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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#!/usr/bin/env ruby
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#
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# color_scheme_na.rb - A Bio::ColorScheme demo script for Nucleic Acids
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# sequences.
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#
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# Usage:
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#
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# % ruby color_scheme_na.rb > cs-seq-fna.html
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# % cat seq.fna
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# >DNA_sequence
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# acgtgtgtcatgctagtcgatcgtactagtcgtagctagtca
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# % ruby color_scheme_na.rb seq.fna > colored-seq-fna.html
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#
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#
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# Copyright:: Copyright (C) 2005
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# Mitsuteru C. Nakao <n@bioruby.org>
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# License:: The Ruby License
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#
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# $Id: color_scheme_na.rb,v 1.3 2007/04/05 23:35:42 trevor Exp $
|
|
21
|
+
#
|
|
22
|
+
|
|
23
|
+
require 'bio'
|
|
24
|
+
|
|
25
|
+
|
|
26
|
+
# returns folded sequence with <br>.
|
|
27
|
+
def br(i, width = 80)
|
|
28
|
+
return "<br\n>" if i % width == 0
|
|
29
|
+
""
|
|
30
|
+
end
|
|
31
|
+
|
|
32
|
+
|
|
33
|
+
# returns sequence html doc
|
|
34
|
+
def display(seq, cs)
|
|
35
|
+
html = '<p style="font-family: monospace">'
|
|
36
|
+
postfix = '</span>'
|
|
37
|
+
i = 0
|
|
38
|
+
seq.each_byte do |c|
|
|
39
|
+
color = cs[c.chr]
|
|
40
|
+
prefix = %Q(<span style="background:\##{color};">)
|
|
41
|
+
html += prefix + c.chr + postfix
|
|
42
|
+
html += br(i += 1)
|
|
43
|
+
end
|
|
44
|
+
html + '</p>'
|
|
45
|
+
end
|
|
46
|
+
|
|
47
|
+
|
|
48
|
+
# returns scheme wise html doc
|
|
49
|
+
def display_scheme(scheme, naseq, aaseq)
|
|
50
|
+
html = ''
|
|
51
|
+
cs = eval("Bio::ColorScheme::#{scheme}")
|
|
52
|
+
[naseq, aaseq].each do |seq|
|
|
53
|
+
html += display(seq, cs)
|
|
54
|
+
end
|
|
55
|
+
return ['<div>', "<h3>#{cs}</h3>", html, '</div>']
|
|
56
|
+
end
|
|
57
|
+
|
|
58
|
+
|
|
59
|
+
|
|
60
|
+
if fna = ARGV.shift
|
|
61
|
+
naseq = Bio::FastaFormat.new(File.open(fna, 'r').read).naseq
|
|
62
|
+
aaseq = naseq.translate
|
|
63
|
+
else
|
|
64
|
+
naseq = Bio::Sequence::NA.new('acgtu' * 20).randomize
|
|
65
|
+
aaseq = naseq.translate
|
|
66
|
+
end
|
|
67
|
+
|
|
68
|
+
title = 'Bio::ColorScheme for DNA sequences'
|
|
69
|
+
doc = ['<html>',
|
|
70
|
+
'<header>', '<title>', title, '</title>', '</header>',
|
|
71
|
+
'<body>', '<h1>', title, '</h1>']
|
|
72
|
+
|
|
73
|
+
doc << ['<div>', '<h2>', 'Simple colors', '</h2>']
|
|
74
|
+
['Nucleotide'].each do |scheme|
|
|
75
|
+
doc << display_scheme(scheme, naseq, "")
|
|
76
|
+
end
|
|
77
|
+
doc << ['</div>']
|
|
78
|
+
|
|
79
|
+
['Zappo', 'Taylor' ].each do |scheme|
|
|
80
|
+
doc << display_scheme(scheme, "", aaseq)
|
|
81
|
+
end
|
|
82
|
+
doc << ['</div>']
|
|
83
|
+
|
|
84
|
+
|
|
85
|
+
doc << ['<div>', '<h2>', 'Score colors', '</h2>']
|
|
86
|
+
['Buried', 'Helix', 'Hydropathy', 'Strand', 'Turn'].each do |score|
|
|
87
|
+
doc << display_scheme(score, "", aaseq)
|
|
88
|
+
end
|
|
89
|
+
doc << ['</div>']
|
|
90
|
+
|
|
91
|
+
puts doc + ['</body>','</html>']
|
data/sample/dbget
ADDED
|
@@ -0,0 +1,37 @@
|
|
|
1
|
+
#!/usr/bin/env ruby
|
|
2
|
+
#
|
|
3
|
+
# dbget - DBGET client
|
|
4
|
+
#
|
|
5
|
+
# Interface to GenomeNet DBGET system - http://www.genome.jp/dbget/
|
|
6
|
+
#
|
|
7
|
+
# Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
|
|
8
|
+
#
|
|
9
|
+
# This program is free software; you can redistribute it and/or modify
|
|
10
|
+
# it under the terms of the GNU General Public License as published by
|
|
11
|
+
# the Free Software Foundation; either version 2 of the License, or
|
|
12
|
+
# (at your option) any later version.
|
|
13
|
+
#
|
|
14
|
+
# This program is distributed in the hope that it will be useful,
|
|
15
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
16
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
17
|
+
# GNU General Public License for more details.
|
|
18
|
+
#
|
|
19
|
+
# You should have received a copy of the GNU General Public License
|
|
20
|
+
# along with this program; if not, write to the Free Software
|
|
21
|
+
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
|
|
22
|
+
#
|
|
23
|
+
# $Id: dbget,v 1.7 2004/08/24 00:09:24 k Exp $
|
|
24
|
+
#
|
|
25
|
+
|
|
26
|
+
require "bio/io/dbget"
|
|
27
|
+
|
|
28
|
+
# DBGET command
|
|
29
|
+
com = File.basename($0) # e.g. $PATH/bget db entry
|
|
30
|
+
com = ARGV.shift if com == "dbget" # e.g. $PATH/dbget bget db entry
|
|
31
|
+
|
|
32
|
+
# DBGET query strings
|
|
33
|
+
arg = ARGV.join(" ")
|
|
34
|
+
|
|
35
|
+
# DBGET result
|
|
36
|
+
print Bio::DBGET.dbget(com, arg)
|
|
37
|
+
|
data/sample/enzymes.rb
ADDED
|
@@ -0,0 +1,78 @@
|
|
|
1
|
+
#!/usr/bin/env ruby
|
|
2
|
+
#
|
|
3
|
+
# enzymes.rb - cut input file using enzyme on command line
|
|
4
|
+
#
|
|
5
|
+
# Copyright (C) 2006 Pjotr Prins <p@bioruby.org> and Trevor Wennblom <trevor@corevx.com>
|
|
6
|
+
#
|
|
7
|
+
# This program is free software; you can redistribute it and/or modify
|
|
8
|
+
# it under the terms of the GNU General Public License as published by
|
|
9
|
+
# the Free Software Foundation; either version 2 of the License, or
|
|
10
|
+
# (at your option) any later version.
|
|
11
|
+
#
|
|
12
|
+
# This program is distributed in the hope that it will be useful,
|
|
13
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
14
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
15
|
+
# GNU General Public License for more details.
|
|
16
|
+
#
|
|
17
|
+
# $Id: enzymes.rb,v 1.1 2006/03/03 15:31:06 pjotr Exp $
|
|
18
|
+
#
|
|
19
|
+
|
|
20
|
+
require 'bio/io/flatfile'
|
|
21
|
+
require 'bio/util/restriction_enzyme'
|
|
22
|
+
|
|
23
|
+
include Bio
|
|
24
|
+
|
|
25
|
+
usage = <<USAGE
|
|
26
|
+
|
|
27
|
+
Usage: enzymes.rb enzyme1 [enzyme2] infiles
|
|
28
|
+
|
|
29
|
+
Examples:
|
|
30
|
+
|
|
31
|
+
Output the primary sequences cut using both BstYI and MseI:
|
|
32
|
+
|
|
33
|
+
./enzymes.rb BstYI MseI *.seq
|
|
34
|
+
|
|
35
|
+
or using the actual formats
|
|
36
|
+
|
|
37
|
+
./enzymes.rb "r^gatcy" "t^taa" *.seq
|
|
38
|
+
|
|
39
|
+
USAGE
|
|
40
|
+
|
|
41
|
+
if ARGV.size < 2
|
|
42
|
+
print usage
|
|
43
|
+
exit 1
|
|
44
|
+
end
|
|
45
|
+
|
|
46
|
+
enzyme1 = ARGV.shift
|
|
47
|
+
# ---- Fetch enzyme2 if it is not a file
|
|
48
|
+
arg2 = ARGV[0]
|
|
49
|
+
if arg2 and !File.exist?(arg2)
|
|
50
|
+
enzyme2 = ARGV.shift
|
|
51
|
+
end
|
|
52
|
+
|
|
53
|
+
re1 = Bio::RestrictionEnzyme::DoubleStranded.new(enzyme1)
|
|
54
|
+
puts "Enzyme #{enzyme1}: " + re1.primary.with_cut_symbols # e.g. r^gatcy
|
|
55
|
+
if (enzyme2)
|
|
56
|
+
re2 = Bio::RestrictionEnzyme::DoubleStranded.new(enzyme2)
|
|
57
|
+
puts "Enzyme #{enzyme2}: " + re2.primary.with_cut_symbols # e.g. t^taa
|
|
58
|
+
end
|
|
59
|
+
|
|
60
|
+
ARGV.each do | fn |
|
|
61
|
+
ff = Bio::FlatFile.auto(fn)
|
|
62
|
+
ff.each_entry do |entry|
|
|
63
|
+
seq = Bio::Sequence::NA.new(entry.seq)
|
|
64
|
+
# puts seq.inspect
|
|
65
|
+
seq.cut_with_enzyme(enzyme1).each do | frag1 |
|
|
66
|
+
frag = frag1
|
|
67
|
+
if enzyme2
|
|
68
|
+
seq = Bio::Sequence::NA.new(frag1.primary)
|
|
69
|
+
frags2 = seq.cut_with_enzyme(enzyme2)
|
|
70
|
+
next if frags2.size == 0
|
|
71
|
+
frag = frags2.shift # pick up first fragment
|
|
72
|
+
end
|
|
73
|
+
print '> '+entry.definition+"\n"
|
|
74
|
+
print frag.primary,"\n"
|
|
75
|
+
end
|
|
76
|
+
end
|
|
77
|
+
end
|
|
78
|
+
|
data/sample/fasta2tab.rb
ADDED
|
@@ -0,0 +1,99 @@
|
|
|
1
|
+
#!/usr/bin/env ruby
|
|
2
|
+
#
|
|
3
|
+
# fasta2tab.rb - convert FASTA (-m 6) output into tab delimited data for MySQL
|
|
4
|
+
#
|
|
5
|
+
# Usage:
|
|
6
|
+
#
|
|
7
|
+
# % fasta2tab.rb FASTA-output-file[s] > fasta_results.tab
|
|
8
|
+
# % mysql < fasta_results.sql (use sample at the end of this file)
|
|
9
|
+
#
|
|
10
|
+
# Format accepted:
|
|
11
|
+
#
|
|
12
|
+
# % fasta3[3][_t] -Q -H -m 6 query.f target.f ktup > FASTA-output-file
|
|
13
|
+
#
|
|
14
|
+
# Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
|
|
15
|
+
#
|
|
16
|
+
# This program is free software; you can redistribute it and/or modify
|
|
17
|
+
# it under the terms of the GNU General Public License as published by
|
|
18
|
+
# the Free Software Foundation; either version 2 of the License, or
|
|
19
|
+
# (at your option) any later version.
|
|
20
|
+
#
|
|
21
|
+
# This program is distributed in the hope that it will be useful,
|
|
22
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
23
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
24
|
+
# GNU General Public License for more details.
|
|
25
|
+
#
|
|
26
|
+
# $Id: fasta2tab.rb,v 0.1 2001/06/21 08:21:58 katayama Exp $
|
|
27
|
+
#
|
|
28
|
+
|
|
29
|
+
while gets
|
|
30
|
+
|
|
31
|
+
# query
|
|
32
|
+
if /^\S+: (\d+) aa$/
|
|
33
|
+
q_len = $1
|
|
34
|
+
end
|
|
35
|
+
|
|
36
|
+
# each hit
|
|
37
|
+
if /^>>([^>]\S+).*\((\d+) aa\)$/
|
|
38
|
+
target = $1
|
|
39
|
+
t_len = $2
|
|
40
|
+
|
|
41
|
+
# d = dummy variable
|
|
42
|
+
d, d, initn, d, init1, d, opt, d, zscore, d, bits, d, evalue =
|
|
43
|
+
gets.split(/\s+/)
|
|
44
|
+
d, d, sw, ident, d, ugident, d, d, overlap, d, d, lap =
|
|
45
|
+
gets.split(/\s+/)
|
|
46
|
+
|
|
47
|
+
# query-hit pair
|
|
48
|
+
print "#{$FILENAME}\t#{q_len}\t#{target}\t#{t_len}"
|
|
49
|
+
|
|
50
|
+
# pick up values
|
|
51
|
+
ary = [
|
|
52
|
+
initn,
|
|
53
|
+
init1,
|
|
54
|
+
opt,
|
|
55
|
+
zscore,
|
|
56
|
+
bits,
|
|
57
|
+
evalue,
|
|
58
|
+
sw,
|
|
59
|
+
ident,
|
|
60
|
+
ugident,
|
|
61
|
+
overlap,
|
|
62
|
+
lap
|
|
63
|
+
]
|
|
64
|
+
|
|
65
|
+
# print values
|
|
66
|
+
for i in ary
|
|
67
|
+
i.tr!('^0-9.:e\-','')
|
|
68
|
+
print "\t#{i}"
|
|
69
|
+
end
|
|
70
|
+
|
|
71
|
+
print "\n"
|
|
72
|
+
|
|
73
|
+
end
|
|
74
|
+
end
|
|
75
|
+
|
|
76
|
+
=begin MySQL fasta_results.sql sample
|
|
77
|
+
|
|
78
|
+
CREATE DATABASE IF NOT EXISTS db_name;
|
|
79
|
+
CREATE TABLE IF NOT EXISTS db_name.table_name (
|
|
80
|
+
query varchar(25) not NULL,
|
|
81
|
+
q_len integer unsigned default 0,
|
|
82
|
+
target varchar(25) not NULL,
|
|
83
|
+
t_len integer unsigned default 0,
|
|
84
|
+
initn integer unsigned default 0,
|
|
85
|
+
init1 integer unsigned default 0,
|
|
86
|
+
opt integer unsigned default 0,
|
|
87
|
+
zscore float default 0.0,
|
|
88
|
+
bits float default 0.0,
|
|
89
|
+
evalue float default 0.0,
|
|
90
|
+
sw integer unsigned default 0,
|
|
91
|
+
ident float default 0.0,
|
|
92
|
+
ugident float default 0.0,
|
|
93
|
+
overlap integer unsigned default 0,
|
|
94
|
+
lap_at varchar(25) default NULL
|
|
95
|
+
);
|
|
96
|
+
LOAD DATA LOCAL INFILE 'fasta_results.tab' INTO TABLE db_name.table_name;
|
|
97
|
+
|
|
98
|
+
=end
|
|
99
|
+
|
data/sample/fastagrep.rb
ADDED
|
@@ -0,0 +1,72 @@
|
|
|
1
|
+
#!/usr/bin/env ruby
|
|
2
|
+
#
|
|
3
|
+
# fastagrep: Greps a FASTA file (in fact it can use any flat file input supported
|
|
4
|
+
# by BIORUBY) and outputs sorted FASTA
|
|
5
|
+
#
|
|
6
|
+
# Copyright (C) 2008 KATAYAMA Toshiaki <k@bioruby.org> & Pjotr Prins
|
|
7
|
+
#
|
|
8
|
+
# This program is free software; you can redistribute it and/or modify
|
|
9
|
+
# it under the terms of the GNU General Public License as published by
|
|
10
|
+
# the Free Software Foundation; either version 2 of the License, or
|
|
11
|
+
# (at your option) any later version.
|
|
12
|
+
#
|
|
13
|
+
# This program is distributed in the hope that it will be useful,
|
|
14
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
15
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
16
|
+
# GNU General Public License for more details.
|
|
17
|
+
#
|
|
18
|
+
# $Id: fastagrep.rb,v 1.1 2008/05/19 12:22:05 pjotr Exp $
|
|
19
|
+
#
|
|
20
|
+
|
|
21
|
+
require 'bio'
|
|
22
|
+
|
|
23
|
+
include Bio
|
|
24
|
+
|
|
25
|
+
usage = <<USAGE
|
|
26
|
+
|
|
27
|
+
Usage: fastagrep.rb [--skip] [regex] infiles
|
|
28
|
+
|
|
29
|
+
-v Invert the sense of matching, to select non-matching lines.
|
|
30
|
+
|
|
31
|
+
Examples:
|
|
32
|
+
|
|
33
|
+
Output all sequence descriptors containing 'Arabidopsis' or 'Drosophila'
|
|
34
|
+
regardless of case
|
|
35
|
+
|
|
36
|
+
fastagrep.rb "/Arabidopsis|Drosophila/i" *.seq > reduced.fasta
|
|
37
|
+
|
|
38
|
+
As the result is a FASTA stream you could pipe it for sorting:
|
|
39
|
+
|
|
40
|
+
fastagrep.rb "/Arabidopsis|Drosophila/i" *.seq | fastasort.rb
|
|
41
|
+
USAGE
|
|
42
|
+
|
|
43
|
+
if ARGV.size == 0
|
|
44
|
+
print usage
|
|
45
|
+
exit 1
|
|
46
|
+
end
|
|
47
|
+
|
|
48
|
+
skip = (ARGV[0] == '-v')
|
|
49
|
+
ARGV.shift if skip
|
|
50
|
+
|
|
51
|
+
# ---- Valid regular expression - if it is not a file
|
|
52
|
+
regex = ARGV[0]
|
|
53
|
+
if regex=~/^\// and !File.exist?(regex)
|
|
54
|
+
ARGV.shift
|
|
55
|
+
else
|
|
56
|
+
print usage
|
|
57
|
+
exit 1
|
|
58
|
+
end
|
|
59
|
+
|
|
60
|
+
ARGV.each do | fn |
|
|
61
|
+
Bio::FlatFile.auto(fn).each do | item |
|
|
62
|
+
if skip
|
|
63
|
+
next if eval("item.definition =~ #{regex}")
|
|
64
|
+
else
|
|
65
|
+
next if eval("item.definition !~ #{regex}")
|
|
66
|
+
end
|
|
67
|
+
rec = Bio::FastaFormat.new('> '+item.definition.strip+"\n"+item.data)
|
|
68
|
+
print rec
|
|
69
|
+
end
|
|
70
|
+
end
|
|
71
|
+
|
|
72
|
+
|
data/sample/fastasort.rb
ADDED
|
@@ -0,0 +1,54 @@
|
|
|
1
|
+
#!/usr/bin/env ruby
|
|
2
|
+
#
|
|
3
|
+
# fastasort: Sorts a FASTA file (in fact it can use any flat file input supported
|
|
4
|
+
# by BIORUBY) while modifying the definition of each record in the
|
|
5
|
+
# process so it is suitable for processing with (for example) pal2nal
|
|
6
|
+
# and PAML.
|
|
7
|
+
#
|
|
8
|
+
# Copyright (C) 2008 KATAYAMA Toshiaki <k@bioruby.org> & Pjotr Prins
|
|
9
|
+
#
|
|
10
|
+
# This program is free software; you can redistribute it and/or modify
|
|
11
|
+
# it under the terms of the GNU General Public License as published by
|
|
12
|
+
# the Free Software Foundation; either version 2 of the License, or
|
|
13
|
+
# (at your option) any later version.
|
|
14
|
+
#
|
|
15
|
+
# This program is distributed in the hope that it will be useful,
|
|
16
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
17
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
18
|
+
# GNU General Public License for more details.
|
|
19
|
+
#
|
|
20
|
+
# $Id: fastasort.rb,v 1.2 2008/05/19 12:22:05 pjotr Exp $
|
|
21
|
+
#
|
|
22
|
+
|
|
23
|
+
require 'bio'
|
|
24
|
+
|
|
25
|
+
include Bio
|
|
26
|
+
|
|
27
|
+
table = Hash.new # table to sort objects
|
|
28
|
+
ARGV.each do | fn |
|
|
29
|
+
Bio::FlatFile.auto(fn).each do | item |
|
|
30
|
+
# Some procession of the definition for external programs (just
|
|
31
|
+
# an example):
|
|
32
|
+
|
|
33
|
+
# strip JALView extension from definition e.g. .../1-212
|
|
34
|
+
if item.definition =~ /\/\d+-\d+$/
|
|
35
|
+
item.definition = $`
|
|
36
|
+
end
|
|
37
|
+
# substitute slashes:
|
|
38
|
+
definition = item.definition.gsub(/\//,'-')
|
|
39
|
+
# substitute quotes and ampersands:
|
|
40
|
+
definition = item.definition.gsub(/['"&]/,'x')
|
|
41
|
+
# prefix letters if the first position is a number:
|
|
42
|
+
definition = 'seq'+definition if definition =~ /^\d/
|
|
43
|
+
|
|
44
|
+
# Now add the data to the sort table
|
|
45
|
+
table[definition] = item.data
|
|
46
|
+
end
|
|
47
|
+
end
|
|
48
|
+
|
|
49
|
+
# Output sorted table
|
|
50
|
+
table.sort.each do | definition, data |
|
|
51
|
+
rec = Bio::FastaFormat.new('> '+definition.strip+"\n"+data)
|
|
52
|
+
print rec
|
|
53
|
+
end
|
|
54
|
+
|
data/sample/fsplit.rb
ADDED
|
@@ -0,0 +1,51 @@
|
|
|
1
|
+
#!/usr/bin/env ruby
|
|
2
|
+
#
|
|
3
|
+
# fsplit.rb - split FASTA file by each n entries
|
|
4
|
+
#
|
|
5
|
+
# Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
|
|
6
|
+
#
|
|
7
|
+
# This program is free software; you can redistribute it and/or modify
|
|
8
|
+
# it under the terms of the GNU General Public License as published by
|
|
9
|
+
# the Free Software Foundation; either version 2 of the License, or
|
|
10
|
+
# (at your option) any later version.
|
|
11
|
+
#
|
|
12
|
+
# This program is distributed in the hope that it will be useful,
|
|
13
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
14
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
15
|
+
# GNU General Public License for more details.
|
|
16
|
+
#
|
|
17
|
+
# $Id: fsplit.rb,v 0.1 2001/06/21 08:22:29 katayama Exp $
|
|
18
|
+
#
|
|
19
|
+
|
|
20
|
+
if ARGV.length != 2
|
|
21
|
+
|
|
22
|
+
print <<-USAGE
|
|
23
|
+
fsplit.rb - split FASTA file by each n entries
|
|
24
|
+
|
|
25
|
+
Usage :
|
|
26
|
+
|
|
27
|
+
% ./fsplit.rb 2000 seq.f
|
|
28
|
+
|
|
29
|
+
This will produce seq.f.1, seq.f.2, ... with containing 2000 sequences
|
|
30
|
+
in each file.
|
|
31
|
+
|
|
32
|
+
USAGE
|
|
33
|
+
exit 1
|
|
34
|
+
|
|
35
|
+
end
|
|
36
|
+
|
|
37
|
+
count = ARGV.shift.to_i
|
|
38
|
+
|
|
39
|
+
i = -1
|
|
40
|
+
|
|
41
|
+
while gets
|
|
42
|
+
if /^>/
|
|
43
|
+
i += 1
|
|
44
|
+
if i % count == 0
|
|
45
|
+
n = i / count
|
|
46
|
+
out = File.new("#{$FILENAME}.#{n+1}", "w+")
|
|
47
|
+
end
|
|
48
|
+
end
|
|
49
|
+
out.print
|
|
50
|
+
end
|
|
51
|
+
|