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 +1,158 @@
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#
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# = sample/demo_sequence.rb - demonstration of sequence manipulation
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#
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# Copyright:: Copyright (C) 2000-2006
|
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# Toshiaki Katayama <k@bioruby.org>,
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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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# $Id:$
|
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#
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# == Description
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#
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# Demonstration of biological sequence manipulation.
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#
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# == Usage
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#
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# Simply run this script.
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#
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# $ ruby demo_sequence.rb
|
20
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#
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21
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# == Development information
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#
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# The code was moved from lib/bio/sequence.rb.
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#
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25
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require 'bio'
|
27
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|
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#if __FILE__ == $0
|
29
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puts "== Test Bio::Sequence::NA.new"
|
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p Bio::Sequence::NA.new('')
|
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p na = Bio::Sequence::NA.new('atgcatgcATGCATGCAAAA')
|
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p rna = Bio::Sequence::NA.new('augcaugcaugcaugcaaaa')
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34
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|
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puts "\n== Test Bio::Sequence::AA.new"
|
36
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p Bio::Sequence::AA.new('')
|
37
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p aa = Bio::Sequence::AA.new('ACDEFGHIKLMNPQRSTVWYU')
|
38
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+
|
39
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puts "\n== Test Bio::Sequence#to_s"
|
40
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p na.to_s
|
41
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p aa.to_s
|
42
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+
|
43
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puts "\n== Test Bio::Sequence#subseq(2,6)"
|
44
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p na
|
45
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p na.subseq(2,6)
|
46
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+
|
47
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puts "\n== Test Bio::Sequence#[2,6]"
|
48
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p na
|
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p na[2,6]
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50
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+
|
51
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puts "\n== Test Bio::Sequence#to_fasta('hoge', 8)"
|
52
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puts na.to_fasta('hoge', 8)
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53
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|
54
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puts "\n== Test Bio::Sequence#window_search(15)"
|
55
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p na
|
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na.window_search(15) {|x| p x}
|
57
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|
58
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puts "\n== Test Bio::Sequence#total({'a'=>0.1,'t'=>0.2,'g'=>0.3,'c'=>0.4})"
|
59
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p na.total({'a'=>0.1,'t'=>0.2,'g'=>0.3,'c'=>0.4})
|
60
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+
|
61
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puts "\n== Test Bio::Sequence#composition"
|
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p na
|
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p na.composition
|
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p rna
|
65
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p rna.composition
|
66
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|
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puts "\n== Test Bio::Sequence::NA#splicing('complement(join(1..5,16..20))')"
|
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p na
|
69
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p na.splicing("complement(join(1..5,16..20))")
|
70
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+
p rna
|
71
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p rna.splicing("complement(join(1..5,16..20))")
|
72
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+
|
73
|
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puts "\n== Test Bio::Sequence::NA#complement"
|
74
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+
p na.complement
|
75
|
+
p rna.complement
|
76
|
+
p Bio::Sequence::NA.new('tacgyrkmhdbvswn').complement
|
77
|
+
p Bio::Sequence::NA.new('uacgyrkmhdbvswn').complement
|
78
|
+
|
79
|
+
puts "\n== Test Bio::Sequence::NA#translate"
|
80
|
+
p na
|
81
|
+
p na.translate
|
82
|
+
p rna
|
83
|
+
p rna.translate
|
84
|
+
|
85
|
+
puts "\n== Test Bio::Sequence::NA#gc_percent"
|
86
|
+
p na.gc_percent
|
87
|
+
p rna.gc_percent
|
88
|
+
|
89
|
+
puts "\n== Test Bio::Sequence::NA#illegal_bases"
|
90
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+
p na.illegal_bases
|
91
|
+
p Bio::Sequence::NA.new('tacgyrkmhdbvswn').illegal_bases
|
92
|
+
p Bio::Sequence::NA.new('abcdefghijklmnopqrstuvwxyz-!%#$@').illegal_bases
|
93
|
+
|
94
|
+
puts "\n== Test Bio::Sequence::NA#molecular_weight"
|
95
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+
p na
|
96
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+
p na.molecular_weight
|
97
|
+
p rna
|
98
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+
p rna.molecular_weight
|
99
|
+
|
100
|
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puts "\n== Test Bio::Sequence::NA#to_re"
|
101
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+
p Bio::Sequence::NA.new('atgcrymkdhvbswn')
|
102
|
+
p Bio::Sequence::NA.new('atgcrymkdhvbswn').to_re
|
103
|
+
p Bio::Sequence::NA.new('augcrymkdhvbswn')
|
104
|
+
p Bio::Sequence::NA.new('augcrymkdhvbswn').to_re
|
105
|
+
|
106
|
+
puts "\n== Test Bio::Sequence::NA#names"
|
107
|
+
p na.names
|
108
|
+
|
109
|
+
puts "\n== Test Bio::Sequence::NA#pikachu"
|
110
|
+
p na.pikachu
|
111
|
+
|
112
|
+
puts "\n== Test Bio::Sequence::NA#randomize"
|
113
|
+
print "Orig : "; p na
|
114
|
+
print "Rand : "; p na.randomize
|
115
|
+
print "Rand : "; p na.randomize
|
116
|
+
print "Rand : "; p na.randomize.randomize
|
117
|
+
print "Block : "; na.randomize do |x| print x end; puts
|
118
|
+
|
119
|
+
print "Orig : "; p rna
|
120
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+
print "Rand : "; p rna.randomize
|
121
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+
print "Rand : "; p rna.randomize
|
122
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+
print "Rand : "; p rna.randomize.randomize
|
123
|
+
print "Block : "; rna.randomize do |x| print x end; puts
|
124
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+
|
125
|
+
puts "\n== Test Bio::Sequence::NA.randomize(counts)"
|
126
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+
print "Count : "; p counts = {'a'=>10,'c'=>20,'g'=>30,'t'=>40}
|
127
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+
print "Rand : "; p Bio::Sequence::NA.randomize(counts)
|
128
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+
print "Count : "; p counts = {'a'=>10,'c'=>20,'g'=>30,'u'=>40}
|
129
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+
print "Rand : "; p Bio::Sequence::NA.randomize(counts)
|
130
|
+
print "Block : "; Bio::Sequence::NA.randomize(counts) {|x| print x}; puts
|
131
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+
|
132
|
+
puts "\n== Test Bio::Sequence::AA#codes"
|
133
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+
p aa
|
134
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p aa.codes
|
135
|
+
|
136
|
+
puts "\n== Test Bio::Sequence::AA#names"
|
137
|
+
p aa
|
138
|
+
p aa.names
|
139
|
+
|
140
|
+
puts "\n== Test Bio::Sequence::AA#molecular_weight"
|
141
|
+
p aa.subseq(1,20)
|
142
|
+
p aa.subseq(1,20).molecular_weight
|
143
|
+
|
144
|
+
puts "\n== Test Bio::Sequence::AA#randomize"
|
145
|
+
aaseq = 'MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA'
|
146
|
+
s = Bio::Sequence::AA.new(aaseq)
|
147
|
+
print "Orig : "; p s
|
148
|
+
print "Rand : "; p s.randomize
|
149
|
+
print "Rand : "; p s.randomize
|
150
|
+
print "Rand : "; p s.randomize.randomize
|
151
|
+
print "Block : "; s.randomize {|x| print x}; puts
|
152
|
+
|
153
|
+
puts "\n== Test Bio::Sequence::AA.randomize(counts)"
|
154
|
+
print "Count : "; p counts = s.composition
|
155
|
+
print "Rand : "; puts Bio::Sequence::AA.randomize(counts)
|
156
|
+
print "Block : "; Bio::Sequence::AA.randomize(counts) {|x| print x}; puts
|
157
|
+
|
158
|
+
#end
|
data/sample/enzymes.rb
ADDED
@@ -0,0 +1,78 @@
|
|
1
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+
#!/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
|
+
|
data/sample/gb2fasta.rb
ADDED
@@ -0,0 +1,30 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
#
|
3
|
+
# gb2fasta.rb - convert GenBank entry into FASTA format (nuc)
|
4
|
+
#
|
5
|
+
# Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
|
6
|
+
# Copyright (C) 2002 Yoshinori K. Okuji <o@bioruby.org>
|
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: gb2fasta.rb,v 0.6 2008/02/05 12:11:11 pjotr Exp $
|
19
|
+
#
|
20
|
+
|
21
|
+
require 'bio'
|
22
|
+
|
23
|
+
include Bio
|
24
|
+
|
25
|
+
ff = FlatFile.new(GenBank, ARGF)
|
26
|
+
|
27
|
+
while gb = ff.next_entry
|
28
|
+
print gb.seq.to_fasta("gb:#{gb.entry_id} #{gb.definition}", 70)
|
29
|
+
end
|
30
|
+
|