jandot-bio 1.2.1
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- data/bin/bioruby +44 -0
- data/bin/br_biofetch.rb +47 -0
- data/bin/br_bioflat.rb +282 -0
- data/bin/br_biogetseq.rb +45 -0
- data/bin/br_pmfetch.rb +421 -0
- data/doc/Changes-0.7.rd +369 -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/lib/bio.rb +279 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +351 -0
- data/lib/bio/appl/blast/format0.rb +1438 -0
- data/lib/bio/appl/blast/format8.rb +83 -0
- data/lib/bio/appl/blast/report.rb +516 -0
- data/lib/bio/appl/blast/rexml.rb +135 -0
- data/lib/bio/appl/blast/rpsblast.rb +176 -0
- data/lib/bio/appl/blast/wublast.rb +550 -0
- data/lib/bio/appl/blast/xmlparser.rb +228 -0
- data/lib/bio/appl/blat/report.rb +489 -0
- data/lib/bio/appl/clustalw.rb +219 -0
- data/lib/bio/appl/clustalw/report.rb +152 -0
- data/lib/bio/appl/emboss.rb +203 -0
- data/lib/bio/appl/fasta.rb +237 -0
- data/lib/bio/appl/fasta/format10.rb +325 -0
- data/lib/bio/appl/gcg/msf.rb +212 -0
- data/lib/bio/appl/gcg/seq.rb +195 -0
- data/lib/bio/appl/genscan/report.rb +552 -0
- data/lib/bio/appl/hmmer.rb +126 -0
- data/lib/bio/appl/hmmer/report.rb +683 -0
- data/lib/bio/appl/iprscan/report.rb +374 -0
- data/lib/bio/appl/mafft.rb +259 -0
- data/lib/bio/appl/mafft/report.rb +226 -0
- data/lib/bio/appl/muscle.rb +52 -0
- data/lib/bio/appl/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.rb +548 -0
- data/lib/bio/appl/psort/report.rb +457 -0
- data/lib/bio/appl/pts1.rb +263 -0
- data/lib/bio/appl/sim4.rb +124 -0
- data/lib/bio/appl/sim4/report.rb +485 -0
- data/lib/bio/appl/sosui/report.rb +151 -0
- data/lib/bio/appl/spidey/report.rb +593 -0
- data/lib/bio/appl/targetp/report.rb +267 -0
- data/lib/bio/appl/tcoffee.rb +55 -0
- data/lib/bio/appl/tmhmm/report.rb +222 -0
- data/lib/bio/command.rb +337 -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.rb +329 -0
- data/lib/bio/db/aaindex.rb +357 -0
- data/lib/bio/db/embl/common.rb +336 -0
- data/lib/bio/db/embl/embl.rb +402 -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 +599 -0
- data/lib/bio/db/fasta.rb +907 -0
- data/lib/bio/db/genbank/common.rb +290 -0
- data/lib/bio/db/genbank/ddbj.rb +22 -0
- data/lib/bio/db/genbank/genbank.rb +215 -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 +174 -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 +170 -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 +323 -0
- data/lib/bio/db/nbrf.rb +191 -0
- data/lib/bio/db/newick.rb +658 -0
- data/lib/bio/db/nexus.rb +1854 -0
- data/lib/bio/db/pdb.rb +29 -0
- data/lib/bio/db/pdb/atom.rb +77 -0
- data/lib/bio/db/pdb/chain.rb +210 -0
- data/lib/bio/db/pdb/chemicalcomponent.rb +224 -0
- data/lib/bio/db/pdb/model.rb +148 -0
- data/lib/bio/db/pdb/pdb.rb +1911 -0
- data/lib/bio/db/pdb/residue.rb +176 -0
- data/lib/bio/db/pdb/utils.rb +399 -0
- data/lib/bio/db/prosite.rb +597 -0
- data/lib/bio/db/rebase.rb +457 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/feature.rb +226 -0
- data/lib/bio/io/das.rb +461 -0
- data/lib/bio/io/dbget.rb +194 -0
- data/lib/bio/io/ddbjxml.rb +581 -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 +181 -0
- data/lib/bio/io/flatfile.rb +1309 -0
- data/lib/bio/io/flatfile/bdb.rb +253 -0
- data/lib/bio/io/flatfile/index.rb +1371 -0
- data/lib/bio/io/flatfile/indexer.rb +787 -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 +256 -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 +365 -0
- data/lib/bio/location.rb +772 -0
- data/lib/bio/map.rb +410 -0
- data/lib/bio/pathway.rb +854 -0
- data/lib/bio/reference.rb +623 -0
- data/lib/bio/sequence.rb +475 -0
- data/lib/bio/sequence/aa.rb +125 -0
- data/lib/bio/sequence/common.rb +333 -0
- data/lib/bio/sequence/compat.rb +123 -0
- data/lib/bio/sequence/format.rb +181 -0
- data/lib/bio/sequence/generic.rb +24 -0
- data/lib/bio/sequence/na.rb +491 -0
- data/lib/bio/shell.rb +44 -0
- data/lib/bio/shell/core.rb +578 -0
- data/lib/bio/shell/demo.rb +146 -0
- data/lib/bio/shell/interface.rb +218 -0
- data/lib/bio/shell/irb.rb +95 -0
- data/lib/bio/shell/object.rb +71 -0
- data/lib/bio/shell/plugin/blast.rb +42 -0
- data/lib/bio/shell/plugin/codon.rb +218 -0
- data/lib/bio/shell/plugin/das.rb +58 -0
- data/lib/bio/shell/plugin/emboss.rb +23 -0
- data/lib/bio/shell/plugin/entry.rb +105 -0
- data/lib/bio/shell/plugin/flatfile.rb +101 -0
- data/lib/bio/shell/plugin/keggapi.rb +181 -0
- data/lib/bio/shell/plugin/midi.rb +430 -0
- data/lib/bio/shell/plugin/obda.rb +45 -0
- data/lib/bio/shell/plugin/psort.rb +56 -0
- data/lib/bio/shell/plugin/seq.rb +247 -0
- data/lib/bio/shell/plugin/soap.rb +87 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb +29 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml +27 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml +11 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml +7 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif +0 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb +144 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb +47 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml +10 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml +26 -0
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif +0 -0
- data/lib/bio/shell/script.rb +25 -0
- data/lib/bio/shell/setup.rb +109 -0
- data/lib/bio/shell/web.rb +102 -0
- data/lib/bio/tree.rb +850 -0
- data/lib/bio/util/color_scheme.rb +191 -0
- data/lib/bio/util/color_scheme/buried.rb +59 -0
- data/lib/bio/util/color_scheme/helix.rb +59 -0
- data/lib/bio/util/color_scheme/hydropathy.rb +64 -0
- data/lib/bio/util/color_scheme/nucleotide.rb +31 -0
- data/lib/bio/util/color_scheme/strand.rb +59 -0
- data/lib/bio/util/color_scheme/taylor.rb +50 -0
- data/lib/bio/util/color_scheme/turn.rb +59 -0
- data/lib/bio/util/color_scheme/zappo.rb +50 -0
- data/lib/bio/util/contingency_table.rb +370 -0
- data/lib/bio/util/restriction_enzyme.rb +228 -0
- data/lib/bio/util/restriction_enzyme/analysis.rb +249 -0
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +217 -0
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +107 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +321 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +130 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +103 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +38 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +76 -0
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +107 -0
- data/lib/bio/util/restriction_enzyme/enzymes.yaml +7061 -0
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +24 -0
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +47 -0
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +67 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +257 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +242 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +51 -0
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +41 -0
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +77 -0
- data/lib/bio/util/restriction_enzyme/single_strand.rb +199 -0
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +135 -0
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +23 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +111 -0
- data/lib/bio/util/sirna.rb +288 -0
- data/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/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/test/data/HMMER/hmmpfam.out +64 -0
- data/test/data/HMMER/hmmsearch.out +88 -0
- data/test/data/SOSUI/sample.report +11 -0
- data/test/data/TMHMM/sample.report +21 -0
- data/test/data/aaindex/DAYM780301 +30 -0
- data/test/data/aaindex/PRAM900102 +20 -0
- data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq +53 -0
- data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq +37 -0
- data/test/data/blast/2.2.15.blastp.m7 +876 -0
- data/test/data/blast/b0002.faa +15 -0
- data/test/data/blast/b0002.faa.m0 +128 -0
- data/test/data/blast/b0002.faa.m7 +65 -0
- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/embl/AB090716.embl +65 -0
- data/test/data/embl/AB090716.embl.rel89 +63 -0
- data/test/data/fasta/example1.txt +75 -0
- data/test/data/fasta/example2.txt +21 -0
- data/test/data/genscan/sample.report +63 -0
- data/test/data/iprscan/merged.raw +32 -0
- data/test/data/iprscan/merged.txt +74 -0
- data/test/data/prosite/prosite.dat +2233 -0
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/soft/GDS100_partial.soft +92 -0
- data/test/data/soft/GSE3457_family_partial.soft +874 -0
- data/test/data/uniprot/p53_human.uniprot +1456 -0
- data/test/functional/bio/io/test_ensembl.rb +186 -0
- data/test/functional/bio/io/test_soapwsdl.rb +52 -0
- data/test/runner.rb +14 -0
- data/test/unit/bio/appl/bl2seq/test_report.rb +134 -0
- data/test/unit/bio/appl/blast/test_report.rb +417 -0
- data/test/unit/bio/appl/blast/test_xmlparser.rb +388 -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/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 +163 -0
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_pts1.rb +140 -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_sptr.rb +1775 -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 +127 -0
- data/test/unit/bio/db/test_lasergene.rb +95 -0
- data/test/unit/bio/db/test_newick.rb +293 -0
- data/test/unit/bio/db/test_nexus.rb +360 -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/test_ddbjxml.rb +75 -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 +237 -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 +174 -0
- data/test/unit/bio/sequence/test_compat.rb +69 -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 +288 -0
- data/test/unit/bio/test_db.rb +96 -0
- data/test/unit/bio/test_feature.rb +116 -0
- data/test/unit/bio/test_location.rb +39 -0
- data/test/unit/bio/test_map.rb +230 -0
- data/test/unit/bio/test_pathway.rb +473 -0
- data/test/unit/bio/test_reference.rb +224 -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 +479 -0
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VERSION=1.00
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[embl]
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protocol=biofetch
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location=http://bioruby.org/cgi-bin/biofetch.rb
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dbname=embl
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[embl-upd]
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protocol=biofetch
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location=http://bioruby.org/cgi-bin/biofetch.rb
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dbname=embl-upd
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[embl_biofetch]
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protocol=biofetch
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location=http://www.ebi.ac.uk/cgi-bin/dbfetch
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dbname=embl
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[embl_biosql]
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protocol=biosql
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location=localhost
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dbname=biosql
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driver=postgres
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user=hack
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pass=
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biodbname=embl
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26
|
+
|
27
|
+
[embl_biocorba]
|
28
|
+
protocol=bsane-corba
|
29
|
+
location=sqldbsrv.ior
|
30
|
+
|
31
|
+
[embl_xembl]
|
32
|
+
protocol=xembl
|
33
|
+
location=http://www.ebi.ac.uk/xembl/XEMBL.wsdl
|
34
|
+
format=Bsml
|
35
|
+
|
36
|
+
[embl_flat]
|
37
|
+
protcol=flat
|
38
|
+
location=/export/database/
|
39
|
+
dbname=embl
|
40
|
+
|
41
|
+
[genbank_bdb]
|
42
|
+
protcol=flat
|
43
|
+
location=/export/database/
|
44
|
+
dbname=genbank
|
45
|
+
|
46
|
+
[swissprot]
|
47
|
+
protocol=biofetch
|
48
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
49
|
+
dbname=swissprot
|
50
|
+
|
51
|
+
[swissprot-upd]
|
52
|
+
protocol=biofetch
|
53
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
54
|
+
dbname=swissprot-upd
|
55
|
+
|
56
|
+
[swissprot_biofetch]
|
57
|
+
protocol=biofetch
|
58
|
+
location=http://www.ebi.ac.uk/cgi-bin/dbfetch
|
59
|
+
dbname=swall
|
60
|
+
|
61
|
+
[swissprot_biosql]
|
62
|
+
protocol=biosql
|
63
|
+
location=db.bioruby.org
|
64
|
+
dbname=biosql
|
65
|
+
driver=mysql
|
66
|
+
user=root
|
67
|
+
pass=
|
68
|
+
biodbname=sp
|
69
|
+
|
70
|
+
|
71
|
+
[genbank]
|
72
|
+
protocol=biofetch
|
73
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
74
|
+
dbname=genbank
|
75
|
+
|
76
|
+
[genbank-upd]
|
77
|
+
protocol=biofetch
|
78
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
79
|
+
dbname=genbank-upd
|
80
|
+
|
81
|
+
[genbank_biosql]
|
82
|
+
protocol=biosql
|
83
|
+
location=db.bioruby.org
|
84
|
+
dbname=biosql
|
85
|
+
driver=mysql
|
86
|
+
user=root
|
87
|
+
pass=
|
88
|
+
biodbname=gb
|
89
|
+
|
90
|
+
|
91
|
+
[refseq]
|
92
|
+
protocol=biofetch
|
93
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
94
|
+
dbname=refseq
|
95
|
+
|
96
|
+
[refseq_biosql]
|
97
|
+
protocol=biosql
|
98
|
+
location=db.bioruby.org
|
99
|
+
dbname=biosql
|
100
|
+
driver=mysql
|
101
|
+
user=
|
102
|
+
pass=
|
103
|
+
biodbname=rs
|
104
|
+
|
105
|
+
|
106
|
+
[kegg-pathway]
|
107
|
+
protocol=biofetch
|
108
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
109
|
+
dbname=pathway
|
110
|
+
|
111
|
+
[kegg-genome]
|
112
|
+
protocol=biofetch
|
113
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
114
|
+
dbname=genome
|
115
|
+
|
116
|
+
[kegg-genes]
|
117
|
+
protocol=biofetch
|
118
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
119
|
+
dbname=genes
|
120
|
+
|
121
|
+
[kegg-vgenes]
|
122
|
+
protocol=biofetch
|
123
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
124
|
+
dbname=vgenes
|
125
|
+
|
126
|
+
[aaindex]
|
127
|
+
protocol=biofetch
|
128
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
129
|
+
dbname=aaindex
|
130
|
+
|
131
|
+
[blocks]
|
132
|
+
protocol=biofetch
|
133
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
134
|
+
dbname=blocks
|
135
|
+
|
136
|
+
[enzyme]
|
137
|
+
protocol=biofetch
|
138
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
139
|
+
dbname=enzyme
|
140
|
+
|
141
|
+
[epd]
|
142
|
+
protocol=biofetch
|
143
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
144
|
+
dbname=epd
|
145
|
+
|
146
|
+
[litdb]
|
147
|
+
protocol=biofetch
|
148
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
149
|
+
dbname=litdb
|
150
|
+
|
151
|
+
[omim]
|
152
|
+
protocol=biofetch
|
153
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
154
|
+
dbname=omim
|
155
|
+
|
156
|
+
[pdb]
|
157
|
+
protocol=biofetch
|
158
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
159
|
+
dbname=pdb
|
160
|
+
|
161
|
+
[pdbstr]
|
162
|
+
protocol=biofetch
|
163
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
164
|
+
dbname=pdbstr
|
165
|
+
|
166
|
+
[pfam]
|
167
|
+
protocol=biofetch
|
168
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
169
|
+
dbname=pfam
|
170
|
+
|
171
|
+
[pir]
|
172
|
+
protocol=biofetch
|
173
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
174
|
+
dbname=pir
|
175
|
+
|
176
|
+
[pmd]
|
177
|
+
protocol=biofetch
|
178
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
179
|
+
dbname=pmd
|
180
|
+
|
181
|
+
[prf]
|
182
|
+
protocol=biofetch
|
183
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
184
|
+
dbname=prf
|
185
|
+
|
186
|
+
[prints]
|
187
|
+
protocol=biofetch
|
188
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
189
|
+
dbname=prints
|
190
|
+
|
191
|
+
[prodom]
|
192
|
+
protocol=biofetch
|
193
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
194
|
+
dbname=prodom
|
195
|
+
|
196
|
+
[prosdoc]
|
197
|
+
protocol=biofetch
|
198
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
199
|
+
dbname=prosdoc
|
200
|
+
|
201
|
+
[prosite]
|
202
|
+
protocol=biofetch
|
203
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
204
|
+
dbname=prosite
|
205
|
+
|
206
|
+
[transfac]
|
207
|
+
protocol=biofetch
|
208
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
209
|
+
dbname=transfac
|
210
|
+
|
data/lib/bio.rb
ADDED
@@ -0,0 +1,279 @@
|
|
1
|
+
#
|
2
|
+
# = bio.rb - Loading all BioRuby modules
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2001-2007
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: bio.rb,v 1.89 2008/01/09 17:18:17 k Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
module Bio
|
12
|
+
|
13
|
+
BIORUBY_VERSION = [1, 2, 1].extend(Comparable)
|
14
|
+
|
15
|
+
### Basic data types
|
16
|
+
|
17
|
+
## Sequence
|
18
|
+
|
19
|
+
autoload :Sequence, 'bio/sequence'
|
20
|
+
|
21
|
+
## Locations/Location
|
22
|
+
|
23
|
+
autoload :Location, 'bio/location'
|
24
|
+
autoload :Locations, 'bio/location'
|
25
|
+
|
26
|
+
## Features/Feature
|
27
|
+
|
28
|
+
autoload :Feature, 'bio/feature'
|
29
|
+
autoload :Features, 'bio/feature'
|
30
|
+
|
31
|
+
## References/Reference
|
32
|
+
|
33
|
+
autoload :Reference, 'bio/reference'
|
34
|
+
autoload :References, 'bio/reference'
|
35
|
+
|
36
|
+
## Pathway/Relation
|
37
|
+
|
38
|
+
autoload :Pathway, 'bio/pathway'
|
39
|
+
autoload :Relation, 'bio/pathway'
|
40
|
+
|
41
|
+
## Alignment
|
42
|
+
|
43
|
+
autoload :Alignment, 'bio/alignment'
|
44
|
+
|
45
|
+
## Tree
|
46
|
+
autoload :Tree, 'bio/tree'
|
47
|
+
|
48
|
+
## Map
|
49
|
+
autoload :Map, 'bio/map'
|
50
|
+
|
51
|
+
### Constants
|
52
|
+
|
53
|
+
autoload :NucleicAcid, 'bio/data/na'
|
54
|
+
autoload :AminoAcid, 'bio/data/aa'
|
55
|
+
autoload :CodonTable, 'bio/data/codontable'
|
56
|
+
|
57
|
+
|
58
|
+
### DB parsers
|
59
|
+
|
60
|
+
autoload :DB, 'bio/db'
|
61
|
+
autoload :NCBIDB, 'bio/db'
|
62
|
+
autoload :KEGGDB, 'bio/db'
|
63
|
+
autoload :EMBLDB, 'bio/db'
|
64
|
+
|
65
|
+
## GenBank/RefSeq/DDBJ
|
66
|
+
|
67
|
+
autoload :GenBank, 'bio/db/genbank/genbank'
|
68
|
+
autoload :GenPept, 'bio/db/genbank/genpept'
|
69
|
+
autoload :RefSeq, 'bio/db/genbank/refseq'
|
70
|
+
autoload :DDBJ, 'bio/db/genbank/ddbj'
|
71
|
+
## below are described in bio/db/genbank/ddbj.rb
|
72
|
+
#class DDBJ
|
73
|
+
# autoload :XML, 'bio/io/ddbjxml'
|
74
|
+
#end
|
75
|
+
|
76
|
+
## EMBL/TrEMBL/Swiss-Prot/SPTR
|
77
|
+
|
78
|
+
autoload :EMBL, 'bio/db/embl/embl'
|
79
|
+
autoload :SPTR, 'bio/db/embl/sptr'
|
80
|
+
autoload :TrEMBL, 'bio/db/embl/trembl'
|
81
|
+
autoload :UniProt, 'bio/db/embl/uniprot'
|
82
|
+
autoload :SwissProt, 'bio/db/embl/swissprot'
|
83
|
+
|
84
|
+
## KEGG
|
85
|
+
|
86
|
+
class KEGG
|
87
|
+
autoload :GENOME, 'bio/db/kegg/genome'
|
88
|
+
autoload :GENES, 'bio/db/kegg/genes'
|
89
|
+
autoload :ENZYME, 'bio/db/kegg/enzyme'
|
90
|
+
autoload :COMPOUND, 'bio/db/kegg/compound'
|
91
|
+
autoload :DRUG, 'bio/db/kegg/drug'
|
92
|
+
autoload :GLYCAN, 'bio/db/kegg/glycan'
|
93
|
+
autoload :REACTION, 'bio/db/kegg/reaction'
|
94
|
+
autoload :BRITE, 'bio/db/kegg/brite'
|
95
|
+
autoload :CELL, 'bio/db/kegg/cell'
|
96
|
+
autoload :EXPRESSION, 'bio/db/kegg/expression'
|
97
|
+
autoload :ORTHOLOGY, 'bio/db/kegg/orthology'
|
98
|
+
autoload :KGML, 'bio/db/kegg/kgml'
|
99
|
+
autoload :Taxonomy, 'bio/db/kegg/taxonomy'
|
100
|
+
end
|
101
|
+
|
102
|
+
## other formats
|
103
|
+
|
104
|
+
autoload :FastaFormat, 'bio/db/fasta'
|
105
|
+
autoload :FastaNumericFormat, 'bio/db/fasta' # change to FastaFormat::Numeric ?
|
106
|
+
autoload :FastaDefline, 'bio/db/fasta' # change to FastaFormat::Defline
|
107
|
+
autoload :GFF, 'bio/db/gff'
|
108
|
+
autoload :AAindex, 'bio/db/aaindex'
|
109
|
+
autoload :AAindex1, 'bio/db/aaindex' # change to AAindex::AAindex1 ?
|
110
|
+
autoload :AAindex2, 'bio/db/aaindex' # change to AAindex::AAindex2 ?
|
111
|
+
autoload :TRANSFAC, 'bio/db/transfac'
|
112
|
+
autoload :PROSITE, 'bio/db/prosite'
|
113
|
+
autoload :LITDB, 'bio/db/litdb'
|
114
|
+
autoload :MEDLINE, 'bio/db/medline'
|
115
|
+
autoload :FANTOM, 'bio/db/fantom'
|
116
|
+
autoload :GO, 'bio/db/go'
|
117
|
+
autoload :PDB, 'bio/db/pdb'
|
118
|
+
autoload :NBRF, 'bio/db/nbrf'
|
119
|
+
autoload :REBASE, 'bio/db/rebase'
|
120
|
+
autoload :SOFT, 'bio/db/soft'
|
121
|
+
autoload :Lasergene, 'bio/db/lasergene'
|
122
|
+
|
123
|
+
autoload :Newick, 'bio/db/newick'
|
124
|
+
autoload :Nexus, 'bio/db/nexus'
|
125
|
+
|
126
|
+
### IO interface modules
|
127
|
+
|
128
|
+
autoload :Registry, 'bio/io/registry'
|
129
|
+
autoload :Fetch, 'bio/io/fetch'
|
130
|
+
autoload :SQL, 'bio/io/sql'
|
131
|
+
autoload :SOAPWSDL, 'bio/io/soapwsdl'
|
132
|
+
autoload :FlatFile, 'bio/io/flatfile'
|
133
|
+
autoload :FlatFileIndex, 'bio/io/flatfile/index' # chage to FlatFile::Index ?
|
134
|
+
## below are described in bio/io/flatfile/index.rb
|
135
|
+
#class FlatFileIndex
|
136
|
+
# autoload :Indexer, 'bio/io/flatfile/indexer'
|
137
|
+
# autoload :BDBdefault, 'bio/io/flatfile/bdb'
|
138
|
+
# autoload :BDBwrapper, 'bio/io/flatfile/bdb'
|
139
|
+
# autoload :BDB_1, 'bio/io/flatfile/bdb'
|
140
|
+
#end
|
141
|
+
|
142
|
+
autoload :PubMed, 'bio/io/pubmed'
|
143
|
+
autoload :DAS, 'bio/io/das'
|
144
|
+
autoload :DBGET, 'bio/io/dbget'
|
145
|
+
|
146
|
+
autoload :Ensembl, 'bio/io/ensembl'
|
147
|
+
autoload :Hinv, 'bio/io/hinv'
|
148
|
+
|
149
|
+
## below are described in bio/appl/blast.rb
|
150
|
+
#class Blast
|
151
|
+
# autoload :Fastacmd, 'bio/io/fastacmd'
|
152
|
+
#end
|
153
|
+
|
154
|
+
class KEGG
|
155
|
+
autoload :API, 'bio/io/keggapi'
|
156
|
+
end
|
157
|
+
|
158
|
+
## below are described in bio/db/genbank/ddbj.rb
|
159
|
+
#class DDBJ
|
160
|
+
# autoload :XML, 'bio/io/ddbjxml'
|
161
|
+
#end
|
162
|
+
|
163
|
+
class HGC
|
164
|
+
autoload :HiGet, 'bio/io/higet'
|
165
|
+
end
|
166
|
+
|
167
|
+
class EBI
|
168
|
+
autoload :SOAP, 'bio/io/ebisoap'
|
169
|
+
end
|
170
|
+
|
171
|
+
class NCBI
|
172
|
+
autoload :SOAP, 'bio/io/ncbisoap'
|
173
|
+
end
|
174
|
+
|
175
|
+
|
176
|
+
### Applications
|
177
|
+
|
178
|
+
autoload :Fasta, 'bio/appl/fasta'
|
179
|
+
## below are described in bio/appl/fasta.rb
|
180
|
+
#class Fasta
|
181
|
+
# autoload :Report, 'bio/appl/fasta/format10'
|
182
|
+
#end
|
183
|
+
|
184
|
+
autoload :Blast, 'bio/appl/blast'
|
185
|
+
## below are described in bio/appl/blast.rb
|
186
|
+
#class Blast
|
187
|
+
# autoload :Fastacmd, 'bio/io/fastacmd'
|
188
|
+
# autoload :Report, 'bio/appl/blast/report'
|
189
|
+
# autoload :Default, 'bio/appl/blast/format0'
|
190
|
+
# autoload :WU, 'bio/appl/blast/wublast'
|
191
|
+
# autoload :Bl2seq, 'bio/appl/bl2seq/report'
|
192
|
+
#end
|
193
|
+
|
194
|
+
autoload :HMMER, 'bio/appl/hmmer'
|
195
|
+
## below are described in bio/appl/hmmer.rb
|
196
|
+
#class HMMER
|
197
|
+
# autoload :Report, 'bio/appl/hmmer/report'
|
198
|
+
#end
|
199
|
+
|
200
|
+
autoload :EMBOSS, 'bio/appl/emboss' # use bio/command, improve
|
201
|
+
|
202
|
+
autoload :PSORT, 'bio/appl/psort'
|
203
|
+
## below are described in bio/appl/psort.rb
|
204
|
+
#class PSORT
|
205
|
+
# class PSORT1
|
206
|
+
# autoload :Report, 'bio/appl/psort/report'
|
207
|
+
# end
|
208
|
+
# class PSORT2
|
209
|
+
# autoload :Report, 'bio/appl/psort/report'
|
210
|
+
# end
|
211
|
+
#end
|
212
|
+
|
213
|
+
autoload :TMHMM, 'bio/appl/tmhmm/report'
|
214
|
+
autoload :TargetP, 'bio/appl/targetp/report'
|
215
|
+
autoload :SOSUI, 'bio/appl/sosui/report'
|
216
|
+
autoload :Genscan, 'bio/appl/genscan/report'
|
217
|
+
|
218
|
+
autoload :ClustalW, 'bio/appl/clustalw'
|
219
|
+
## below are described in bio/appl/clustalw.rb
|
220
|
+
#class ClustalW
|
221
|
+
# autoload :Report, 'bio/appl/clustalw/report'
|
222
|
+
#end
|
223
|
+
|
224
|
+
autoload :MAFFT, 'bio/appl/mafft'
|
225
|
+
## below are described in bio/appl/mafft.rb
|
226
|
+
#class MAFFT
|
227
|
+
# autoload :Report, 'bio/appl/mafft/report'
|
228
|
+
#end
|
229
|
+
|
230
|
+
autoload :Tcoffee, 'bio/appl/tcoffee'
|
231
|
+
autoload :Muscle, 'bio/appl/muscle'
|
232
|
+
autoload :Probcons, 'bio/appl/probcons'
|
233
|
+
|
234
|
+
autoload :Sim4, 'bio/appl/sim4'
|
235
|
+
## below are described in bio/appl/sim4.rb
|
236
|
+
#class Sim4
|
237
|
+
# autoload :Report, 'bio/appl/sim4/report'
|
238
|
+
#end
|
239
|
+
|
240
|
+
autoload :Spidey, 'bio/appl/spidey/report'
|
241
|
+
autoload :Blat, 'bio/appl/blat/report'
|
242
|
+
|
243
|
+
module GCG
|
244
|
+
autoload :Msf, 'bio/appl/gcg/msf'
|
245
|
+
autoload :Seq, 'bio/appl/gcg/seq'
|
246
|
+
end
|
247
|
+
|
248
|
+
module Phylip
|
249
|
+
autoload :PhylipFormat, 'bio/appl/phylip/alignment'
|
250
|
+
autoload :DistanceMatrix, 'bio/appl/phylip/distance_matrix'
|
251
|
+
end
|
252
|
+
|
253
|
+
autoload :Iprscan, 'bio/appl/iprscan/report'
|
254
|
+
|
255
|
+
### Utilities
|
256
|
+
|
257
|
+
autoload :SiRNA, 'bio/util/sirna'
|
258
|
+
autoload :ColorScheme, 'bio/util/color_scheme'
|
259
|
+
autoload :ContingencyTable, 'bio/util/contingency_table'
|
260
|
+
autoload :RestrictionEnzyme, 'bio/util/restriction_enzyme'
|
261
|
+
|
262
|
+
### Service libraries
|
263
|
+
autoload :Command, 'bio/command'
|
264
|
+
|
265
|
+
### Provide BioRuby shell 'command' also as 'Bio.command' (like ChemRuby)
|
266
|
+
|
267
|
+
def self.method_missing(*args)
|
268
|
+
require 'bio/shell'
|
269
|
+
extend Bio::Shell
|
270
|
+
public_class_method(*Bio::Shell.private_instance_methods)
|
271
|
+
if Bio.respond_to?(args.first)
|
272
|
+
Bio.send(*args)
|
273
|
+
else
|
274
|
+
raise NameError
|
275
|
+
end
|
276
|
+
end
|
277
|
+
|
278
|
+
end
|
279
|
+
|