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 +1,144 @@
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#
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# = bio/appl/blast/rexml.rb - BLAST XML output (-m 7) parser by REXML
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#
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# Copyright:: Copyright (C) 2002, 2003 Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id:$
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#
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# == Note
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#
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# This file is automatically loaded by bio/appl/blast/report.rb
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#
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begin
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require 'rexml/document'
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rescue LoadError
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end
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module Bio
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class Blast
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class Report
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private
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def rexml_parse(xml)
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dom = REXML::Document.new(xml)
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rexml_parse_program(dom)
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dom.elements.each("*//Iteration") do |e|
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@iterations.push(rexml_parse_iteration(e))
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end
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end
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def rexml_parse_program(dom)
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hash = {}
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dom.root.each_element_with_text do |e|
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name, text = e.name, e.text
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case name
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when 'BlastOutput_param'
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e.elements["Parameters"].each_element_with_text do |p|
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xml_set_parameter(p.name, p.text)
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end
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else
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hash[name] = text if text.strip.size > 0
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end
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end
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@program = hash['BlastOutput_program']
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@version = hash['BlastOutput_version']
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@reference = hash['BlastOutput_reference']
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@db = hash['BlastOutput_db']
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@query_id = hash['BlastOutput_query-ID']
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@query_def = hash['BlastOutput_query-def']
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@query_len = hash['BlastOutput_query-len'].to_i
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end
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def rexml_parse_iteration(e)
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iteration = Iteration.new
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e.elements.each do |i|
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case i.name
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when 'Iteration_iter-num'
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iteration.num = i.text.to_i
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when 'Iteration_hits'
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i.elements.each("Hit") do |h|
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iteration.hits.push(rexml_parse_hit(h))
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end
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when 'Iteration_message'
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iteration.message = i.text
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when 'Iteration_stat'
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i.elements["Statistics"].each_element_with_text do |s|
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k = s.name.sub(/Statistics_/, '')
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v = s.text =~ /\D/ ? s.text.to_f : s.text.to_i
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iteration.statistics[k] = v
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end
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# for new BLAST XML format
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when 'Iteration_query-ID'
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iteration.query_id = i.text
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when 'Iteration_query-def'
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iteration.query_def = i.text
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when 'Iteration_query-len'
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iteration.query_len = i.text.to_i
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end
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end #case i.name
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return iteration
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end
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def rexml_parse_hit(e)
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hit = Hit.new
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hash = {}
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hit.query_id = @query_id
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hit.query_def = @query_def
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hit.query_len = @query_len
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e.elements.each do |h|
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case h.name
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when 'Hit_hsps'
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h.elements.each("Hsp") do |s|
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hit.hsps.push(rexml_parse_hsp(s))
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end
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else
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hash[h.name] = h.text
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end
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end
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hit.num = hash['Hit_num'].to_i
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hit.hit_id = hash['Hit_id']
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hit.len = hash['Hit_len'].to_i
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hit.definition = hash['Hit_def']
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hit.accession = hash['Hit_accession']
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return hit
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end
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def rexml_parse_hsp(e)
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hsp = Hsp.new
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hash = {}
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e.each_element_with_text do |h|
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hash[h.name] = h.text
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end
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hsp.num = hash['Hsp_num'].to_i
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hsp.bit_score = hash['Hsp_bit-score'].to_f
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hsp.score = hash['Hsp_score'].to_i
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hsp.evalue = hash['Hsp_evalue'].to_f
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hsp.query_from = hash['Hsp_query-from'].to_i
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hsp.query_to = hash['Hsp_query-to'].to_i
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hsp.hit_from = hash['Hsp_hit-from'].to_i
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hsp.hit_to = hash['Hsp_hit-to'].to_i
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hsp.pattern_from = hash['Hsp_pattern-from'].to_i
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hsp.pattern_to = hash['Hsp_pattern-to'].to_i
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hsp.query_frame = hash['Hsp_query-frame'].to_i
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hsp.hit_frame = hash['Hsp_hit-frame'].to_i
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hsp.identity = hash['Hsp_identity'].to_i
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hsp.positive = hash['Hsp_positive'].to_i
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hsp.gaps = hash['Hsp_gaps'].to_i
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hsp.align_len = hash['Hsp_align-len'].to_i
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hsp.density = hash['Hsp_density'].to_i
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hsp.qseq = hash['Hsp_qseq']
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hsp.hseq = hash['Hsp_hseq']
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hsp.midline = hash['Hsp_midline']
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return hsp
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end
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end
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end
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end
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@@ -0,0 +1,277 @@
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#
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# = bio/appl/blast/rpsblast.rb - NCBI RPS Blast default output parser
|
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#
|
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# Copyright:: Copyright (C) 2008 Naohisa Goto <ng@bioruby.org>
|
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# License:: The Ruby License
|
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#
|
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# $Id:$
|
8
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#
|
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# == Description
|
10
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#
|
11
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# NCBI RPS Blast (Reversed Position Specific Blast) default
|
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# (-m 0 option) output parser class, Bio::Blast::RPSBlast::Report
|
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# and related classes/modules.
|
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#
|
15
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# == References
|
16
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#
|
17
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# * Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
|
18
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# Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
|
19
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# "Gapped BLAST and PSI-BLAST: a new generation of protein database search
|
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# programs", Nucleic Acids Res. 25:3389-3402.
|
21
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# * ftp://ftp.ncbi.nih.gov/blast/documents/rpsblast.html
|
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# * http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml
|
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#
|
24
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|
25
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require 'bio/appl/blast/format0'
|
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require 'bio/io/flatfile'
|
27
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|
28
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module Bio
|
29
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+
class Blast
|
30
|
+
|
31
|
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# NCBI RPS Blast (Reversed Position Specific Blast) namespace.
|
32
|
+
# Currently, this module is existing only for separating namespace.
|
33
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+
# To parse RPSBlast results, see Bio::Blast::RPSBlast::Report documents.
|
34
|
+
module RPSBlast
|
35
|
+
|
36
|
+
# Flatfile splitter for RPS-BLAST reports.
|
37
|
+
# It is internally used when reading RPS-BLAST report.
|
38
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+
# Normally, users do not need to use it directly.
|
39
|
+
#
|
40
|
+
# Note for Windows: RPS-BLAST results generated in Microsoft Windows
|
41
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+
# may not be parsed correctly due to the line feed code problem.
|
42
|
+
# For a workaroud, convert line feed codes from Windows(DOS) to UNIX.
|
43
|
+
#
|
44
|
+
class RPSBlastSplitter < Bio::FlatFile::Splitter::Template
|
45
|
+
|
46
|
+
# Separator used to distinguish start of each report
|
47
|
+
ReportHead = /\A\n*(RPS\-BLAST|Query\=)/
|
48
|
+
|
49
|
+
# Delimiter used for IO#gets
|
50
|
+
Delimiter = "\n\n"
|
51
|
+
|
52
|
+
# creates a new splitter object
|
53
|
+
def initialize(klass, bstream)
|
54
|
+
super(klass, bstream)
|
55
|
+
@entry_head = nil
|
56
|
+
end
|
57
|
+
|
58
|
+
# Skips leader of the entry.
|
59
|
+
# In this class, only skips space characters.
|
60
|
+
def skip_leader
|
61
|
+
stream.skip_spaces
|
62
|
+
return nil
|
63
|
+
end
|
64
|
+
|
65
|
+
# Rewinds the stream
|
66
|
+
def rewind
|
67
|
+
@entry_head = nil
|
68
|
+
super
|
69
|
+
end
|
70
|
+
|
71
|
+
# gets an entry
|
72
|
+
def get_entry
|
73
|
+
p0 = stream_pos()
|
74
|
+
pieces = []
|
75
|
+
flag_head = false # reached to start of header
|
76
|
+
flag_body = false # reached to start of body (Query=...)
|
77
|
+
while x = stream.gets(Delimiter)
|
78
|
+
if ReportHead =~ x then
|
79
|
+
case $1
|
80
|
+
when 'RPS-BLAST'
|
81
|
+
if pieces.empty? then
|
82
|
+
@entry_head = nil
|
83
|
+
flag_head = true
|
84
|
+
else
|
85
|
+
stream.ungets(x)
|
86
|
+
break
|
87
|
+
end
|
88
|
+
when 'Query='
|
89
|
+
if flag_body then
|
90
|
+
stream.ungets(x)
|
91
|
+
break
|
92
|
+
else
|
93
|
+
@entry_head = pieces.join('') if flag_head
|
94
|
+
flag_body = true
|
95
|
+
end
|
96
|
+
else
|
97
|
+
raise 'Bug: should not reach here'
|
98
|
+
end
|
99
|
+
end #if ReportHead...
|
100
|
+
pieces.push x
|
101
|
+
end #while
|
102
|
+
p1 = stream_pos()
|
103
|
+
|
104
|
+
self.entry_start_pos = p0
|
105
|
+
self.entry =
|
106
|
+
if pieces.empty? then
|
107
|
+
nil
|
108
|
+
elsif !flag_head and @entry_head then
|
109
|
+
@entry_head + pieces.join('')
|
110
|
+
else
|
111
|
+
pieces.join('')
|
112
|
+
end
|
113
|
+
self.entry_ended_pos = p1
|
114
|
+
return self.entry
|
115
|
+
end
|
116
|
+
end #class RPSBlastSplitter
|
117
|
+
|
118
|
+
# NCBI RPS Blast (Reversed Position Specific Blast)
|
119
|
+
# default output parser.
|
120
|
+
#
|
121
|
+
# It supports defalut (-m 0 option) output of the "rpsblast" command.
|
122
|
+
#
|
123
|
+
# Because this class inherits Bio::Blast::Default::Report,
|
124
|
+
# almost all methods are eqaul to Bio::Blast::Default::Report.
|
125
|
+
# Only DELIMITER (and RS) and few methods are different.
|
126
|
+
#
|
127
|
+
# By using Bio::FlatFile, (for example, Bio::FlatFile.open),
|
128
|
+
# rpsblast result generated from multiple query sequences is
|
129
|
+
# automatically splitted into multiple
|
130
|
+
# Bio::BLast::RPSBlast::Report objects corresponding to
|
131
|
+
# query sequences.
|
132
|
+
#
|
133
|
+
# Note for multi-fasta results WITH using Bio::FlatFile:
|
134
|
+
# Each splitted result is concatenated with header of the
|
135
|
+
# result which describes RPS-BLAST version and database
|
136
|
+
# information, if possible.
|
137
|
+
#
|
138
|
+
# Note for multi-fasta results WITHOUT using Bio::FlatFile:
|
139
|
+
# When parsing an output of rpsblast command running with
|
140
|
+
# multi-fasta sequences WITHOUT using Bio::FlatFile,
|
141
|
+
# each query's result is stored as an "iteration" of PSI-Blast.
|
142
|
+
# This behavior may be changed in the future.
|
143
|
+
#
|
144
|
+
# Note for nucleotide results: This class is not tested with
|
145
|
+
# nucleotide query and/or nucleotide databases.
|
146
|
+
#
|
147
|
+
class Report < Bio::Blast::Default::Report
|
148
|
+
# Delimter of each entry for RPS-BLAST.
|
149
|
+
DELIMITER = RS = "\nRPS-BLAST"
|
150
|
+
|
151
|
+
# (Integer) excess read size included in DELIMITER.
|
152
|
+
DELIMITER_OVERRUN = 9 # "RPS-BLAST"
|
153
|
+
|
154
|
+
# splitter for Bio::FlatFile support
|
155
|
+
FLATFILE_SPLITTER = RPSBlastSplitter
|
156
|
+
|
157
|
+
# Creates a new Report object from a string.
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+
#
|
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+
# Using Bio::FlatFile.open (or some other methods)
|
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+
# is recommended instead of using this method directly.
|
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+
# Refer Bio::Blast::RPSBlast::Report document for more information.
|
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|
+
#
|
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|
+
# Note for multi-fasta results WITHOUT using Bio::FlatFile:
|
164
|
+
# When parsing an output of rpsblast command running with
|
165
|
+
# multi-fasta sequences WITHOUT using Bio::FlatFile,
|
166
|
+
# each query's result is stored as an "iteration" of PSI-Blast.
|
167
|
+
# This behavior may be changed in the future.
|
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|
+
#
|
169
|
+
# Note for nucleotide results: This class is not tested with
|
170
|
+
# nucleotide query and/or nucleotide databases.
|
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|
+
#
|
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|
+
def initialize(str)
|
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|
+
str = str.sub(/\A\s+/, '')
|
174
|
+
# remove trailing entries for sure
|
175
|
+
str.sub!(/\n(RPS\-BLAST.*)/m, "\n")
|
176
|
+
@entry_overrun = $1
|
177
|
+
@entry = str
|
178
|
+
data = str.split(/(?:^[ \t]*\n)+/)
|
179
|
+
|
180
|
+
if data[0] and /\AQuery\=/ !~ data[0] then
|
181
|
+
format0_split_headers(data)
|
182
|
+
end
|
183
|
+
@iterations = format0_split_search(data)
|
184
|
+
format0_split_stat_params(data)
|
185
|
+
end
|
186
|
+
|
187
|
+
# Returns definition of the query.
|
188
|
+
# For a result of multi-fasta input, the first query's definition
|
189
|
+
# is returned (The same as <tt>iterations.first.query_def</tt>).
|
190
|
+
def query_def
|
191
|
+
iterations.first.query_def
|
192
|
+
end
|
193
|
+
|
194
|
+
# Returns length of the query.
|
195
|
+
# For a result of multi-fasta input, the first query's length
|
196
|
+
# is returned (The same as <tt>iterations.first.query_len</tt>).
|
197
|
+
def query_len
|
198
|
+
iterations.first.query_len
|
199
|
+
end
|
200
|
+
|
201
|
+
private
|
202
|
+
|
203
|
+
# Splits headers into the first line, reference, query line and
|
204
|
+
# database line.
|
205
|
+
def format0_split_headers(data)
|
206
|
+
@f0header = data.shift
|
207
|
+
@f0references = []
|
208
|
+
while data[0] and /\ADatabase\:/ !~ data[0]
|
209
|
+
@f0references.push data.shift
|
210
|
+
end
|
211
|
+
@f0database = data.shift
|
212
|
+
# In special case, a void line is inserted after database name.
|
213
|
+
if /\A +[\d\,]+ +sequences\; +[\d\,]+ total +letters\s*\z/ =~ data[0] then
|
214
|
+
@f0database.concat "\n"
|
215
|
+
@f0database.concat data.shift
|
216
|
+
end
|
217
|
+
end
|
218
|
+
|
219
|
+
# Splits the search results.
|
220
|
+
def format0_split_search(data)
|
221
|
+
iterations = []
|
222
|
+
dummystr = 'Searching..................................................done'
|
223
|
+
if r = data[0] and /^Searching/ =~ r then
|
224
|
+
dummystr = data.shift
|
225
|
+
end
|
226
|
+
while r = data[0] and /^Query\=/ =~ r
|
227
|
+
iterations << Iteration.new(data, dummystr)
|
228
|
+
end
|
229
|
+
iterations
|
230
|
+
end
|
231
|
+
|
232
|
+
# Iteration class for RPS-Blast.
|
233
|
+
# Though RPS-Blast does not iterate like PSI-BLAST,
|
234
|
+
# it aims to store a result of single query sequence.
|
235
|
+
#
|
236
|
+
# Normally, the instance of the class is generated
|
237
|
+
# by Bio::Blast::RPSBlast::Report object.
|
238
|
+
#
|
239
|
+
class Iteration < Bio::Blast::Default::Report::Iteration
|
240
|
+
# Creates a new Iteration object.
|
241
|
+
# It is designed to be called only internally from
|
242
|
+
# the Bio::Blast::RPSBlast::Report class.
|
243
|
+
# Users shall not use the method directly.
|
244
|
+
def initialize(data, dummystr)
|
245
|
+
if /\AQuery\=/ =~ data[0] then
|
246
|
+
sc = StringScanner.new(data.shift)
|
247
|
+
sc.skip(/\s*/)
|
248
|
+
if sc.skip_until(/Query\= */) then
|
249
|
+
q = []
|
250
|
+
begin
|
251
|
+
q << sc.scan(/.*/)
|
252
|
+
sc.skip(/\s*^ ?/)
|
253
|
+
end until !sc.rest or r = sc.skip(/ *\( *([\,\d]+) *letters *\)\s*\z/)
|
254
|
+
@query_len = sc[1].delete(',').to_i if r
|
255
|
+
@query_def = q.join(' ')
|
256
|
+
end
|
257
|
+
end
|
258
|
+
data.unshift(dummystr)
|
259
|
+
|
260
|
+
super(data)
|
261
|
+
end
|
262
|
+
|
263
|
+
# definition of the query
|
264
|
+
attr_reader :query_def
|
265
|
+
|
266
|
+
# length of the query sequence
|
267
|
+
attr_reader :query_len
|
268
|
+
|
269
|
+
end #class Iteration
|
270
|
+
|
271
|
+
end #class Report
|
272
|
+
|
273
|
+
end #module RPSBlast
|
274
|
+
|
275
|
+
end #module Blast
|
276
|
+
end #module Bio
|
277
|
+
|