wwood-bioruby 1.2.11
Sign up to get free protection for your applications and to get access to all the features.
- 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
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +11 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +7 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +47 -0
- 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
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +10 -0
- 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
- data/test/data/blast/b0002.faa.m0 +128 -0
- data/test/data/blast/b0002.faa.m7 +65 -0
- 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 +1,112 @@
|
|
1
|
+
#
|
2
|
+
# = test/unit/bio/appl/blast/test_ncbioptions.rb - Unit test for Bio::Blast::NCBIOptions
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>
|
5
|
+
# License:: The Ruby License
|
6
|
+
#
|
7
|
+
# $Id:$
|
8
|
+
#
|
9
|
+
|
10
|
+
require 'pathname'
|
11
|
+
libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
|
12
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
13
|
+
|
14
|
+
require 'test/unit'
|
15
|
+
require 'bio/appl/blast/ncbioptions'
|
16
|
+
|
17
|
+
module Bio
|
18
|
+
|
19
|
+
class TestBlastNCBIOptions < Test::Unit::TestCase
|
20
|
+
|
21
|
+
def setup
|
22
|
+
@str = '-p blastn -m0 -m 1 -m2 -m 3 -F T -m 4 m5 -pblastx -m 6 -m 7'
|
23
|
+
@options = %w( -p blastn -m0 -m 1 -m2 -m 3 -F T -m 4 m5
|
24
|
+
-pblastx -m 6 -m 7 )
|
25
|
+
@normalized_options = %w( -F T m5 -p blastx -m 7 )
|
26
|
+
@obj = Bio::Blast::NCBIOptions.parse(@str)
|
27
|
+
end
|
28
|
+
|
29
|
+
def test_parse
|
30
|
+
str = '-p tblastx -d cdna_human -i est001.fst -o test.blastn -e 0.1'
|
31
|
+
options = %w( -p tblastx -d cdna_human -i est001.fst
|
32
|
+
-o test.blastn -e 0.1 )
|
33
|
+
obj = Bio::Blast::NCBIOptions.parse(str)
|
34
|
+
assert_equal(options, obj.options)
|
35
|
+
end
|
36
|
+
|
37
|
+
def test_normalize!
|
38
|
+
assert_nothing_raised { @obj.normalize! }
|
39
|
+
assert_equal(@normalized_options, @obj.options)
|
40
|
+
end
|
41
|
+
|
42
|
+
def test_get
|
43
|
+
assert_equal('blastx', @obj.get('-p'))
|
44
|
+
assert_equal('blastx', @obj.get('p'))
|
45
|
+
|
46
|
+
assert_equal('7', @obj.get('-m'))
|
47
|
+
assert_equal('7', @obj.get('m'))
|
48
|
+
|
49
|
+
assert_equal('T', @obj.get('-F'))
|
50
|
+
assert_equal('T', @obj.get('F'))
|
51
|
+
|
52
|
+
assert_nil(@obj.get('-X'))
|
53
|
+
end
|
54
|
+
|
55
|
+
def test_delete
|
56
|
+
assert_equal('blastx', @obj.delete('-p'))
|
57
|
+
assert_nil(@obj.delete('p'))
|
58
|
+
|
59
|
+
assert_equal('7', @obj.delete('-m'))
|
60
|
+
assert_nil(@obj.delete('m'))
|
61
|
+
|
62
|
+
assert_equal('T', @obj.delete('F'))
|
63
|
+
assert_nil(@obj.delete('-F'))
|
64
|
+
|
65
|
+
assert_nil(@obj.delete('-X'))
|
66
|
+
end
|
67
|
+
|
68
|
+
def test_set
|
69
|
+
assert_equal('blastx', @obj.set('-p', 'blastp'))
|
70
|
+
assert_equal('blastp', @obj.set('p', 'tblastx'))
|
71
|
+
assert_equal('tblastx',@obj.get('p'))
|
72
|
+
|
73
|
+
assert_equal('7', @obj.set('m', '8'))
|
74
|
+
assert_equal('8', @obj.set('-m', '0'))
|
75
|
+
assert_equal('0', @obj.get('m'))
|
76
|
+
|
77
|
+
assert_equal('T', @obj.set('-F', 'F'))
|
78
|
+
assert_equal('F', @obj.get('F'))
|
79
|
+
|
80
|
+
assert_nil(@obj.set('-d', 'nr'))
|
81
|
+
assert_equal('nr', @obj.get('d'))
|
82
|
+
|
83
|
+
assert_nil(@obj.set('i', 'test.fst'))
|
84
|
+
assert_equal('test.fst', @obj.get('-i'))
|
85
|
+
end
|
86
|
+
|
87
|
+
def test_equal_equal
|
88
|
+
obj1 = Bio::Blast::NCBIOptions.parse(@str)
|
89
|
+
assert_equal(true, @obj == obj1)
|
90
|
+
|
91
|
+
obj2 = Bio::Blast::NCBIOptions.parse('-F F')
|
92
|
+
assert_equal(false, @obj == obj2)
|
93
|
+
|
94
|
+
assert_equal(false, @obj == 12345)
|
95
|
+
end
|
96
|
+
|
97
|
+
def test_add_options
|
98
|
+
opts = %w( -p tblastx -m 8 -d cdna -i est.fst -o test.blast -e 0.01 )
|
99
|
+
result_opts = %w( -F T m5 ) + opts
|
100
|
+
assert_nothing_raised { @obj.add_options(opts) }
|
101
|
+
assert_equal(result_opts, @obj.options)
|
102
|
+
end
|
103
|
+
|
104
|
+
def test_make_command_line_options
|
105
|
+
opts = %w( -p tblastx -d cdna -i est.fst -o test.blast -e 0.01 )
|
106
|
+
result_opts = opts + %w( -m 0 -m 1 -m 2 -m 3 -F T -m 4 m5 -m 6 -m 7 )
|
107
|
+
assert_equal(result_opts, @obj.make_command_line_options(opts))
|
108
|
+
end
|
109
|
+
|
110
|
+
end #class TestBlastNCBIOptions
|
111
|
+
|
112
|
+
end #module Bio
|
@@ -0,0 +1,1135 @@
|
|
1
|
+
#
|
2
|
+
# test/unit/bio/appl/blast/test_report.rb - Unit test for Bio::Blast::Report
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005, 2008
|
5
|
+
# Mitsuteru Nakao <n@bioruby.org>,
|
6
|
+
# Naohisa Goto <ng@bioruby.org>
|
7
|
+
# License:: The Ruby License
|
8
|
+
#
|
9
|
+
# $Id:$
|
10
|
+
#
|
11
|
+
|
12
|
+
require 'pathname'
|
13
|
+
libpath = Pathname.new(File.join(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib'))).cleanpath.to_s
|
14
|
+
$:.unshift(libpath) unless $:.include?(libpath)
|
15
|
+
|
16
|
+
require 'test/unit'
|
17
|
+
require 'bio/appl/blast/report'
|
18
|
+
|
19
|
+
|
20
|
+
module Bio
|
21
|
+
|
22
|
+
module TestBlastReportHelper
|
23
|
+
bioruby_root = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5)).cleanpath.to_s
|
24
|
+
TestDataBlast = Pathname.new(File.join(bioruby_root, 'test', 'data', 'blast')).cleanpath.to_s
|
25
|
+
|
26
|
+
private
|
27
|
+
|
28
|
+
def get_input_data(basename = 'b0002.faa')
|
29
|
+
File.open(File.join(TestDataBlast, basename)).read
|
30
|
+
end
|
31
|
+
|
32
|
+
def get_output_data(basename = 'b0002.faa', format = 7)
|
33
|
+
fn = basename + ".m#{format.to_i}"
|
34
|
+
|
35
|
+
# available filenames:
|
36
|
+
# 'b0002.faa.m0'
|
37
|
+
# 'b0002.faa.m7'
|
38
|
+
# 'b0002.faa.m8'
|
39
|
+
|
40
|
+
File.open(File.join(TestDataBlast, fn)).read
|
41
|
+
end
|
42
|
+
|
43
|
+
def create_report_object(basename = 'b0002.faa')
|
44
|
+
case self.class.name.to_s
|
45
|
+
when /XMLParser/i
|
46
|
+
text = get_output_data(basename, 7)
|
47
|
+
Bio::Blast::Report.new(text, :xmlparser)
|
48
|
+
when /REXML/i
|
49
|
+
text = get_output_data(basename, 7)
|
50
|
+
Bio::Blast::Report.new(text, :rexml)
|
51
|
+
when /Default/i
|
52
|
+
text = get_output_data(basename, 0)
|
53
|
+
Bio::Blast::Default::Report.new(text)
|
54
|
+
when /Tab/i
|
55
|
+
text = get_output_data(basename, 8)
|
56
|
+
Bio::Blast::Report.new(text)
|
57
|
+
else
|
58
|
+
text = get_output_data(basename, 7)
|
59
|
+
Bio::Blast::Report.new(text)
|
60
|
+
end
|
61
|
+
end
|
62
|
+
end #module TestBlastReportHelper
|
63
|
+
|
64
|
+
class TestBlastReport < Test::Unit::TestCase
|
65
|
+
include TestBlastReportHelper
|
66
|
+
|
67
|
+
def setup
|
68
|
+
@report = create_report_object
|
69
|
+
end
|
70
|
+
|
71
|
+
def test_iterations
|
72
|
+
assert(@report.iterations)
|
73
|
+
end
|
74
|
+
|
75
|
+
def test_parameters
|
76
|
+
assert_equal('BLOSUM62', @report.parameters['matrix'])
|
77
|
+
assert_equal(10, @report.parameters['expect'])
|
78
|
+
assert_equal(11, @report.parameters['gap-open'])
|
79
|
+
assert_equal(1, @report.parameters['gap-extend'])
|
80
|
+
assert_equal('S', @report.parameters['filter'])
|
81
|
+
end
|
82
|
+
|
83
|
+
def test_program
|
84
|
+
assert_equal('blastp', @report.program)
|
85
|
+
end
|
86
|
+
|
87
|
+
def test_version
|
88
|
+
assert_equal('blastp 2.2.10 [Oct-19-2004]', @report.version)
|
89
|
+
end
|
90
|
+
|
91
|
+
def test_reference
|
92
|
+
xml_quoted_str = "~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs", Nucleic Acids Res. 25:3389-3402."
|
93
|
+
text_str = '~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs", Nucleic Acids Res. 25:3389-3402.'
|
94
|
+
# assert_equal(xml_quoted_str, @report.reference)
|
95
|
+
assert_equal(text_str, @report.reference)
|
96
|
+
end
|
97
|
+
|
98
|
+
def test_db
|
99
|
+
assert_equal('b0002.faa', @report.db)
|
100
|
+
end
|
101
|
+
|
102
|
+
def test_query_id
|
103
|
+
assert_equal('lcl|QUERY', @report.query_id)
|
104
|
+
end
|
105
|
+
|
106
|
+
def test_query_def
|
107
|
+
assert_equal('eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)', @report.query_def)
|
108
|
+
end
|
109
|
+
|
110
|
+
def test_query_len
|
111
|
+
assert_equal(820, @report.query_len)
|
112
|
+
end
|
113
|
+
|
114
|
+
def test_matrix
|
115
|
+
assert_equal('BLOSUM62', @report.matrix)
|
116
|
+
end
|
117
|
+
|
118
|
+
def test_expect
|
119
|
+
assert_equal(10, @report.expect)
|
120
|
+
end
|
121
|
+
|
122
|
+
def test_inclusion
|
123
|
+
assert_nothing_raised { @report.inclusion }
|
124
|
+
end
|
125
|
+
|
126
|
+
def test_sc_match
|
127
|
+
assert_nothing_raised { @report.sc_match }
|
128
|
+
end
|
129
|
+
|
130
|
+
def test_sc_mismatch
|
131
|
+
assert_nothing_raised { @report.sc_mismatch }
|
132
|
+
end
|
133
|
+
|
134
|
+
def test_gap_open
|
135
|
+
assert_equal(11, @report.gap_open)
|
136
|
+
end
|
137
|
+
|
138
|
+
def test_gap_extend
|
139
|
+
assert_equal(1, @report.gap_extend)
|
140
|
+
end
|
141
|
+
|
142
|
+
def test_filter
|
143
|
+
assert_equal('S', @report.filter)
|
144
|
+
end
|
145
|
+
|
146
|
+
def test_pattern
|
147
|
+
assert_equal(nil, @report.pattern)
|
148
|
+
end
|
149
|
+
|
150
|
+
def test_entrez_query
|
151
|
+
assert_equal(nil, @report.entrez_query)
|
152
|
+
end
|
153
|
+
|
154
|
+
def test_each_iteration
|
155
|
+
assert_nothing_raised {
|
156
|
+
@report.each_iteration { |itr| }
|
157
|
+
}
|
158
|
+
end
|
159
|
+
|
160
|
+
def test_each_hit
|
161
|
+
assert_nothing_raised {
|
162
|
+
@report.each_hit { |hit| }
|
163
|
+
}
|
164
|
+
end
|
165
|
+
|
166
|
+
def test_hits
|
167
|
+
assert(@report.hits)
|
168
|
+
end
|
169
|
+
|
170
|
+
def test_statistics
|
171
|
+
assert_equal({"kappa"=>0.041, "db-num"=>1, "eff-space"=>605284.0, "hsp-len"=>42, "db-len"=>820, "lambda"=>0.267, "entropy"=>0.14}, @report.statistics)
|
172
|
+
end
|
173
|
+
|
174
|
+
def test_db_num
|
175
|
+
assert_equal(1, @report.db_num)
|
176
|
+
end
|
177
|
+
|
178
|
+
def test_db_len
|
179
|
+
assert_equal(820, @report.db_len)
|
180
|
+
end
|
181
|
+
|
182
|
+
def test_hsp_len
|
183
|
+
assert_equal(42, @report.hsp_len)
|
184
|
+
end
|
185
|
+
|
186
|
+
def test_eff_space
|
187
|
+
assert_equal(605284, @report.eff_space)
|
188
|
+
end
|
189
|
+
|
190
|
+
def test_kappa
|
191
|
+
assert_equal(0.041, @report.kappa)
|
192
|
+
end
|
193
|
+
|
194
|
+
def test_lambda
|
195
|
+
assert_equal(0.267, @report.lambda)
|
196
|
+
end
|
197
|
+
|
198
|
+
def test_entropy
|
199
|
+
assert_equal(0.14, @report.entropy)
|
200
|
+
end
|
201
|
+
|
202
|
+
def test_message
|
203
|
+
assert_equal(nil, @report.message)
|
204
|
+
end
|
205
|
+
end
|
206
|
+
|
207
|
+
class TestBlastReportIteration < Test::Unit::TestCase
|
208
|
+
include TestBlastReportHelper
|
209
|
+
|
210
|
+
def setup
|
211
|
+
report = create_report_object
|
212
|
+
@itr = report.iterations.first
|
213
|
+
end
|
214
|
+
|
215
|
+
def test_hits
|
216
|
+
assert(@itr.hits)
|
217
|
+
end
|
218
|
+
|
219
|
+
def test_statistics
|
220
|
+
stat = {"kappa" => 0.041, "eff-space" => 605284, "db-num" => 1,
|
221
|
+
"hsp-len" => 42, "db-len" => 820, "lambda" => 0.267,
|
222
|
+
"entropy" => 0.14}
|
223
|
+
assert_equal(stat, @itr.statistics)
|
224
|
+
end
|
225
|
+
|
226
|
+
def test_num
|
227
|
+
assert_equal(1, @itr.num)
|
228
|
+
end
|
229
|
+
|
230
|
+
def test_message
|
231
|
+
assert_equal(nil, @itr.message)
|
232
|
+
end
|
233
|
+
end
|
234
|
+
|
235
|
+
class TestBlastReportHit < Test::Unit::TestCase
|
236
|
+
include TestBlastReportHelper
|
237
|
+
|
238
|
+
def setup
|
239
|
+
report = create_report_object
|
240
|
+
@hit = report.hits.first
|
241
|
+
end
|
242
|
+
|
243
|
+
def test_Hit_hsps
|
244
|
+
assert(@hit.hsps)
|
245
|
+
end
|
246
|
+
|
247
|
+
def test_Hit_query_id
|
248
|
+
assert_equal('lcl|QUERY', @hit.query_id)
|
249
|
+
end
|
250
|
+
|
251
|
+
def test_Hit_query_def
|
252
|
+
assert_equal('eco:b0002 thrA, Hs, thrD, thrA2, thrA1; bifunctional: aspartokinase I (N-terminal); homoserine dehydrogenase I (C-terminal) [EC:2.7.2.4 1.1.1.3]; K00003 homoserine dehydrogenase; K00928 aspartate kinase (A)', @hit.query_def)
|
253
|
+
end
|
254
|
+
|
255
|
+
def test_Hit_query_len
|
256
|
+
assert_equal(820, @hit.query_len)
|
257
|
+
end
|
258
|
+
|
259
|
+
def test_Hit_num
|
260
|
+
assert(@hit.num)
|
261
|
+
end
|
262
|
+
|
263
|
+
def test_Hit_hit_id
|
264
|
+
assert_equal('gnl|BL_ORD_ID|0', @hit.hit_id)
|
265
|
+
end
|
266
|
+
|
267
|
+
def test_Hit_len
|
268
|
+
assert_equal(820, @hit.len)
|
269
|
+
end
|
270
|
+
|
271
|
+
def test_Hit_target_len
|
272
|
+
assert_equal(820, @hit.target_len)
|
273
|
+
end
|
274
|
+
|
275
|
+
def test_Hit_definition
|
276
|
+
assert(@hit.definition)
|
277
|
+
end
|
278
|
+
|
279
|
+
def test_Hit_taeget_def
|
280
|
+
assert(@hit.target_def)
|
281
|
+
end
|
282
|
+
|
283
|
+
def test_Hit_accession
|
284
|
+
assert(@hit.accession)
|
285
|
+
end
|
286
|
+
|
287
|
+
def test_Hit_target_id
|
288
|
+
assert(@hit.target_id)
|
289
|
+
end
|
290
|
+
|
291
|
+
def test_Hit_evalue
|
292
|
+
assert_equal(0, @hit.evalue)
|
293
|
+
end
|
294
|
+
|
295
|
+
def test_Hit_bit_score
|
296
|
+
assert_equal(1567.75, @hit.bit_score)
|
297
|
+
end
|
298
|
+
|
299
|
+
def test_Hit_identity
|
300
|
+
assert_equal(820, @hit.identity)
|
301
|
+
end
|
302
|
+
|
303
|
+
def test_Hit_overlap
|
304
|
+
assert_equal(820, @hit.overlap)
|
305
|
+
end
|
306
|
+
|
307
|
+
def test_Hit_query_seq
|
308
|
+
seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
|
309
|
+
assert_equal(seq, @hit.query_seq)
|
310
|
+
end
|
311
|
+
|
312
|
+
def test_Hit_target_seq
|
313
|
+
seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
|
314
|
+
assert_equal(seq, @hit.target_seq)
|
315
|
+
end
|
316
|
+
|
317
|
+
def test_Hit_midline
|
318
|
+
seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
|
319
|
+
assert_equal(seq, @hit.midline)
|
320
|
+
end
|
321
|
+
|
322
|
+
def test_Hit_query_start
|
323
|
+
assert_equal(1, @hit.query_start)
|
324
|
+
# assert_equal(1, @hit.query_from)
|
325
|
+
end
|
326
|
+
|
327
|
+
def test_Hit_query_end
|
328
|
+
assert_equal(820, @hit.query_end)
|
329
|
+
# assert_equal(820, @hit.query_to)
|
330
|
+
end
|
331
|
+
|
332
|
+
def test_Hit_target_start
|
333
|
+
assert_equal(1, @hit.target_start)
|
334
|
+
# assert_equal(1, @hit.hit_from)
|
335
|
+
end
|
336
|
+
|
337
|
+
def test_Hit_target_end
|
338
|
+
assert_equal(820, @hit.target_end)
|
339
|
+
# assert_equal(820, @hit.hit_to)
|
340
|
+
end
|
341
|
+
|
342
|
+
def test_Hit_lap_at
|
343
|
+
assert_equal([1, 820, 1, 820], @hit.lap_at)
|
344
|
+
end
|
345
|
+
end
|
346
|
+
|
347
|
+
class TestBlastReportHsp < Test::Unit::TestCase
|
348
|
+
include TestBlastReportHelper
|
349
|
+
|
350
|
+
def setup
|
351
|
+
report = create_report_object
|
352
|
+
@hsp = report.hits.first.hsps.first
|
353
|
+
end
|
354
|
+
|
355
|
+
def test_Hsp_num
|
356
|
+
assert_equal(1, @hsp.num)
|
357
|
+
end
|
358
|
+
|
359
|
+
def test_Hsp_bit_score
|
360
|
+
assert_equal(1567.75, @hsp.bit_score)
|
361
|
+
end
|
362
|
+
|
363
|
+
def test_Hsp_score
|
364
|
+
assert_equal(4058, @hsp.score)
|
365
|
+
end
|
366
|
+
|
367
|
+
def test_Hsp_evalue
|
368
|
+
assert_equal(0, @hsp.evalue)
|
369
|
+
end
|
370
|
+
|
371
|
+
def test_Hsp_identity
|
372
|
+
assert_equal(820, @hsp.identity)
|
373
|
+
end
|
374
|
+
|
375
|
+
def test_Hsp_gaps
|
376
|
+
assert_nothing_raised { @hsp.gaps }
|
377
|
+
end
|
378
|
+
|
379
|
+
def test_Hsp_positive
|
380
|
+
assert_equal(820, @hsp.positive)
|
381
|
+
end
|
382
|
+
|
383
|
+
def test_Hsp_align_len
|
384
|
+
assert_equal(820, @hsp.align_len)
|
385
|
+
end
|
386
|
+
|
387
|
+
def test_Hsp_density
|
388
|
+
assert(@hsp.density)
|
389
|
+
end
|
390
|
+
|
391
|
+
def test_Hsp_query_frame
|
392
|
+
assert_equal(1, @hsp.query_frame)
|
393
|
+
end
|
394
|
+
|
395
|
+
def test_Hsp_query_from
|
396
|
+
assert_equal(1, @hsp.query_from)
|
397
|
+
end
|
398
|
+
|
399
|
+
def test_Hsp_query_to
|
400
|
+
assert_equal(820, @hsp.query_to)
|
401
|
+
end
|
402
|
+
|
403
|
+
def test_Hsp_hit_frame
|
404
|
+
assert_equal(1, @hsp.hit_frame)
|
405
|
+
end
|
406
|
+
|
407
|
+
def test_Hsp_hit_from
|
408
|
+
assert_equal(1, @hsp.hit_from)
|
409
|
+
end
|
410
|
+
|
411
|
+
def test_Hsp_hit_to
|
412
|
+
assert_equal(820, @hsp.hit_to)
|
413
|
+
end
|
414
|
+
|
415
|
+
def test_Hsp_pattern_from
|
416
|
+
assert_nothing_raised { @hsp.pattern_from }
|
417
|
+
end
|
418
|
+
|
419
|
+
def test_Hsp_pattern_to
|
420
|
+
assert_nothing_raised { @hsp.pattern_to }
|
421
|
+
end
|
422
|
+
|
423
|
+
def test_Hsp_qseq
|
424
|
+
seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
|
425
|
+
assert_equal(seq, @hsp.qseq)
|
426
|
+
end
|
427
|
+
|
428
|
+
def test_Hsp_midline
|
429
|
+
seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
|
430
|
+
assert_equal(seq, @hsp.midline)
|
431
|
+
end
|
432
|
+
|
433
|
+
def test_Hsp_hseq
|
434
|
+
seq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
|
435
|
+
assert_equal(seq, @hsp.hseq)
|
436
|
+
end
|
437
|
+
|
438
|
+
def test_Hsp_percent_identity
|
439
|
+
assert_nothing_raised { @hsp.percent_identity }
|
440
|
+
end
|
441
|
+
|
442
|
+
def test_Hsp_mismatch_count
|
443
|
+
assert_nothing_raised { @hsp.mismatch_count }
|
444
|
+
end
|
445
|
+
|
446
|
+
end
|
447
|
+
|
448
|
+
class TestBlastReportREXML < TestBlastReport
|
449
|
+
end
|
450
|
+
|
451
|
+
class TestBlastReportIterationREXML < TestBlastReportIteration
|
452
|
+
end
|
453
|
+
|
454
|
+
class TestBlastReportHitREXML < TestBlastReportHit
|
455
|
+
end
|
456
|
+
|
457
|
+
class TestBlastReportHspREXML < TestBlastReportHsp
|
458
|
+
end
|
459
|
+
|
460
|
+
if defined? XMLParser then
|
461
|
+
|
462
|
+
class TestBlastReportXMLParser < TestBlastReport
|
463
|
+
end
|
464
|
+
|
465
|
+
class TestBlastReportIterationXMLParser < TestBlastReportIteration
|
466
|
+
end
|
467
|
+
|
468
|
+
class TestBlastReportHitXMLParser < TestBlastReportHit
|
469
|
+
end
|
470
|
+
|
471
|
+
class TestBlastReportHspXMLParser < TestBlastReportHsp
|
472
|
+
end
|
473
|
+
|
474
|
+
end #if defined? XMLParser
|
475
|
+
|
476
|
+
class TestBlastReportDefault < TestBlastReport
|
477
|
+
undef test_entrez_query
|
478
|
+
undef test_filter
|
479
|
+
undef test_hsp_len
|
480
|
+
undef test_inclusion
|
481
|
+
undef test_parameters
|
482
|
+
undef test_query_id
|
483
|
+
undef test_statistics
|
484
|
+
|
485
|
+
def test_program
|
486
|
+
assert_equal('BLASTP', @report.program)
|
487
|
+
end
|
488
|
+
|
489
|
+
def test_reference
|
490
|
+
text_str = 'Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.'
|
491
|
+
assert_equal(text_str, @report.reference)
|
492
|
+
end
|
493
|
+
|
494
|
+
def test_version
|
495
|
+
assert_equal('BLASTP 2.2.10 [Oct-19-2004]', @report.version)
|
496
|
+
end
|
497
|
+
|
498
|
+
def test_kappa
|
499
|
+
assert_equal(0.134, @report.kappa)
|
500
|
+
end
|
501
|
+
|
502
|
+
def test_lambda
|
503
|
+
assert_equal(0.319, @report.lambda)
|
504
|
+
end
|
505
|
+
|
506
|
+
def test_entropy
|
507
|
+
assert_equal(0.383, @report.entropy)
|
508
|
+
end
|
509
|
+
|
510
|
+
def test_gapped_kappa
|
511
|
+
assert_equal(0.0410, @report.gapped_kappa)
|
512
|
+
end
|
513
|
+
|
514
|
+
def test_gapped_lambda
|
515
|
+
assert_equal(0.267, @report.gapped_lambda)
|
516
|
+
end
|
517
|
+
|
518
|
+
def test_gapped_entropy
|
519
|
+
assert_equal(0.140, @report.gapped_entropy)
|
520
|
+
end
|
521
|
+
end
|
522
|
+
|
523
|
+
class TestBlastReportIterationDefault < TestBlastReportIteration
|
524
|
+
undef test_statistics
|
525
|
+
end
|
526
|
+
|
527
|
+
class TestBlastReportHitDefault < TestBlastReportHit
|
528
|
+
undef test_Hit_accession
|
529
|
+
undef test_Hit_hit_id
|
530
|
+
undef test_Hit_num
|
531
|
+
undef test_Hit_query_def
|
532
|
+
undef test_Hit_query_id
|
533
|
+
undef test_Hit_query_len
|
534
|
+
|
535
|
+
def setup
|
536
|
+
@filtered_query_sequence = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQxxxxxxxxxxxxxxALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
|
537
|
+
super
|
538
|
+
end
|
539
|
+
|
540
|
+
def test_Hit_bit_score
|
541
|
+
# differs from XML because of truncation in the default format
|
542
|
+
assert_equal(1567.0, @hit.bit_score)
|
543
|
+
end
|
544
|
+
|
545
|
+
def test_Hit_identity
|
546
|
+
# differs from XML because filtered residues are not counted in the
|
547
|
+
# default format
|
548
|
+
assert_equal(806, @hit.identity)
|
549
|
+
end
|
550
|
+
|
551
|
+
def test_Hit_midline
|
552
|
+
# differs from XML because filtered residues are not specified in XML
|
553
|
+
seq = @filtered_query_sequence.gsub(/x/, ' ')
|
554
|
+
assert_equal(seq, @hit.midline)
|
555
|
+
end
|
556
|
+
|
557
|
+
def test_Hit_query_seq
|
558
|
+
# differs from XML because filtered residues are not specified in XML
|
559
|
+
seq = @filtered_query_sequence.gsub(/x/, 'X')
|
560
|
+
assert_equal(seq, @hit.query_seq)
|
561
|
+
end
|
562
|
+
end
|
563
|
+
|
564
|
+
class TestBlastReportHspDefault < TestBlastReportHsp
|
565
|
+
undef test_Hsp_density
|
566
|
+
undef test_Hsp_mismatch_count
|
567
|
+
undef test_Hsp_num
|
568
|
+
undef test_Hsp_pattern_from
|
569
|
+
undef test_Hsp_pattern_to
|
570
|
+
|
571
|
+
def setup
|
572
|
+
@filtered_query_sequence = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHYLESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAVTERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQMLFNTDQxxxxxxxxxxxxxxALLEQLKRQQSWLKNKHIDLRVCGVANSKALLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYADFLREGFHVVTPNKKANTSSMDYYHQLRYAAEKSRRKFLYDTNVGAGLPVIENLQNLLNAGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARKLLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEGKVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV'
|
573
|
+
super
|
574
|
+
end
|
575
|
+
|
576
|
+
def test_Hsp_identity
|
577
|
+
# differs from XML because filtered residues are not counted in the
|
578
|
+
# default format
|
579
|
+
assert_equal(806, @hsp.identity)
|
580
|
+
end
|
581
|
+
|
582
|
+
def test_Hsp_positive
|
583
|
+
# differs from XML because filtered residues are not counted in the
|
584
|
+
# default format
|
585
|
+
assert_equal(806, @hsp.positive)
|
586
|
+
end
|
587
|
+
|
588
|
+
def test_Hsp_midline
|
589
|
+
# differs from XML because filtered residues are not specified in XML
|
590
|
+
seq = @filtered_query_sequence.gsub(/x/, ' ')
|
591
|
+
assert_equal(seq, @hsp.midline)
|
592
|
+
end
|
593
|
+
|
594
|
+
def test_Hsp_qseq
|
595
|
+
# differs from XML because filtered residues are not specified in XML
|
596
|
+
seq = @filtered_query_sequence.gsub(/x/, 'X')
|
597
|
+
assert_equal(seq, @hsp.qseq)
|
598
|
+
end
|
599
|
+
|
600
|
+
def test_Hsp_bit_score
|
601
|
+
# differs from XML because of truncation in the default format
|
602
|
+
assert_equal(1567.0, @hsp.bit_score)
|
603
|
+
end
|
604
|
+
|
605
|
+
def test_Hsp_hit_frame
|
606
|
+
# differs from XML because not available in the default BLASTP format
|
607
|
+
assert_equal(nil, @hsp.hit_frame)
|
608
|
+
end
|
609
|
+
|
610
|
+
def test_Hsp_query_frame
|
611
|
+
# differs from XML because not available in the default BLASTP format
|
612
|
+
assert_equal(nil, @hsp.query_frame)
|
613
|
+
end
|
614
|
+
end
|
615
|
+
|
616
|
+
########################################################################
|
617
|
+
# Tests for new BLAST XML format (blastall 2.2.14 or later)
|
618
|
+
# with the result of multiple query sequences
|
619
|
+
########################################################################
|
620
|
+
|
621
|
+
class TestBlastReportMulti < Test::Unit::TestCase
|
622
|
+
include TestBlastReportHelper
|
623
|
+
|
624
|
+
def setup
|
625
|
+
@report = create_report_object('blastp-multi')
|
626
|
+
@overall = [ @report ] + @report.reports
|
627
|
+
end
|
628
|
+
|
629
|
+
def test_reports
|
630
|
+
assert_equal(5, @report.reports.size)
|
631
|
+
end
|
632
|
+
|
633
|
+
def test_iterations
|
634
|
+
assert_equal(1, @report.iterations.size)
|
635
|
+
assert_equal([ 1, 1, 1, 1, 1],
|
636
|
+
@report.reports.collect { |x| x.iterations.size })
|
637
|
+
end
|
638
|
+
|
639
|
+
def test_parameters
|
640
|
+
@overall.each do |r|
|
641
|
+
assert_equal('BLOSUM62', r.parameters['matrix'])
|
642
|
+
assert_equal(0.001, r.parameters['expect'])
|
643
|
+
assert_equal(11, r.parameters['gap-open'])
|
644
|
+
assert_equal(1, r.parameters['gap-extend'])
|
645
|
+
assert_equal('F', r.parameters['filter'])
|
646
|
+
end
|
647
|
+
end
|
648
|
+
|
649
|
+
def test_program
|
650
|
+
@overall.each do |r|
|
651
|
+
assert_equal('blastp', r.program)
|
652
|
+
end
|
653
|
+
end
|
654
|
+
|
655
|
+
def test_version
|
656
|
+
@overall.each do |r|
|
657
|
+
assert_equal('blastp 2.2.18 [Mar-02-2008]', r.version)
|
658
|
+
end
|
659
|
+
end
|
660
|
+
|
661
|
+
def test_reference
|
662
|
+
text_str = '~Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, ~Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), ~"Gapped BLAST and PSI-BLAST: a new generation of protein database search~programs", Nucleic Acids Res. 25:3389-3402.'
|
663
|
+
|
664
|
+
@overall.each do |r|
|
665
|
+
assert_equal(text_str, r.reference)
|
666
|
+
end
|
667
|
+
end
|
668
|
+
|
669
|
+
def test_db
|
670
|
+
@overall.each do |r|
|
671
|
+
assert_equal('BA000007.faa', r.db)
|
672
|
+
end
|
673
|
+
end
|
674
|
+
|
675
|
+
def test_query_id
|
676
|
+
qids = [ 'lcl|1_0', 'lcl|2_0', 'lcl|3_0', nil, 'lcl|5_0' ]
|
677
|
+
assert_equal(qids[0], @report.query_id)
|
678
|
+
assert_equal(qids,
|
679
|
+
@report.reports.collect { |r| r.query_id })
|
680
|
+
end
|
681
|
+
|
682
|
+
def test_query_def
|
683
|
+
qdefs =
|
684
|
+
[ 'gi|1790845|gb|AAC77338.1| predicted DNA-binding transcriptional regulator [Escherichia coli str. K-12 substr. MG1655]',
|
685
|
+
'gi|1790846|gb|AAC77339.1| lipoate-protein ligase A [Escherichia coli str. K-12',
|
686
|
+
'gi|1790847|gb|AAC77340.1| conserved protein [Escherichia coli str. K-12 substr. MG1655]',
|
687
|
+
nil,
|
688
|
+
'gi|1790849|gb|AAC77341.1| 3-phosphoserine phosphatase [Escherichia coli str. K-12 substr. MG1655]'
|
689
|
+
]
|
690
|
+
assert_equal(qdefs[0], @report.query_def)
|
691
|
+
assert_equal(qdefs,
|
692
|
+
@report.reports.collect { |r| r.query_def })
|
693
|
+
end
|
694
|
+
|
695
|
+
def test_query_len
|
696
|
+
qlens = [ 443, 346, 214, nil, 322 ]
|
697
|
+
assert_equal(qlens[0], @report.query_len)
|
698
|
+
assert_equal(qlens,
|
699
|
+
@report.reports.collect { |r| r.query_len })
|
700
|
+
end
|
701
|
+
|
702
|
+
def test_matrix
|
703
|
+
@overall.each do |r|
|
704
|
+
assert_equal('BLOSUM62', r.matrix)
|
705
|
+
end
|
706
|
+
end
|
707
|
+
|
708
|
+
def test_expect
|
709
|
+
@overall.each do |r|
|
710
|
+
assert_equal(0.001, r.expect)
|
711
|
+
end
|
712
|
+
end
|
713
|
+
|
714
|
+
def test_gap_open
|
715
|
+
@overall.each do |r|
|
716
|
+
assert_equal(11, r.gap_open)
|
717
|
+
end
|
718
|
+
end
|
719
|
+
|
720
|
+
def test_gap_extend
|
721
|
+
@overall.each do |r|
|
722
|
+
assert_equal(1, r.gap_extend)
|
723
|
+
end
|
724
|
+
end
|
725
|
+
|
726
|
+
def test_filter
|
727
|
+
@overall.each do |r|
|
728
|
+
assert_equal('F', r.filter)
|
729
|
+
end
|
730
|
+
end
|
731
|
+
|
732
|
+
def test_pattern
|
733
|
+
@overall.each do |r|
|
734
|
+
assert_equal(nil, r.pattern)
|
735
|
+
end
|
736
|
+
end
|
737
|
+
|
738
|
+
def test_each_iteration
|
739
|
+
@overall.each do |r|
|
740
|
+
count = 0
|
741
|
+
assert_nothing_raised {
|
742
|
+
r.each_iteration { |itr| count += 1 }
|
743
|
+
}
|
744
|
+
assert_equal(1, count)
|
745
|
+
end
|
746
|
+
end
|
747
|
+
|
748
|
+
def test_each_hit
|
749
|
+
@overall.each do |r|
|
750
|
+
assert_nothing_raised {
|
751
|
+
r.each_hit { |hit| }
|
752
|
+
}
|
753
|
+
end
|
754
|
+
end
|
755
|
+
|
756
|
+
def test_hits
|
757
|
+
hsizes = [ 0, 1, 1, 0, 2 ]
|
758
|
+
assert_equal(hsizes[0], @report.hits.size)
|
759
|
+
assert_equal(hsizes,
|
760
|
+
@report.reports.collect { |r| r.hits.size })
|
761
|
+
end
|
762
|
+
|
763
|
+
def test_statistics
|
764
|
+
assert_equal({}, @report.statistics)
|
765
|
+
|
766
|
+
stat = {
|
767
|
+
"kappa" => 0.041, "eff-space" => 0, "db-num" => 5361,
|
768
|
+
"hsp-len" => 0, "db-len" => 1609188, "lambda" => 0.267,
|
769
|
+
"entropy" => 0.14
|
770
|
+
}
|
771
|
+
stats = [ {}, stat, stat, {}, stat ]
|
772
|
+
@report.reports.each do |r|
|
773
|
+
assert_equal(stats.shift, r.statistics)
|
774
|
+
end
|
775
|
+
end
|
776
|
+
|
777
|
+
def test_db_num
|
778
|
+
assert_equal(nil, @report.db_num)
|
779
|
+
ary = [ nil, 5361, 5361, nil, 5361 ]
|
780
|
+
@report.reports.each do |r|
|
781
|
+
assert_equal(ary.shift, r.db_num)
|
782
|
+
end
|
783
|
+
end
|
784
|
+
|
785
|
+
def test_db_len
|
786
|
+
assert_equal(nil, @report.db_len)
|
787
|
+
ary = [ nil, 1609188, 1609188, nil, 1609188 ]
|
788
|
+
@report.reports.each do |r|
|
789
|
+
assert_equal(ary.shift, r.db_len)
|
790
|
+
end
|
791
|
+
end
|
792
|
+
|
793
|
+
def test_hsp_len
|
794
|
+
assert_equal(nil, @report.hsp_len)
|
795
|
+
ary = [ nil, 0, 0, nil, 0 ]
|
796
|
+
@report.reports.each do |r|
|
797
|
+
assert_equal(ary.shift, r.hsp_len)
|
798
|
+
end
|
799
|
+
end
|
800
|
+
|
801
|
+
def test_eff_space
|
802
|
+
assert_equal(nil, @report.eff_space)
|
803
|
+
ary = [ nil, 0, 0, nil, 0 ]
|
804
|
+
@report.reports.each do |r|
|
805
|
+
assert_equal(ary.shift, r.eff_space)
|
806
|
+
end
|
807
|
+
end
|
808
|
+
|
809
|
+
def test_kappa
|
810
|
+
assert_equal(nil, @report.kappa)
|
811
|
+
ary = [ nil, 0.041, 0.041, nil, 0.041 ]
|
812
|
+
@report.reports.each do |r|
|
813
|
+
assert_equal(ary.shift, r.kappa)
|
814
|
+
end
|
815
|
+
end
|
816
|
+
|
817
|
+
def test_lambda
|
818
|
+
assert_equal(nil, @report.lambda)
|
819
|
+
ary = [ nil, 0.267, 0.267, nil, 0.267 ]
|
820
|
+
@report.reports.each do |r|
|
821
|
+
assert_equal(ary.shift, r.lambda)
|
822
|
+
end
|
823
|
+
end
|
824
|
+
|
825
|
+
def test_entropy
|
826
|
+
assert_equal(nil, @report.entropy)
|
827
|
+
ary = [ nil, 0.14, 0.14, nil, 0.14 ]
|
828
|
+
@report.reports.each do |r|
|
829
|
+
assert_equal(ary.shift, r.entropy)
|
830
|
+
end
|
831
|
+
end
|
832
|
+
|
833
|
+
def test_message
|
834
|
+
@overall.each do |r|
|
835
|
+
assert_equal(nil, r.message)
|
836
|
+
end
|
837
|
+
end
|
838
|
+
end
|
839
|
+
|
840
|
+
class TestBlastReportIterationMulti < Test::Unit::TestCase
|
841
|
+
include TestBlastReportHelper
|
842
|
+
|
843
|
+
def setup
|
844
|
+
report = create_report_object('blastp-multi')
|
845
|
+
@itr = report.reports[4].iterations[0]
|
846
|
+
end
|
847
|
+
|
848
|
+
def test_query_id
|
849
|
+
assert_equal('lcl|5_0', @itr.query_id)
|
850
|
+
end
|
851
|
+
|
852
|
+
def test_query_def
|
853
|
+
assert_equal('gi|1790849|gb|AAC77341.1| 3-phosphoserine phosphatase [Escherichia coli str. K-12 substr. MG1655]', @itr.query_def)
|
854
|
+
end
|
855
|
+
|
856
|
+
def test_query_len
|
857
|
+
assert_equal(322, @itr.query_len)
|
858
|
+
end
|
859
|
+
|
860
|
+
def test_hits
|
861
|
+
assert_equal(2, @itr.hits.size)
|
862
|
+
end
|
863
|
+
|
864
|
+
def test_each
|
865
|
+
count = 0
|
866
|
+
assert_nothing_raised {
|
867
|
+
@itr.each { |hit| count += 1 }
|
868
|
+
}
|
869
|
+
assert_equal(2, count)
|
870
|
+
end
|
871
|
+
|
872
|
+
def test_statistics
|
873
|
+
stat = {
|
874
|
+
"kappa" => 0.041, "eff-space" => 0, "db-num" => 5361,
|
875
|
+
"hsp-len" => 0, "db-len" => 1609188, "lambda" => 0.267,
|
876
|
+
"entropy" => 0.14
|
877
|
+
}
|
878
|
+
assert_equal(stat, @itr.statistics)
|
879
|
+
end
|
880
|
+
|
881
|
+
def test_num
|
882
|
+
assert_equal(5, @itr.num)
|
883
|
+
end
|
884
|
+
|
885
|
+
def test_message
|
886
|
+
assert_equal(nil, @itr.message)
|
887
|
+
end
|
888
|
+
end
|
889
|
+
|
890
|
+
class TestBlastReportHitMulti < Test::Unit::TestCase
|
891
|
+
include TestBlastReportHelper
|
892
|
+
|
893
|
+
def setup
|
894
|
+
report = create_report_object('blastp-multi')
|
895
|
+
@hit = report.reports[4].iterations[0].hits[1]
|
896
|
+
end
|
897
|
+
|
898
|
+
def test_Hit_hsps
|
899
|
+
assert_equal(1, @hit.hsps.size)
|
900
|
+
end
|
901
|
+
|
902
|
+
def test_Hit_query_id
|
903
|
+
assert_equal('lcl|5_0', @hit.query_id)
|
904
|
+
end
|
905
|
+
|
906
|
+
def test_Hit_query_def
|
907
|
+
assert_equal('gi|1790849|gb|AAC77341.1| 3-phosphoserine phosphatase [Escherichia coli str. K-12 substr. MG1655]', @hit.query_def)
|
908
|
+
end
|
909
|
+
|
910
|
+
def test_Hit_query_len
|
911
|
+
assert_equal(322, @hit.query_len)
|
912
|
+
end
|
913
|
+
|
914
|
+
def test_Hit_num
|
915
|
+
assert_equal(2, @hit.num)
|
916
|
+
end
|
917
|
+
|
918
|
+
def test_Hit_hit_id
|
919
|
+
assert_equal('gi|13363792|dbj|BAB37741.1|', @hit.hit_id)
|
920
|
+
end
|
921
|
+
|
922
|
+
def test_Hit_len
|
923
|
+
assert_equal(732, @hit.len)
|
924
|
+
end
|
925
|
+
|
926
|
+
def test_Hit_target_len
|
927
|
+
assert_equal(732, @hit.target_len)
|
928
|
+
end
|
929
|
+
|
930
|
+
def test_Hit_definition
|
931
|
+
assert_equal('zinc-transporting ATPase [Escherichia coli O157:H7 str. Sakai]', @hit.definition)
|
932
|
+
end
|
933
|
+
|
934
|
+
def test_Hit_taeget_def
|
935
|
+
assert_equal('zinc-transporting ATPase [Escherichia coli O157:H7 str. Sakai]', @hit.target_def)
|
936
|
+
end
|
937
|
+
|
938
|
+
def test_Hit_accession
|
939
|
+
assert_equal('BAB37741', @hit.accession)
|
940
|
+
end
|
941
|
+
|
942
|
+
def test_Hit_target_id
|
943
|
+
#assert_equal('gi|13363792|dbj|BAB37741.1|', @hit.target_id)
|
944
|
+
assert_equal('BAB37741', @hit.target_id)
|
945
|
+
end
|
946
|
+
|
947
|
+
def test_Hit_evalue
|
948
|
+
assert_equal(0.000899657, @hit.evalue)
|
949
|
+
end
|
950
|
+
|
951
|
+
def test_Hit_bit_score
|
952
|
+
assert_equal(38.1206, @hit.bit_score)
|
953
|
+
end
|
954
|
+
|
955
|
+
def test_Hit_identity
|
956
|
+
assert_equal(39, @hit.identity)
|
957
|
+
end
|
958
|
+
|
959
|
+
def test_Hit_overlap
|
960
|
+
# alignment length
|
961
|
+
assert_equal(123, @hit.overlap)
|
962
|
+
end
|
963
|
+
|
964
|
+
def test_Hit_query_seq
|
965
|
+
seq = 'VLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVN-EKAEVTIRHADLMGV'
|
966
|
+
assert_equal(seq, @hit.query_seq)
|
967
|
+
end
|
968
|
+
|
969
|
+
def test_Hit_target_seq
|
970
|
+
seq = 'ISELNALGVKGVILTG----------DNPRAAAAIAGELGL---EFKAGLL-----PEDKVKAVTELNQHA--PLAM---VGDGINDAPAMKAAAIGIAMGSGTDVALETADAALTHNHLRGL'
|
971
|
+
assert_equal(seq, @hit.target_seq)
|
972
|
+
end
|
973
|
+
|
974
|
+
def test_Hit_midline
|
975
|
+
seq = '+ +L LG K I +G D R A +A EL + +F ++ + K K +T L Q PLA +GDG ND P +KAA +GIA + V E A+ + H L G+'
|
976
|
+
assert_equal(seq, @hit.midline)
|
977
|
+
end
|
978
|
+
|
979
|
+
def test_Hit_query_start
|
980
|
+
assert_equal(190, @hit.query_start)
|
981
|
+
# assert_equal(190, @hit.query_from)
|
982
|
+
end
|
983
|
+
|
984
|
+
def test_Hit_query_end
|
985
|
+
assert_equal(311, @hit.query_end)
|
986
|
+
# assert_equal(311, @hit.query_to)
|
987
|
+
end
|
988
|
+
|
989
|
+
def test_Hit_target_start
|
990
|
+
assert_equal(569, @hit.target_start)
|
991
|
+
# assert_equal(569, @hit.hit_from)
|
992
|
+
end
|
993
|
+
|
994
|
+
def test_Hit_target_end
|
995
|
+
assert_equal(668, @hit.target_end)
|
996
|
+
# assert_equal(668, @hit.hit_to)
|
997
|
+
end
|
998
|
+
|
999
|
+
def test_Hit_lap_at
|
1000
|
+
assert_equal([190, 311, 569, 668], @hit.lap_at)
|
1001
|
+
end
|
1002
|
+
end
|
1003
|
+
|
1004
|
+
class TestBlastReportHspMulti < Test::Unit::TestCase
|
1005
|
+
include TestBlastReportHelper
|
1006
|
+
|
1007
|
+
def setup
|
1008
|
+
report = create_report_object('blastp-multi')
|
1009
|
+
@hsp = report.reports[4].iterations[0].hits[1].hsps[0]
|
1010
|
+
end
|
1011
|
+
|
1012
|
+
def test_Hsp_num
|
1013
|
+
assert_equal(1, @hsp.num)
|
1014
|
+
end
|
1015
|
+
|
1016
|
+
def test_Hsp_bit_score
|
1017
|
+
assert_equal(38.1206, @hsp.bit_score)
|
1018
|
+
end
|
1019
|
+
|
1020
|
+
def test_Hsp_score
|
1021
|
+
assert_equal(87, @hsp.score)
|
1022
|
+
end
|
1023
|
+
|
1024
|
+
def test_Hsp_evalue
|
1025
|
+
assert_equal(0.000899657, @hsp.evalue)
|
1026
|
+
end
|
1027
|
+
|
1028
|
+
def test_Hsp_identity
|
1029
|
+
assert_equal(39, @hsp.identity)
|
1030
|
+
end
|
1031
|
+
|
1032
|
+
def test_Hsp_gaps
|
1033
|
+
assert_equal(24, @hsp.gaps)
|
1034
|
+
end
|
1035
|
+
|
1036
|
+
def test_Hsp_positive
|
1037
|
+
assert_equal(56, @hsp.positive)
|
1038
|
+
end
|
1039
|
+
|
1040
|
+
def test_Hsp_align_len
|
1041
|
+
assert_equal(123, @hsp.align_len)
|
1042
|
+
end
|
1043
|
+
|
1044
|
+
def test_Hsp_density
|
1045
|
+
assert_nothing_raised { @hsp.density }
|
1046
|
+
end
|
1047
|
+
|
1048
|
+
def test_Hsp_query_frame
|
1049
|
+
assert_equal(1, @hsp.query_frame)
|
1050
|
+
end
|
1051
|
+
|
1052
|
+
def test_Hsp_query_from
|
1053
|
+
assert_equal(190, @hsp.query_from)
|
1054
|
+
end
|
1055
|
+
|
1056
|
+
def test_Hsp_query_to
|
1057
|
+
assert_equal(311, @hsp.query_to)
|
1058
|
+
end
|
1059
|
+
|
1060
|
+
def test_Hsp_hit_frame
|
1061
|
+
assert_equal(1, @hsp.hit_frame)
|
1062
|
+
end
|
1063
|
+
|
1064
|
+
def test_Hsp_hit_from
|
1065
|
+
assert_equal(569, @hsp.hit_from)
|
1066
|
+
end
|
1067
|
+
|
1068
|
+
def test_Hsp_hit_to
|
1069
|
+
assert_equal(668, @hsp.hit_to)
|
1070
|
+
end
|
1071
|
+
|
1072
|
+
def test_Hsp_pattern_from
|
1073
|
+
assert_nothing_raised { @hsp.pattern_from }
|
1074
|
+
end
|
1075
|
+
|
1076
|
+
def test_Hsp_pattern_to
|
1077
|
+
assert_nothing_raised { @hsp.pattern_to }
|
1078
|
+
end
|
1079
|
+
|
1080
|
+
def test_Hsp_qseq
|
1081
|
+
seq = 'VLKLETLGWKVAIASGGFTFFAEYLRDKLRLTAVVANELEIMDGKFTGNVIGDIVDAQYKAKTLTRLAQEYEIPLAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVN-EKAEVTIRHADLMGV'
|
1082
|
+
assert_equal(seq, @hsp.qseq)
|
1083
|
+
end
|
1084
|
+
|
1085
|
+
def test_Hsp_midline
|
1086
|
+
seq = '+ +L LG K I +G D R A +A EL + +F ++ + K K +T L Q PLA +GDG ND P +KAA +GIA + V E A+ + H L G+'
|
1087
|
+
assert_equal(seq, @hsp.midline)
|
1088
|
+
end
|
1089
|
+
|
1090
|
+
def test_Hsp_hseq
|
1091
|
+
seq = 'ISELNALGVKGVILTG----------DNPRAAAAIAGELGL---EFKAGLL-----PEDKVKAVTELNQHA--PLAM---VGDGINDAPAMKAAAIGIAMGSGTDVALETADAALTHNHLRGL'
|
1092
|
+
assert_equal(seq, @hsp.hseq)
|
1093
|
+
end
|
1094
|
+
|
1095
|
+
def test_Hsp_percent_identity
|
1096
|
+
assert_nothing_raised { @hsp.percent_identity }
|
1097
|
+
end
|
1098
|
+
|
1099
|
+
def test_Hsp_mismatch_count
|
1100
|
+
assert_nothing_raised { @hsp.mismatch_count }
|
1101
|
+
end
|
1102
|
+
|
1103
|
+
end
|
1104
|
+
|
1105
|
+
# Tests for REXML version
|
1106
|
+
class TestBlastReportMultiREXML < TestBlastReportMulti
|
1107
|
+
end
|
1108
|
+
|
1109
|
+
class TestBlastReportIterationMultiREXML < TestBlastReportIterationMulti
|
1110
|
+
end
|
1111
|
+
|
1112
|
+
class TestBlastReportHitMultiREXML < TestBlastReportHitMulti
|
1113
|
+
end
|
1114
|
+
|
1115
|
+
class TestBlastReportHspMultiREXML < TestBlastReportHspMulti
|
1116
|
+
end
|
1117
|
+
|
1118
|
+
# Tests for XMLParser version
|
1119
|
+
if defined? XMLParser then
|
1120
|
+
|
1121
|
+
class TestBlastReportMultiXMLParser < TestBlastReportMulti
|
1122
|
+
end
|
1123
|
+
|
1124
|
+
class TestBlastReportIterationMultiXMLParser < TestBlastReportIterationMulti
|
1125
|
+
end
|
1126
|
+
|
1127
|
+
class TestBlastReportHitMultiXMLParser < TestBlastReportHitMulti
|
1128
|
+
end
|
1129
|
+
|
1130
|
+
class TestBlastReportHspMultiXMLParser < TestBlastReportHspMulti
|
1131
|
+
end
|
1132
|
+
|
1133
|
+
end #if defined? XMLParser
|
1134
|
+
|
1135
|
+
end # module Bio
|