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 +1,23 @@
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#
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# = bio/shell/plugin/emboss.rb - methods to use EMBOSS
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#
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# Copyright:: Copyright (C) 2005
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# Toshiaki Katayama <k@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: emboss.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
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#
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module Bio::Shell
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private
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def seqret(usa)
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Bio::EMBOSS.seqret(usa)
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end
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def entret(usa)
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Bio::EMBOSS.entret(usa)
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end
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end
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#
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# = bio/shell/plugin/entry.rb - extract entry and sequence
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#
|
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# Copyright:: Copyright (C) 2005
|
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# Toshiaki Katayama <k@bioruby.org>
|
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# License:: The Ruby License
|
7
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#
|
8
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# $Id: entry.rb,v 1.10 2007/04/05 23:35:41 trevor Exp $
|
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#
|
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module Bio::Shell
|
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private
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# Read a text file and collect the first word of each line in array
|
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def readlist(filename)
|
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list = []
|
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File.open(filename).each do |line|
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list << line[/^\S+/]
|
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end
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return list
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end
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# Obtain a Bio::Sequence::NA (DNA) or a Bio::Sequence::AA (Amino Acid)
|
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# sequence from
|
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# * String -- "atgcatgc" or "MQKKP"
|
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# * IO -- io = IO.popen("gzip -dc db.gz") (first entry only)
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# * "filename" -- "gbvrl.gbk" (first entry only)
|
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# * "db:entry" -- "embl:BUM" (entry is retrieved by the ent method)
|
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def getseq(arg)
|
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seq = ""
|
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if arg.kind_of?(Bio::Sequence)
|
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seq = arg
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elsif arg.respond_to?(:gets) or File.exists?(arg)
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ent = flatauto(arg)
|
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elsif arg[/:/]
|
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ent = getobj(arg)
|
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else
|
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tmp = arg
|
40
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+
end
|
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|
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if ent.respond_to?(:seq)
|
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tmp = ent.seq
|
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elsif ent.respond_to?(:naseq)
|
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#seq = ent.naseq
|
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tmp = ent.naseq
|
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elsif ent.respond_to?(:aaseq)
|
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#seq = ent.aaseq
|
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tmp = ent.aaseq
|
50
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+
end
|
51
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|
52
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if tmp and tmp.is_a?(String) and not tmp.empty?
|
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#seq = Bio::Sequence.auto(tmp).seq
|
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seq = Bio::Sequence.auto(tmp)
|
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end
|
56
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return seq
|
57
|
+
end
|
58
|
+
|
59
|
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# Obtain a database entry from
|
60
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# * IO -- IO object (first entry only)
|
61
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# * "filename" -- local file (first entry only)
|
62
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# * "db:entry" -- local BioFlat, OBDA, EMBOSS, KEGG API
|
63
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+
def getent(arg)
|
64
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entry = ""
|
65
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db, entry_id = arg.to_s.strip.split(/:/)
|
66
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+
|
67
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# local file
|
68
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if arg.respond_to?(:gets) or File.exists?(arg)
|
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puts "Retrieving entry from file (#{arg})"
|
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entry = flatfile(arg)
|
71
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+
|
72
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# BioFlat in ./.bioruby/bioflat/ or ~/.bioinformatics/.bioruby/bioflat/
|
73
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elsif Bio::Shell.find_flat_dir(db)
|
74
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+
puts "Retrieving entry from local BioFlat database (#{arg})"
|
75
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+
entry = flatsearch(db, entry_id)
|
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+
|
77
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# OBDA in ~/.bioinformatics/seqdatabase.ini
|
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elsif obdadbs.include?(db)
|
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puts "Retrieving entry from OBDA (#{arg})"
|
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entry = obdaentry(db, entry_id)
|
81
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+
|
82
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else
|
83
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# EMBOSS USA in ~/.embossrc
|
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str = entret(arg)
|
85
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if $?.exitstatus == 0 and str.length != 0
|
86
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puts "Retrieving entry from EMBOSS (#{arg})"
|
87
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+
entry = str
|
88
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+
|
89
|
+
# KEGG API at http://www.genome.jp/kegg/soap/
|
90
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+
else
|
91
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+
puts "Retrieving entry from KEGG API (#{arg})"
|
92
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+
entry = bget(arg)
|
93
|
+
end
|
94
|
+
end
|
95
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+
|
96
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return entry
|
97
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+
end
|
98
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+
|
99
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+
# Obtain a parsed object from sources that ent() supports.
|
100
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+
def getobj(arg)
|
101
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str = getent(arg)
|
102
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flatparse(str)
|
103
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+
end
|
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|
105
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+
end
|
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|
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#
|
2
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# = bio/shell/plugin/flatfile.rb - plugin for flatfile database
|
3
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+
#
|
4
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# Copyright:: Copyright (C) 2005
|
5
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+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: flatfile.rb,v 1.13 2007/04/05 23:45:11 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
module Bio::Shell
|
12
|
+
|
13
|
+
private
|
14
|
+
|
15
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+
def flatfile(filename)
|
16
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+
if block_given?
|
17
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+
Bio::FlatFile.auto(filename) do |flat|
|
18
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+
flat.each do |entry|
|
19
|
+
yield flat.entry_raw
|
20
|
+
end
|
21
|
+
end
|
22
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+
else
|
23
|
+
entry = ''
|
24
|
+
Bio::FlatFile.auto(filename) do |flat|
|
25
|
+
flat.next_entry
|
26
|
+
entry = flat.entry_raw
|
27
|
+
end
|
28
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+
return entry
|
29
|
+
end
|
30
|
+
end
|
31
|
+
|
32
|
+
def flatauto(filename)
|
33
|
+
if block_given?
|
34
|
+
Bio::FlatFile.auto(filename) do |flat|
|
35
|
+
flat.each do |entry|
|
36
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+
yield entry
|
37
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+
end
|
38
|
+
end
|
39
|
+
else
|
40
|
+
entry = ''
|
41
|
+
Bio::FlatFile.auto(filename) do |flat|
|
42
|
+
entry = flat.next_entry
|
43
|
+
end
|
44
|
+
return entry
|
45
|
+
end
|
46
|
+
end
|
47
|
+
|
48
|
+
def flatparse(entry)
|
49
|
+
if cls = Bio::FlatFile.autodetect(entry)
|
50
|
+
return cls.new(entry)
|
51
|
+
end
|
52
|
+
end
|
53
|
+
|
54
|
+
def flatfasta(fastafile, *flatfiles)
|
55
|
+
puts "Saving fasta file (#{fastafile}) ... "
|
56
|
+
File.open(fastafile, "w") do |fasta|
|
57
|
+
flatfiles.each do |flatfile|
|
58
|
+
puts " converting -- #{flatfile}"
|
59
|
+
Bio::FlatFile.auto(flatfile) do |flat|
|
60
|
+
flat.each do |entry|
|
61
|
+
header = "#{entry.entry_id} #{entry.definition}"
|
62
|
+
fasta.puts entry.seq.to_fasta(header, 50)
|
63
|
+
end
|
64
|
+
end
|
65
|
+
end
|
66
|
+
end
|
67
|
+
puts "done"
|
68
|
+
end
|
69
|
+
|
70
|
+
def flatindex(dbname, *flatfiles)
|
71
|
+
begin
|
72
|
+
dir = Bio::Shell.create_flat_dir(dbname)
|
73
|
+
print "Creating BioFlat index (#{dir}) ... "
|
74
|
+
bdb = format = options = nil
|
75
|
+
Bio::FlatFileIndex.makeindex(bdb, dir, format, options, *flatfiles)
|
76
|
+
puts "done"
|
77
|
+
rescue
|
78
|
+
warn "Error: Failed to create index (#{dir}) : #{$!}"
|
79
|
+
end
|
80
|
+
end
|
81
|
+
|
82
|
+
def flatsearch(dbname, keyword)
|
83
|
+
dir = Bio::Shell.find_flat_dir(dbname)
|
84
|
+
unless dir
|
85
|
+
warn "Error: Failed to open database (#{dbname})"
|
86
|
+
return
|
87
|
+
end
|
88
|
+
entry = ''
|
89
|
+
Bio::FlatFileIndex.open(dir) do |db|
|
90
|
+
if results = db.include?(keyword)
|
91
|
+
results.each do |entry_id|
|
92
|
+
entry << db.search_primary(entry_id).to_s
|
93
|
+
end
|
94
|
+
else
|
95
|
+
warn "Error: No hits found in #{dbname} (#{keyword})"
|
96
|
+
end
|
97
|
+
end
|
98
|
+
return entry
|
99
|
+
end
|
100
|
+
|
101
|
+
end
|
@@ -0,0 +1,181 @@
|
|
1
|
+
#
|
2
|
+
# = bio/shell/plugin/keggapi.rb - plugin for KEGG API
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: keggapi.rb,v 1.12 2007/04/05 23:35:41 trevor Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
module Bio::Shell
|
12
|
+
|
13
|
+
module Private
|
14
|
+
|
15
|
+
module_function
|
16
|
+
|
17
|
+
def keggapi_definition2tab(list)
|
18
|
+
ary = []
|
19
|
+
list.each do |entry|
|
20
|
+
ary << "#{entry.entry_id}\t#{entry.definition}"
|
21
|
+
end
|
22
|
+
return ary
|
23
|
+
end
|
24
|
+
end
|
25
|
+
|
26
|
+
private
|
27
|
+
|
28
|
+
def keggapi(wsdl = nil)
|
29
|
+
if wsdl
|
30
|
+
@keggapi = Bio::KEGG::API.new(wsdl)
|
31
|
+
else
|
32
|
+
@keggapi ||= Bio::KEGG::API.new
|
33
|
+
end
|
34
|
+
return @keggapi
|
35
|
+
end
|
36
|
+
|
37
|
+
# DBGET
|
38
|
+
|
39
|
+
def binfo(db = "all")
|
40
|
+
result = keggapi.binfo(db)
|
41
|
+
puts result
|
42
|
+
return result
|
43
|
+
end
|
44
|
+
|
45
|
+
def bfind(str)
|
46
|
+
result = keggapi.bfind(str)
|
47
|
+
return result
|
48
|
+
end
|
49
|
+
|
50
|
+
def bget(str)
|
51
|
+
result = keggapi.bget(str)
|
52
|
+
if block_given?
|
53
|
+
yield result
|
54
|
+
else
|
55
|
+
puts result
|
56
|
+
return result
|
57
|
+
end
|
58
|
+
end
|
59
|
+
|
60
|
+
def btit(str)
|
61
|
+
result = keggapi.btit(str)
|
62
|
+
puts result
|
63
|
+
return result
|
64
|
+
end
|
65
|
+
|
66
|
+
def bconv(str)
|
67
|
+
result = keggapi.bconv(str)
|
68
|
+
puts result
|
69
|
+
return result
|
70
|
+
end
|
71
|
+
|
72
|
+
# DATABASES
|
73
|
+
|
74
|
+
def keggdbs
|
75
|
+
list = keggapi.list_databases
|
76
|
+
result = Bio::Shell::Private.keggapi_definition2tab(list).join("\n")
|
77
|
+
puts result
|
78
|
+
return list.map {|x| x.entry_id}
|
79
|
+
end
|
80
|
+
|
81
|
+
def keggorgs
|
82
|
+
list = keggapi.list_organisms
|
83
|
+
result = Bio::Shell::Private.keggapi_definition2tab(list).sort.join("\n")
|
84
|
+
puts result
|
85
|
+
return list.map {|x| x.entry_id}
|
86
|
+
end
|
87
|
+
|
88
|
+
def keggpathways(org = "map")
|
89
|
+
list = keggapi.list_pathways(org)
|
90
|
+
result = Bio::Shell::Private.keggapi_definition2tab(list).join("\n")
|
91
|
+
puts result
|
92
|
+
return list.map {|x| x.entry_id}
|
93
|
+
end
|
94
|
+
|
95
|
+
# use KEGG DAS insetad
|
96
|
+
def kegggenomeseq(org)
|
97
|
+
result = ""
|
98
|
+
require 'net/ftp'
|
99
|
+
Net::FTP.open("ftp.genome.jp", "anonymous") do |ftp|
|
100
|
+
path = "/pub/kegg/genomes/#{org}"
|
101
|
+
list = ftp.nlst(path)
|
102
|
+
file = list.grep(/.*genome$/).shift
|
103
|
+
if file
|
104
|
+
open("ftp://ftp.genome.jp/#{file}") do |file|
|
105
|
+
result = file.read
|
106
|
+
end
|
107
|
+
end
|
108
|
+
end
|
109
|
+
return result
|
110
|
+
end
|
111
|
+
|
112
|
+
end
|
113
|
+
|
114
|
+
=begin
|
115
|
+
|
116
|
+
== BioRuby extensions
|
117
|
+
|
118
|
+
--- get_all_best_best_neighbors_by_gene(genes_id)
|
119
|
+
--- get_all_best_neighbors_by_gene(genes_id)
|
120
|
+
--- get_all_reverse_best_neighbors_by_gene(genes_id)
|
121
|
+
--- get_all_paralogs_by_gene(genes_id)
|
122
|
+
--- get_all_genes_by_motifs(motif_id_list)
|
123
|
+
--- get_all_oc_members_by_gene(genes_id)
|
124
|
+
--- get_all_pc_members_by_gene(genes_id)
|
125
|
+
--- get_all_genes_by_organism(org)
|
126
|
+
--- get_all_linkdb_by_entry(entry_id, db)
|
127
|
+
--- save_image(url, filename = nil)
|
128
|
+
--- get_entries(ary = [])
|
129
|
+
--- get_aaseqs(ary = [])
|
130
|
+
--- get_naseqs(ary = [])
|
131
|
+
--- get_definitions(ary = [])
|
132
|
+
|
133
|
+
== Original KEGG API methods
|
134
|
+
|
135
|
+
--- get_linkdb_by_entry(entry_id, db, start, max_results)
|
136
|
+
--- get_best_best_neighbors_by_gene(genes_id, start, max_results)
|
137
|
+
--- get_best_neighbors_by_gene(genes_id, start, max_results)
|
138
|
+
--- get_reverse_best_neighbors_by_gene(genes_id, start, max_results)
|
139
|
+
--- get_paralogs_by_gene(genes_id, start, max_results)
|
140
|
+
--- get_motifs_by_gene(genes_id, db)
|
141
|
+
--- get_genes_by_motifs(motif_id_list, start, max_results)
|
142
|
+
--- get_ko_by_gene(genes_id)
|
143
|
+
--- get_ko_by_ko_class(ko_class_id)
|
144
|
+
--- get_genes_by_ko_class(ko_class_id, org, start, max_results)
|
145
|
+
--- get_genes_by_ko(ko_id, org)
|
146
|
+
--- get_oc_members_by_gene(genes_id, start, max_results)
|
147
|
+
--- get_pc_members_by_gene(genes_id, start, max_results)
|
148
|
+
--- mark_pathway_by_objects(pathway_id, object_id_list)
|
149
|
+
--- color_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
|
150
|
+
--- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
|
151
|
+
--- get_html_of_colored_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
|
152
|
+
--- get_genes_by_pathway(pathway_id)
|
153
|
+
--- get_enzymes_by_pathway(pathway_id)
|
154
|
+
--- get_compounds_by_pathway(pathway_id)
|
155
|
+
--- get_glycans_by_pathway(pathway_id)
|
156
|
+
--- get_reactions_by_pathway(pathway_id)
|
157
|
+
--- get_kos_by_pathway(pathway_id)
|
158
|
+
--- get_pathways_by_genes(genes_id_list)
|
159
|
+
--- get_pathways_by_enzymes(enzyme_id_list)
|
160
|
+
--- get_pathways_by_compounds(compound_id_list)
|
161
|
+
--- get_pathways_by_glycans(glycan_id_list)
|
162
|
+
--- get_pathways_by_reactions(reaction_id_list)
|
163
|
+
--- get_pathways_by_kos(ko_id_list, org)
|
164
|
+
--- get_linked_pathways(pathway_id)
|
165
|
+
--- get_genes_by_enzyme(enzyme_id, org)
|
166
|
+
--- get_enzymes_by_gene(genes_id)
|
167
|
+
--- get_enzymes_by_compound(compound_id)
|
168
|
+
--- get_enzymes_by_glycan(glycan_id)
|
169
|
+
--- get_enzymes_by_reaction(reaction_id)
|
170
|
+
--- get_compounds_by_enzyme(enzyme_id)
|
171
|
+
--- get_compounds_by_reaction(reaction_id)
|
172
|
+
--- get_glycans_by_enzyme(enzyme_id)
|
173
|
+
--- get_glycans_by_reaction(reaction_id)
|
174
|
+
--- get_reactions_by_enzyme(enzyme_id)
|
175
|
+
--- get_reactions_by_compound(compound_id)
|
176
|
+
--- get_reactions_by_glycan(glycan_id)
|
177
|
+
--- get_genes_by_organism(org, start, max_results)
|
178
|
+
--- get_number_of_genes_by_organism(org)
|
179
|
+
--- convert_mol_to_kcf(mol_text)
|
180
|
+
|
181
|
+
=end
|