ngoto-bio 1.2.9.9001
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- data/ChangeLog +2046 -0
- data/README.rdoc +223 -0
- data/README_DEV.rdoc +285 -0
- data/Rakefile +70 -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/bioruby.gemspec +463 -0
- data/bioruby.gemspec.erb +79 -0
- data/doc/Changes-0.7.rd +369 -0
- data/doc/Changes-1.3.rdoc +195 -0
- data/doc/KEGG_API.rd +1843 -0
- data/doc/KEGG_API.rd.ja +1834 -0
- data/doc/Tutorial.rd +1296 -0
- data/doc/Tutorial.rd.ja +2640 -0
- data/etc/bioinformatics/seqdatabase.ini +210 -0
- data/extconf.rb +2 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -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 +671 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blast.rb +505 -0
- data/lib/bio/appl/blat/report.rb +530 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/fasta.rb +235 -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/report.rb +683 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/baseml.rb +95 -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/codeml.rb +242 -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/report.rb +32 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/phylip/alignment.rb +129 -0
- data/lib/bio/appl/phylip/distance_matrix.rb +96 -0
- data/lib/bio/appl/probcons.rb +41 -0
- data/lib/bio/appl/psort/report.rb +457 -0
- data/lib/bio/appl/psort.rb +548 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sim4.rb +124 -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 +349 -0
- data/lib/bio/data/codontable.rb +722 -0
- data/lib/bio/data/na.rb +223 -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/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/fasta.rb +410 -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/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/pdb.rb +29 -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.rb +329 -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/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/flatfile.rb +473 -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/aa.rb +125 -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/sequence.rb +456 -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
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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
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- 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/shell.rb +44 -0
- data/lib/bio/tree.rb +852 -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/color_scheme.rb +191 -0
- data/lib/bio/util/contingency_table.rb +370 -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/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/double_stranded.rb +321 -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/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/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -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.rb +200 -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/restriction_enzyme.rb +228 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/lib/bio.rb +300 -0
- data/rdoc.zsh +8 -0
- data/sample/any2fasta.rb +59 -0
- data/sample/biofetch.rb +475 -0
- data/sample/color_scheme_na.rb +91 -0
- data/sample/dbget +37 -0
- data/sample/demo_sequence.rb +158 -0
- data/sample/enzymes.rb +78 -0
- data/sample/fasta2tab.rb +99 -0
- data/sample/fastagrep.rb +72 -0
- data/sample/fastasort.rb +54 -0
- data/sample/fsplit.rb +51 -0
- data/sample/gb2fasta.rb +30 -0
- data/sample/gb2tab.rb +325 -0
- data/sample/gbtab2mysql.rb +161 -0
- data/sample/genes2nuc.rb +33 -0
- data/sample/genes2pep.rb +33 -0
- data/sample/genes2tab.rb +81 -0
- data/sample/genome2rb.rb +29 -0
- data/sample/genome2tab.rb +76 -0
- data/sample/goslim.rb +303 -0
- data/sample/gt2fasta.rb +47 -0
- data/sample/na2aa.rb +34 -0
- data/sample/pmfetch.rb +42 -0
- data/sample/pmsearch.rb +42 -0
- data/sample/psortplot_html.rb +214 -0
- data/sample/ssearch2tab.rb +96 -0
- data/sample/tdiary.rb +158 -0
- data/sample/tfastx2tab.rb +100 -0
- data/sample/vs-genes.rb +212 -0
- data/setup.rb +1596 -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
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- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
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- data/test/data/fasta/example1.txt +75 -0
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- data/test/data/genscan/sample.report +63 -0
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- 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
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- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
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- 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 +23 -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
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- 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/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 +488 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +103 -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 +484 -0
@@ -0,0 +1,364 @@
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#
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# = test/bio/db/nexus.rb - Unit test for Bio::Nexus
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#
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# Copyright:: Copyright (C) 2006 Christian M Zmasek <cmzmasek@yahoo.com>
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#
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# License:: The Ruby License
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#
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# $Id:$
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#
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# == Description
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#
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# This file contains unit tests for Bio::Nexus.
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#
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require 'pathname'
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libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
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$:.unshift(libpath) unless $:.include?(libpath)
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require 'test/unit'
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require 'bio/db/nexus'
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module Bio
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class TestNexus < Test::Unit::TestCase
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NEXUS_STRING_1 = <<-END_OF_NEXUS_STRING
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#NEXUS
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Begin Taxa;
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Dimensions [[comment]] ntax=4;
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TaxLabels "hag fish" [comment] 'african frog'
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[lots of different comment follow]
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[] [a] [[a]] [ a ] [[ a ]] [ [ a ] ] [a ]
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[[a ]] [ [a ] ] [ a] [[ a]] [ [ a] ] [ ]
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[[ ]] [ [ ] ] [ a b ] [[ a b ]] [ [ a b ] ]
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[x[ x [x[ x[[x[[xx[x[ x]] ]x ] []]][x]]x]]]
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[comment_1 comment_3] "rat snake" 'red
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mouse';
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End;
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[yet another comment End; ]
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Begin Characters;
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Dimensions nchar=20
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ntax=4;
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[ ntax=1000; ]
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Format DataType=DNA
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Missing=x
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Gap=- MatchChar=.;
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Matrix [comment]
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fish ACATA GAGGG
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TACCT CTAAG
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frog ACTTA GAGGC TACCT CTAGC
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snake ACTCA CTGGG TACCT TTGCG
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mouse ACTCA GACGG TACCT TTGCG;
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End;
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Begin Trees;
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[comment]
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Tree best=(fish,(frog,(snake,mo
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use)));
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[some long comment]
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Tree
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other=(snake,
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(frog,(fish,mo
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use
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)));
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End;
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Begin Trees;
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[comment]
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Tree worst=(A,(B,(C,D
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)));
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Tree bad=(a,
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(b,(c , d
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)
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) );
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End;
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Begin Distances;
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Dimensions nchar=20 ntax=5;
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Format Triangle=Both;
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Matrix
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taxon_1 0.0 1.0
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2.0 4.0 7.0
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taxon_2 1.0
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0.0 3.0 5.0 8.0
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taxon_3 3.0 4.0 0.0 6.0 9.0
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taxon_4 7.0 3.0 2.0 0.0 9.5
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taxon_5 1.2 1.3 1.4 1.5 0.0;
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End;
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Begin Data;
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Dimensions ntax=5 nchar=14;
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Format Datatype=RNA gap=# MISSING=x MatchChar=^;
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TaxLabels ciona
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cow [comment1 commentX] ape
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'purple urchin' "green lizard";
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Matrix
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[ comment [old comment] ]
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taxon_1 A- CCGTCGA-GTTA
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taxon_2 T- CCG-CGA-GATC
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taxon_3 A- C-GTCGA-GATG
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taxon_4 A- C C TC G
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A - -G T T
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T
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taxon_5
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T-CGGTCGT-CTTA;
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End;
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Begin Private1;
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Something foo=5 bar=20;
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Format Datatype=DNA;
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Matrix
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taxon_1 1111 1111111111
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taxon_2 2222 2222222222
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taxon_3 3333 3333333333
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taxon_4 4444 4444444444
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taxon_5 5555 5555555555;
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End;
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Begin Private1;
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some [boring]
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interesting [
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outdated
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] data be here
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End;
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END_OF_NEXUS_STRING
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DATA_BLOCK_OUTPUT_STRING = <<-DATA_BLOCK_OUTPUT_STRING
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Begin Data;
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Dimensions NTax=5 NChar=14;
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Format DataType=RNA Missing=x Gap=# MatchChar=^;
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TaxLabels ciona cow ape purple_urchin green_lizard;
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Matrix
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taxon_1 A-CCGTCGA-GTTA
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taxon_2 T-CCG-CGA-GATC
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taxon_3 A-C-GTCGA-GATG
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taxon_4 A-CCTCGA--GTTT
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taxon_5 T-CGGTCGT-CTTA;
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End;
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DATA_BLOCK_OUTPUT_STRING
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def test_nexus
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nexus = Bio::Nexus.new( NEXUS_STRING_1 )
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blocks = nexus.get_blocks
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assert_equal( 8, blocks.size )
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private_blocks = nexus.get_blocks_by_name( "private1" )
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data_blocks = nexus.get_data_blocks
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character_blocks = nexus.get_characters_blocks
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trees_blocks = nexus.get_trees_blocks
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distances_blocks = nexus.get_distances_blocks
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taxa_blocks = nexus.get_taxa_blocks
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assert_equal( 2, private_blocks.size )
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assert_equal( 1, data_blocks.size )
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assert_equal( 1, character_blocks.size )
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assert_equal( 2, trees_blocks.size )
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assert_equal( 1, distances_blocks.size )
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assert_equal( 1, taxa_blocks.size )
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taxa_block = taxa_blocks[ 0 ]
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assert_equal( taxa_block.get_number_of_taxa.to_i , 4 )
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assert_equal( taxa_block.get_taxa[ 0 ], "hag_fish" )
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assert_equal( taxa_block.get_taxa[ 1 ], "african_frog" )
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assert_equal( taxa_block.get_taxa[ 2 ], "rat_snake" )
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assert_equal( taxa_block.get_taxa[ 3 ], "red_mouse" )
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chars_block = character_blocks[ 0 ]
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assert_equal( chars_block.get_number_of_taxa.to_i, 4 )
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assert_equal( chars_block.get_number_of_characters.to_i, 20 )
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assert_equal( chars_block.get_datatype, "DNA" )
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assert_equal( chars_block.get_match_character, "." )
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assert_equal( chars_block.get_missing, "x" )
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assert_equal( chars_block.get_gap_character, "-" )
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assert_equal( chars_block.get_matrix.get_value( 0, 0 ), "fish" )
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assert_equal( chars_block.get_matrix.get_value( 1, 0 ), "frog" )
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assert_equal( chars_block.get_matrix.get_value( 2, 0 ), "snake" )
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assert_equal( chars_block.get_matrix.get_value( 3, 0 ), "mouse" )
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assert_equal( chars_block.get_matrix.get_value( 0, 20 ), "G" )
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assert_equal( chars_block.get_matrix.get_value( 1, 20 ), "C" )
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assert_equal( chars_block.get_matrix.get_value( 2, 20 ), "G" )
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assert_equal( chars_block.get_matrix.get_value( 3, 20 ), "G" )
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assert_equal( chars_block.get_characters_strings_by_name( "fish" )[ 0 ], "ACATAGAGGGTACCTCTAAG" )
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assert_equal( chars_block.get_characters_strings_by_name( "frog" )[ 0 ], "ACTTAGAGGCTACCTCTAGC" )
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assert_equal( chars_block.get_characters_strings_by_name( "snake" )[ 0 ], "ACTCACTGGGTACCTTTGCG" )
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assert_equal( chars_block.get_characters_strings_by_name( "mouse" )[ 0 ], "ACTCAGACGGTACCTTTGCG" )
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assert_equal( chars_block.get_characters_string( 0 ), "ACATAGAGGGTACCTCTAAG" )
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assert_equal( chars_block.get_characters_string( 1 ), "ACTTAGAGGCTACCTCTAGC" )
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assert_equal( chars_block.get_characters_string( 2 ), "ACTCACTGGGTACCTTTGCG" )
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assert_equal( chars_block.get_characters_string( 3 ), "ACTCAGACGGTACCTTTGCG" )
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assert_equal( chars_block.get_row_name( 1 ), "frog" )
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assert_equal( chars_block.get_sequences_by_name( "fish" )[ 0 ].seq.to_s.downcase, "ACATAGAGGGTACCTCTAAG".downcase )
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assert_equal( chars_block.get_sequences_by_name( "frog" )[ 0 ].seq.to_s.downcase, "ACTTAGAGGCTACCTCTAGC".downcase )
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assert_equal( chars_block.get_sequences_by_name( "snake" )[ 0 ].seq.to_s.downcase, "ACTCACTGGGTACCTTTGCG".downcase )
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assert_equal( chars_block.get_sequences_by_name( "mouse" )[ 0 ].seq.to_s.downcase, "ACTCAGACGGTACCTTTGCG".downcase )
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assert_equal( chars_block.get_sequences_by_name( "fish" )[ 0 ].definition, "fish" )
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assert_equal( chars_block.get_sequences_by_name( "frog" )[ 0 ].definition, "frog" )
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assert_equal( chars_block.get_sequences_by_name( "snake" )[ 0 ].definition, "snake" )
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assert_equal( chars_block.get_sequences_by_name( "mouse" )[ 0 ].definition, "mouse" )
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assert_equal( chars_block.get_sequence( 0 ).seq.to_s.downcase, "ACATAGAGGGTACCTCTAAG".downcase )
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assert_equal( chars_block.get_sequence( 1 ).seq.to_s.downcase, "ACTTAGAGGCTACCTCTAGC".downcase )
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assert_equal( chars_block.get_sequence( 2 ).seq.to_s.downcase, "ACTCACTGGGTACCTTTGCG".downcase )
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assert_equal( chars_block.get_sequence( 3 ).seq.to_s.downcase, "ACTCAGACGGTACCTTTGCG".downcase )
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assert_equal( chars_block.get_sequence( 0 ).definition, "fish" )
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assert_equal( chars_block.get_sequence( 1 ).definition, "frog" )
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assert_equal( chars_block.get_sequence( 2 ).definition, "snake" )
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assert_equal( chars_block.get_sequence( 3 ).definition, "mouse" )
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tree_block_0 = trees_blocks[ 0 ]
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tree_block_1 = trees_blocks[ 1 ]
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assert_equal( tree_block_0.get_tree_names[ 0 ], "best" )
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assert_equal( tree_block_0.get_tree_names[ 1 ], "other" )
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assert_equal( tree_block_0.get_tree_strings_by_name( "best" )[ 0 ], "(fish,(frog,(snake,mouse)));" )
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assert_equal( tree_block_0.get_tree_strings_by_name( "other" )[ 0 ], "(snake,(frog,(fish,mouse)));" )
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best_tree = tree_block_0.get_trees_by_name( "best" )[ 0 ]
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other_tree = tree_block_0.get_trees_by_name( "other" )[ 0 ]
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worst_tree = tree_block_1.get_tree( 0 )
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bad_tree = tree_block_1.get_tree( 1 )
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assert_equal( 6, best_tree.descendents( best_tree.root ).size )
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assert_equal( 4, best_tree.leaves.size)
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assert_equal( 6, other_tree.descendents( other_tree.root ).size )
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assert_equal( 4, other_tree.leaves.size)
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fish_leaf_best = best_tree.nodes.find { |x| x.name == 'fish' }
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assert_equal( 1, best_tree.ancestors( fish_leaf_best ).size )
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fish_leaf_other = other_tree.nodes.find { |x| x.name == 'fish' }
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assert_equal( 3, other_tree.ancestors( fish_leaf_other ).size )
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a_leaf_worst = worst_tree.nodes.find { |x| x.name == 'A' }
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assert_equal( 1, worst_tree.ancestors( a_leaf_worst ).size )
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c_leaf_bad = bad_tree.nodes.find { |x| x.name == 'c' }
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assert_equal( 3, bad_tree.ancestors( c_leaf_bad ).size )
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dist_block = distances_blocks[ 0 ]
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+
assert_equal( dist_block.get_number_of_taxa.to_i, 5 )
|
262
|
+
assert_equal( dist_block.get_number_of_characters.to_i, 20 )
|
263
|
+
assert_equal( dist_block.get_triangle, "Both" )
|
264
|
+
assert_equal( dist_block.get_matrix.get_value( 0, 0 ), "taxon_1" )
|
265
|
+
assert_equal( dist_block.get_matrix.get_value( 1, 0 ), "taxon_2" )
|
266
|
+
assert_equal( dist_block.get_matrix.get_value( 2, 0 ), "taxon_3" )
|
267
|
+
assert_equal( dist_block.get_matrix.get_value( 3, 0 ), "taxon_4" )
|
268
|
+
assert_equal( dist_block.get_matrix.get_value( 4, 0 ), "taxon_5" )
|
269
|
+
assert_equal( dist_block.get_matrix.get_value( 0, 5 ).to_f, 7.0 )
|
270
|
+
assert_equal( dist_block.get_matrix.get_value( 1, 5 ).to_f, 8.0 )
|
271
|
+
assert_equal( dist_block.get_matrix.get_value( 2, 5 ).to_f, 9.0 )
|
272
|
+
assert_equal( dist_block.get_matrix.get_value( 3, 5 ).to_f, 9.5 )
|
273
|
+
assert_equal( dist_block.get_matrix.get_value( 4, 5 ).to_f, 0.0 )
|
274
|
+
|
275
|
+
data_block = data_blocks[ 0 ]
|
276
|
+
assert_equal( data_block.get_number_of_taxa.to_i, 5 )
|
277
|
+
assert_equal( data_block.get_number_of_characters.to_i, 14 )
|
278
|
+
assert_equal( data_block.get_datatype, "RNA" )
|
279
|
+
assert_equal( data_block.get_match_character, "^" )
|
280
|
+
assert_equal( data_block.get_missing, "x" )
|
281
|
+
assert_equal( data_block.get_gap_character, "#" )
|
282
|
+
assert_equal( data_block.get_matrix.get_value( 0, 0 ), "taxon_1" )
|
283
|
+
assert_equal( data_block.get_matrix.get_value( 1, 0 ), "taxon_2" )
|
284
|
+
assert_equal( data_block.get_matrix.get_value( 2, 0 ), "taxon_3" )
|
285
|
+
assert_equal( data_block.get_matrix.get_value( 3, 0 ), "taxon_4" )
|
286
|
+
assert_equal( data_block.get_matrix.get_value( 4, 0 ), "taxon_5" )
|
287
|
+
assert_equal( data_block.get_matrix.get_value( 0, 14 ), "A" )
|
288
|
+
assert_equal( data_block.get_matrix.get_value( 1, 14 ), "C" )
|
289
|
+
assert_equal( data_block.get_matrix.get_value( 2, 14 ), "G" )
|
290
|
+
assert_equal( data_block.get_matrix.get_value( 3, 14 ), "T" )
|
291
|
+
assert_equal( data_block.get_matrix.get_value( 4, 14 ), "A" )
|
292
|
+
assert_equal( data_block.get_taxa[ 0 ], "ciona" )
|
293
|
+
assert_equal( data_block.get_taxa[ 1 ], "cow" )
|
294
|
+
assert_equal( data_block.get_taxa[ 2 ], "ape" )
|
295
|
+
assert_equal( data_block.get_taxa[ 3 ], "purple_urchin" )
|
296
|
+
assert_equal( data_block.get_taxa[ 4 ], "green_lizard" )
|
297
|
+
|
298
|
+
|
299
|
+
assert_equal( data_block.get_characters_strings_by_name( "taxon_1" )[ 0 ], "A-CCGTCGA-GTTA" )
|
300
|
+
assert_equal( data_block.get_characters_strings_by_name( "taxon_2" )[ 0 ], "T-CCG-CGA-GATC" )
|
301
|
+
assert_equal( data_block.get_characters_strings_by_name( "taxon_3" )[ 0 ], "A-C-GTCGA-GATG" )
|
302
|
+
assert_equal( data_block.get_characters_strings_by_name( "taxon_4" )[ 0 ], "A-CCTCGA--GTTT" )
|
303
|
+
assert_equal( data_block.get_characters_strings_by_name( "taxon_5" )[ 0 ], "T-CGGTCGT-CTTA" )
|
304
|
+
|
305
|
+
assert_equal( data_block.get_characters_string( 0 ), "A-CCGTCGA-GTTA" )
|
306
|
+
assert_equal( data_block.get_characters_string( 1 ), "T-CCG-CGA-GATC" )
|
307
|
+
assert_equal( data_block.get_characters_string( 2 ), "A-C-GTCGA-GATG" )
|
308
|
+
assert_equal( data_block.get_characters_string( 3 ), "A-CCTCGA--GTTT" )
|
309
|
+
assert_equal( data_block.get_characters_string( 4 ), "T-CGGTCGT-CTTA" )
|
310
|
+
|
311
|
+
assert_equal( data_block.get_row_name( 0 ), "taxon_1" )
|
312
|
+
assert_equal( data_block.get_row_name( 1 ), "taxon_2" )
|
313
|
+
assert_equal( data_block.get_row_name( 2 ), "taxon_3" )
|
314
|
+
assert_equal( data_block.get_row_name( 3 ), "taxon_4" )
|
315
|
+
assert_equal( data_block.get_row_name( 4 ), "taxon_5" )
|
316
|
+
|
317
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_1" )[ 0 ].seq.to_s.downcase, "A-CCGTCGA-GTTA".downcase )
|
318
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_2" )[ 0 ].seq.to_s.downcase, "T-CCG-CGA-GATC".downcase )
|
319
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_3" )[ 0 ].seq.to_s.downcase, "A-C-GTCGA-GATG".downcase )
|
320
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_4" )[ 0 ].seq.to_s.downcase, "A-CCTCGA--GTTT".downcase )
|
321
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_5" )[ 0 ].seq.to_s.downcase, "T-CGGTCGT-CTTA".downcase )
|
322
|
+
|
323
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_1" )[ 0 ].definition, "taxon_1" )
|
324
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_2" )[ 0 ].definition, "taxon_2" )
|
325
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_3" )[ 0 ].definition, "taxon_3" )
|
326
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_4" )[ 0 ].definition, "taxon_4" )
|
327
|
+
assert_equal( data_block.get_sequences_by_name( "taxon_5" )[ 0 ].definition, "taxon_5" )
|
328
|
+
|
329
|
+
assert_equal( data_block.get_sequence( 0 ).seq.to_s.downcase, "A-CCGTCGA-GTTA".downcase )
|
330
|
+
assert_equal( data_block.get_sequence( 1 ).seq.to_s.downcase, "T-CCG-CGA-GATC".downcase )
|
331
|
+
assert_equal( data_block.get_sequence( 2 ).seq.to_s.downcase, "A-C-GTCGA-GATG".downcase )
|
332
|
+
assert_equal( data_block.get_sequence( 3 ).seq.to_s.downcase, "A-CCTCGA--GTTT".downcase )
|
333
|
+
assert_equal( data_block.get_sequence( 4 ).seq.to_s.downcase, "T-CGGTCGT-CTTA".downcase )
|
334
|
+
|
335
|
+
assert_equal( data_block.get_sequence( 0 ).definition, "taxon_1" )
|
336
|
+
assert_equal( data_block.get_sequence( 1 ).definition, "taxon_2" )
|
337
|
+
assert_equal( data_block.get_sequence( 2 ).definition, "taxon_3" )
|
338
|
+
assert_equal( data_block.get_sequence( 3 ).definition, "taxon_4" )
|
339
|
+
assert_equal( data_block.get_sequence( 4 ).definition, "taxon_5" )
|
340
|
+
|
341
|
+
assert_equal( DATA_BLOCK_OUTPUT_STRING, data_block.to_nexus() )
|
342
|
+
|
343
|
+
generic_0 = private_blocks[ 0 ]
|
344
|
+
generic_1 = private_blocks[ 1 ]
|
345
|
+
assert_equal( generic_0.get_tokens[ 0 ], "Something" )
|
346
|
+
assert_equal( generic_0.get_tokens[ 1 ], "foo" )
|
347
|
+
assert_equal( generic_0.get_tokens[ 2 ], "5" )
|
348
|
+
assert_equal( generic_0.get_tokens[ 3 ], "bar" )
|
349
|
+
assert_equal( generic_0.get_tokens[ 4 ], "20" )
|
350
|
+
assert_equal( generic_0.get_tokens[ 5 ], "Format" )
|
351
|
+
assert_equal( generic_0.get_tokens[ 6 ], "Datatype" )
|
352
|
+
assert_equal( generic_0.get_tokens[ 7 ], "DNA" )
|
353
|
+
assert_equal( generic_0.get_tokens[ 8 ], "Matrix" )
|
354
|
+
assert_equal( generic_0.get_tokens[ 9 ], "taxon_1" )
|
355
|
+
assert_equal( generic_0.get_tokens[10 ], "1111" )
|
356
|
+
assert_equal( generic_1.get_tokens[ 0 ], "some" )
|
357
|
+
assert_equal( generic_1.get_tokens[ 1 ], "interesting" )
|
358
|
+
assert_equal( generic_1.get_tokens[ 2 ], "data" )
|
359
|
+
assert_equal( generic_1.get_tokens[ 3 ], "be" )
|
360
|
+
assert_equal( generic_1.get_tokens[ 4 ], "here" )
|
361
|
+
|
362
|
+
end # test_nexus
|
363
|
+
end # class TestNexus
|
364
|
+
end # module Bio
|