
904
|
+
assert_equal "b", build_na_alignment("y", "s").consensus_iupac, "b #5"
|
905
|
+
assert_equal "b", build_na_alignment("y", "k").consensus_iupac, "b #6"
|
906
|
+
assert_equal "b", build_na_alignment("s", "k").consensus_iupac, "b #7"
|
907
|
+
assert_equal "b", build_na_alignment("s", "k", "y").consensus_iupac, "b #8"
|
908
|
+
assert_equal "b", build_na_alignment("s", "k", "y", "u", "c", "g").consensus_iupac, "b #9"
|
909
|
+
assert_equal "b", build_na_alignment("b", "g").consensus_iupac, "b #10"
|
910
|
+
|
911
|
+
# h = t/u c a y w m
|
912
|
+
assert_equal "h", build_na_alignment("t", "c", "a").consensus_iupac, "h #1"
|
913
|
+
assert_equal "h", build_na_alignment("a", "y").consensus_iupac, "h #2"
|
914
|
+
assert_equal "h", build_na_alignment("c", "w").consensus_iupac, "h #3"
|
915
|
+
assert_equal "h", build_na_alignment("u", "m").consensus_iupac, "h #4"
|
916
|
+
assert_equal "h", build_na_alignment("y", "w").consensus_iupac, "h #5"
|
917
|
+
assert_equal "h", build_na_alignment("y", "m").consensus_iupac, "h #6"
|
918
|
+
assert_equal "h", build_na_alignment("y", "w").consensus_iupac, "h #7"
|
919
|
+
assert_equal "h", build_na_alignment("w", "m", "y").consensus_iupac, "h #8"
|
920
|
+
assert_equal "h", build_na_alignment("w", "m", "y", "t", "c", "a").consensus_iupac, "h #9"
|
921
|
+
assert_equal "h", build_na_alignment("h", "t").consensus_iupac, "h #10"
|
922
|
+
|
923
|
+
# d = t/u g a r w k
|
924
|
+
assert_equal "d", build_na_alignment("t", "g", "a").consensus_iupac, "d #1"
|
925
|
+
assert_equal "d", build_na_alignment("r", "t").consensus_iupac, "d #2"
|
926
|
+
assert_equal "d", build_na_alignment("w", "g").consensus_iupac, "d #3"
|
927
|
+
assert_equal "d", build_na_alignment("k", "a").consensus_iupac, "d #4"
|
928
|
+
assert_equal "d", build_na_alignment("k", "r").consensus_iupac, "d #5"
|
929
|
+
assert_equal "d", build_na_alignment("k", "w").consensus_iupac, "d #6"
|
930
|
+
assert_equal "d", build_na_alignment("r", "w").consensus_iupac, "d #7"
|
931
|
+
assert_equal "d", build_na_alignment("r", "w", "k").consensus_iupac, "d #8"
|
932
|
+
assert_equal "d", build_na_alignment("k", "r", "w", "t", "g", "a").consensus_iupac, "d #9"
|
933
|
+
assert_equal "d", build_na_alignment("d", "t").consensus_iupac, "d #10"
|
934
|
+
|
935
|
+
# n = anything
|
936
|
+
assert_equal "n", build_na_alignment("a", "g", "c", "t").consensus_iupac, "n #1"
|
937
|
+
assert_equal "n", build_na_alignment("a", "g", "c", "u").consensus_iupac, "n #2"
|
938
|
+
assert_equal "n", build_na_alignment("w", "s").consensus_iupac, "n #3"
|
939
|
+
assert_equal "n", build_na_alignment("k", "m").consensus_iupac, "n #4"
|
940
|
+
assert_equal "n", build_na_alignment("r", "y").consensus_iupac, "n #5"
|
941
|
+
end
|
942
|
+
|
943
|
+
def test_consensus_iupac_missing_char
|
944
|
+
alignment = build_na_alignment("a??", "ac?")
|
945
|
+
assert_equal("a??", alignment.consensus_iupac())
|
946
|
+
end
|
947
|
+
|
948
|
+
def test_consensus_iupac_missing_char_option
|
949
|
+
alignment = build_na_alignment("a**t", "ac**")
|
950
|
+
assert_equal("a***", alignment.consensus_iupac(:missing_char => "*"))
|
951
|
+
end
|
952
|
+
|
953
|
+
# Alignment#convert_match
|
954
|
+
|
955
|
+
def test_convert_match
|
956
|
+
alignment = Alignment.new
|
957
|
+
alignment << Sequence::NA.new("agtcgattaa")
|
958
|
+
alignment << Sequence::NA.new("tttcgatgcc")
|
959
|
+
match = alignment.convert_match
|
960
|
+
assert_equal(alignment[0], match[0], "first sequence altered")
|
961
|
+
assert_equal("tt.....gcc", match[1], "wrong match")
|
962
|
+
end
|
963
|
+
|
964
|
+
# Alignment#convert_unmatch
|
965
|
+
|
966
|
+
def test_convert_unmatch
|
967
|
+
alignment = Alignment.new
|
968
|
+
alignment << Sequence::NA.new("agtcgattaa")
|
969
|
+
alignment << Sequence::NA.new("tt.....gcc")
|
970
|
+
unmatched = alignment.convert_unmatch
|
971
|
+
assert_equal("agtcgattaa", unmatched[0], "first changed")
|
972
|
+
assert_equal("tttcgatgcc", unmatched[1], "second wrong")
|
973
|
+
end
|
974
|
+
|
975
|
+
def test_convert_unmatch_multiple_sequences
|
976
|
+
alignment = Alignment.new
|
977
|
+
alignment << Sequence::NA.new("agtcgattaa")
|
978
|
+
alignment << Sequence::NA.new("tt.....gcc")
|
979
|
+
alignment << Sequence::NA.new("c...c..g.c")
|
980
|
+
unmatched = alignment.convert_unmatch
|
981
|
+
assert_equal("agtcgattaa", unmatched[0], "first changed")
|
982
|
+
assert_equal("tttcgatgcc", unmatched[1], "second wrong")
|
983
|
+
assert_equal("cgtccatgac", unmatched[2], "third wrong")
|
984
|
+
end
|
985
|
+
|
986
|
+
def test_convert_unmatch_different_length_sequences_truncates_seq_if_last_matched
|
987
|
+
alignment = Alignment.new
|
988
|
+
alignment << Sequence::NA.new("agtcgatta")
|
989
|
+
alignment << Sequence::NA.new("tt.....gc.")
|
990
|
+
unmatched = alignment.convert_unmatch
|
991
|
+
assert_equal("agtcgatta", unmatched[0], "first changed")
|
992
|
+
assert_equal("tttcgatgc", unmatched[1], "second wrong") #TODO: verify this is correct, and not . at end
|
993
|
+
end
|
994
|
+
|
995
|
+
def test_convert_unmatch_different_match_char
|
996
|
+
alignment = Alignment.new
|
997
|
+
alignment << Sequence::NA.new("agtcga")
|
998
|
+
alignment << Sequence::NA.new("tt====")
|
999
|
+
unmatched = alignment.convert_unmatch('=')
|
1000
|
+
assert_equal("agtcga", unmatched[0], "first changed")
|
1001
|
+
assert_equal("tttcga", unmatched[1], "second wrong")
|
1002
|
+
end
|
1003
|
+
|
1004
|
+
# Alignment#match_line
|
1005
|
+
|
1006
|
+
def test_match_line_protein
|
1007
|
+
alignment = Alignment.new
|
1008
|
+
alignment << Sequence::AA.new("AELFMCF")
|
1009
|
+
alignment << Sequence::AA.new("AKLVNNF")
|
1010
|
+
assert_equal "*:*. *", alignment.match_line
|
1011
|
+
end
|
1012
|
+
|
1013
|
+
#TODO: lots more on the consensus, match, etc.
|
1014
|
+
|
1015
|
+
# Alignment#normalize
|
1016
|
+
|
1017
|
+
def test_normalizebang_extends_sequences_with_gaps
|
1018
|
+
alignment = build_na_alignment("a", "ag", "agc", "agct")
|
1019
|
+
alignment.normalize!
|
1020
|
+
assert_equal({0=>"a---",1=>"ag--",2=>"agc-",3=>"agct"}, alignment.to_hash)
|
1021
|
+
end
|
1022
|
+
|
1023
|
+
# Alignment#to_clustal
|
1024
|
+
end
|
1025
|
+
end
|