wwood-bioruby 1.2.11
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- data/README.rdoc +205 -0
- data/README_DEV.rdoc +285 -0
- data/VERSION.yml +4 -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/lib/bio.rb +306 -0
- data/lib/bio/alignment.rb +2518 -0
- data/lib/bio/appl/bl2seq/report.rb +334 -0
- data/lib/bio/appl/blast.rb +505 -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 +635 -0
- data/lib/bio/appl/blast/xmlparser.rb +236 -0
- data/lib/bio/appl/blat/report.rb +530 -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 +235 -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/paml/baseml.rb +95 -0
- data/lib/bio/appl/paml/baseml/report.rb +32 -0
- data/lib/bio/appl/paml/codeml.rb +242 -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/common.rb +348 -0
- data/lib/bio/appl/paml/common_report.rb +38 -0
- data/lib/bio/appl/paml/yn00.rb +103 -0
- data/lib/bio/appl/paml/yn00/report.rb +32 -0
- data/lib/bio/appl/phylip/alignment.rb +133 -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 +542 -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 +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 +353 -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/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.rb +410 -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/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.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 +456 -0
- data/lib/bio/db/soft.rb +404 -0
- data/lib/bio/db/transfac.rb +375 -0
- data/lib/bio/db/url.rb +42 -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.rb +482 -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/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.rb +456 -0
- data/lib/bio/sequence/aa.rb +152 -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/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
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml +4 -0
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- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css +368 -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
- data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml +8 -0
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- 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 +852 -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 +200 -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/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
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- data/test/data/blast/b0002.faa.m8 +1 -0
- data/test/data/blast/blastp-multi.m7 +188 -0
- data/test/data/command/echoarg2.bat +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/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
- data/test/data/refseq/nm_126355.entret +64 -0
- data/test/data/rpsblast/misc.rpsblast +193 -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/appl/test_pts1.rb +115 -0
- 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 +14 -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
- data/test/unit/bio/appl/test_fasta.rb +130 -0
- data/test/unit/bio/appl/test_psort.rb +57 -0
- 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/db/test_url.rb +36 -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 +505 -0
- data/test/unit/bio/io/test_soapwsdl.rb +32 -0
- data/test/unit/bio/sequence/test_aa.rb +115 -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 +543 -0
data/lib/bio/shell.rb
ADDED
@@ -0,0 +1,44 @@
|
|
1
|
+
#
|
2
|
+
# = bio/shell.rb - Loading all BioRuby shell features
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005, 2006
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: shell.rb,v 1.20 2007/07/09 11:17:09 k Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
require 'bio'
|
12
|
+
require 'yaml'
|
13
|
+
require 'open-uri'
|
14
|
+
require 'fileutils'
|
15
|
+
require 'pp'
|
16
|
+
|
17
|
+
module Bio::Shell
|
18
|
+
|
19
|
+
require 'bio/shell/setup'
|
20
|
+
require 'bio/shell/irb'
|
21
|
+
require 'bio/shell/web'
|
22
|
+
require 'bio/shell/script'
|
23
|
+
require 'bio/shell/core'
|
24
|
+
require 'bio/shell/interface'
|
25
|
+
require 'bio/shell/object'
|
26
|
+
require 'bio/shell/demo'
|
27
|
+
require 'bio/shell/plugin/entry'
|
28
|
+
require 'bio/shell/plugin/seq'
|
29
|
+
require 'bio/shell/plugin/midi'
|
30
|
+
require 'bio/shell/plugin/codon'
|
31
|
+
require 'bio/shell/plugin/flatfile'
|
32
|
+
require 'bio/shell/plugin/obda'
|
33
|
+
require 'bio/shell/plugin/das'
|
34
|
+
require 'bio/shell/plugin/keggapi'
|
35
|
+
require 'bio/shell/plugin/soap'
|
36
|
+
require 'bio/shell/plugin/emboss'
|
37
|
+
require 'bio/shell/plugin/blast'
|
38
|
+
require 'bio/shell/plugin/psort'
|
39
|
+
|
40
|
+
extend Ghost
|
41
|
+
|
42
|
+
end
|
43
|
+
|
44
|
+
|
@@ -0,0 +1,578 @@
|
|
1
|
+
#
|
2
|
+
# = bio/shell/core.rb - internal methods for the BioRuby shell
|
3
|
+
#
|
4
|
+
# Copyright:: Copyright (C) 2005, 2006
|
5
|
+
# Toshiaki Katayama <k@bioruby.org>
|
6
|
+
# License:: The Ruby License
|
7
|
+
#
|
8
|
+
# $Id: core.rb,v 1.27 2007/06/28 11:21:40 k Exp $
|
9
|
+
#
|
10
|
+
|
11
|
+
module Bio::Shell::Core
|
12
|
+
|
13
|
+
SHELLDIR = "shell"
|
14
|
+
DATADIR = "data"
|
15
|
+
SESSION = File.join(SHELLDIR, "session")
|
16
|
+
PLUGIN = File.join(SHELLDIR, "plugin")
|
17
|
+
SCRIPT = File.join(SHELLDIR, "script.rb")
|
18
|
+
CONFIG = File.join(SESSION, "config")
|
19
|
+
OBJECT = File.join(SESSION, "object")
|
20
|
+
HISTORY = File.join(SESSION, "history")
|
21
|
+
BIOFLAT = File.join(DATADIR, "bioflat")
|
22
|
+
|
23
|
+
MARSHAL = [ Marshal::MAJOR_VERSION, Marshal::MINOR_VERSION ]
|
24
|
+
|
25
|
+
MESSAGE = "...BioRuby in the shell..."
|
26
|
+
|
27
|
+
ESC_SEQ = {
|
28
|
+
:k => "\e[30m", :black => "\e[30m",
|
29
|
+
:r => "\e[31m", :red => "\e[31m", :ruby => "\e[31m",
|
30
|
+
:g => "\e[32m", :green => "\e[32m",
|
31
|
+
:y => "\e[33m", :yellow => "\e[33m",
|
32
|
+
:b => "\e[34m", :blue => "\e[34m",
|
33
|
+
:m => "\e[35m", :magenta => "\e[35m",
|
34
|
+
:c => "\e[36m", :cyan => "\e[36m",
|
35
|
+
:w => "\e[37m", :white => "\e[37m",
|
36
|
+
:n => "\e[00m", :none => "\e[00m", :reset => "\e[00m",
|
37
|
+
}
|
38
|
+
|
39
|
+
def colors
|
40
|
+
ESC_SEQ
|
41
|
+
end
|
42
|
+
|
43
|
+
def shell_dir
|
44
|
+
File.join(@cache[:savedir], SHELLDIR)
|
45
|
+
end
|
46
|
+
|
47
|
+
def data_dir
|
48
|
+
File.join(@cache[:savedir], DATADIR)
|
49
|
+
end
|
50
|
+
|
51
|
+
def session_dir
|
52
|
+
File.join(@cache[:savedir], SESSION)
|
53
|
+
end
|
54
|
+
|
55
|
+
def plugin_dir
|
56
|
+
File.join(@cache[:savedir], PLUGIN)
|
57
|
+
end
|
58
|
+
|
59
|
+
def script_file
|
60
|
+
File.join(@cache[:savedir], SCRIPT)
|
61
|
+
end
|
62
|
+
|
63
|
+
def script_dir
|
64
|
+
File.dirname(script_file)
|
65
|
+
end
|
66
|
+
|
67
|
+
def config_file
|
68
|
+
File.join(@cache[:savedir], CONFIG)
|
69
|
+
end
|
70
|
+
|
71
|
+
def object_file
|
72
|
+
File.join(@cache[:savedir], OBJECT)
|
73
|
+
end
|
74
|
+
|
75
|
+
def history_file
|
76
|
+
File.join(@cache[:savedir], HISTORY)
|
77
|
+
end
|
78
|
+
|
79
|
+
def bioflat_dir
|
80
|
+
File.join(@cache[:savedir], BIOFLAT)
|
81
|
+
end
|
82
|
+
|
83
|
+
def ask_yes_or_no(message)
|
84
|
+
loop do
|
85
|
+
STDERR.print "#{message}"
|
86
|
+
answer = gets
|
87
|
+
if answer.nil?
|
88
|
+
# readline support might be broken
|
89
|
+
return false
|
90
|
+
elsif /^\s*[Nn]/.match(answer)
|
91
|
+
return false
|
92
|
+
elsif /^\s*[Yy]/.match(answer)
|
93
|
+
return true
|
94
|
+
else
|
95
|
+
# loop
|
96
|
+
end
|
97
|
+
end
|
98
|
+
end
|
99
|
+
|
100
|
+
end
|
101
|
+
|
102
|
+
|
103
|
+
module Bio::Shell::Ghost
|
104
|
+
|
105
|
+
include Bio::Shell::Core
|
106
|
+
|
107
|
+
# A hash to store persistent configurations
|
108
|
+
attr_accessor :config
|
109
|
+
|
110
|
+
# A hash to store temporal (per session) configurations
|
111
|
+
attr_accessor :cache
|
112
|
+
|
113
|
+
### save/restore the environment
|
114
|
+
|
115
|
+
def configure(savedir)
|
116
|
+
@config = {}
|
117
|
+
@cache = {
|
118
|
+
:savedir => savedir,
|
119
|
+
:workdir => Dir.pwd,
|
120
|
+
}
|
121
|
+
create_save_dir
|
122
|
+
load_config
|
123
|
+
load_plugin
|
124
|
+
end
|
125
|
+
|
126
|
+
def load_session
|
127
|
+
load_object
|
128
|
+
unless @cache[:mode] == :script
|
129
|
+
load_history
|
130
|
+
opening_splash
|
131
|
+
open_history
|
132
|
+
end
|
133
|
+
end
|
134
|
+
|
135
|
+
def save_session
|
136
|
+
unless @cache[:mode] == :script
|
137
|
+
closing_splash
|
138
|
+
end
|
139
|
+
if create_save_dir_ask
|
140
|
+
#save_history # changed to use our own...
|
141
|
+
close_history
|
142
|
+
save_object
|
143
|
+
save_config
|
144
|
+
end
|
145
|
+
#STDERR.puts "Leaving directory '#{@cache[:workdir]}'"
|
146
|
+
end
|
147
|
+
|
148
|
+
### directories
|
149
|
+
|
150
|
+
def create_save_dir
|
151
|
+
create_real_dir(session_dir)
|
152
|
+
create_real_dir(plugin_dir)
|
153
|
+
create_real_dir(data_dir)
|
154
|
+
end
|
155
|
+
|
156
|
+
def create_save_dir_ask
|
157
|
+
if File.directory?(session_dir)
|
158
|
+
@cache[:save] = true
|
159
|
+
end
|
160
|
+
unless @cache[:save]
|
161
|
+
if ask_yes_or_no("Save session in '#{@cache[:workdir]}' directory? [y/n] ")
|
162
|
+
create_real_dir(session_dir)
|
163
|
+
create_real_dir(plugin_dir)
|
164
|
+
create_real_dir(data_dir)
|
165
|
+
create_real_dir(bioflat_dir)
|
166
|
+
@cache[:save] = true
|
167
|
+
else
|
168
|
+
@cache[:save] = false
|
169
|
+
end
|
170
|
+
end
|
171
|
+
return @cache[:save]
|
172
|
+
end
|
173
|
+
|
174
|
+
def create_real_dir(dir)
|
175
|
+
unless File.directory?(dir)
|
176
|
+
begin
|
177
|
+
STDERR.print "Creating directory (#{dir}) ... "
|
178
|
+
FileUtils.makedirs(dir)
|
179
|
+
STDERR.puts "done"
|
180
|
+
rescue
|
181
|
+
warn "Error: Failed to create directory (#{dir}) : #{$!}"
|
182
|
+
end
|
183
|
+
end
|
184
|
+
end
|
185
|
+
|
186
|
+
### bioflat
|
187
|
+
|
188
|
+
def create_flat_dir(dbname)
|
189
|
+
dir = File.join(bioflat_dir, dbname.to_s.strip)
|
190
|
+
unless File.directory?(dir)
|
191
|
+
FileUtils.makedirs(dir)
|
192
|
+
end
|
193
|
+
return dir
|
194
|
+
end
|
195
|
+
|
196
|
+
def find_flat_dir(dbname)
|
197
|
+
dir = File.join(bioflat_dir, dbname.to_s.strip)
|
198
|
+
if File.exists?(dir)
|
199
|
+
return dir
|
200
|
+
else
|
201
|
+
return nil
|
202
|
+
end
|
203
|
+
end
|
204
|
+
|
205
|
+
### config
|
206
|
+
|
207
|
+
def load_config
|
208
|
+
load_config_file(config_file)
|
209
|
+
end
|
210
|
+
|
211
|
+
def load_config_file(file)
|
212
|
+
if File.exists?(file)
|
213
|
+
STDERR.print "Loading config (#{file}) ... "
|
214
|
+
if hash = YAML.load(File.read(file))
|
215
|
+
@config.update(hash)
|
216
|
+
end
|
217
|
+
STDERR.puts "done"
|
218
|
+
end
|
219
|
+
end
|
220
|
+
|
221
|
+
def save_config
|
222
|
+
save_config_file(config_file)
|
223
|
+
end
|
224
|
+
|
225
|
+
def save_config_file(file)
|
226
|
+
begin
|
227
|
+
STDERR.print "Saving config (#{file}) ... "
|
228
|
+
File.open(file, "w") do |f|
|
229
|
+
f.puts @config.to_yaml
|
230
|
+
end
|
231
|
+
STDERR.puts "done"
|
232
|
+
rescue
|
233
|
+
warn "Error: Failed to save (#{file}) : #{$!}"
|
234
|
+
end
|
235
|
+
end
|
236
|
+
|
237
|
+
def config_show
|
238
|
+
@config.each do |k, v|
|
239
|
+
STDERR.puts "#{k}\t= #{v.inspect}"
|
240
|
+
end
|
241
|
+
end
|
242
|
+
|
243
|
+
def config_echo
|
244
|
+
bind = Bio::Shell.cache[:binding]
|
245
|
+
flag = ! @config[:echo]
|
246
|
+
@config[:echo] = IRB.conf[:ECHO] = flag
|
247
|
+
eval("conf.echo = #{flag}", bind)
|
248
|
+
STDERR.puts "Echo #{flag ? 'on' : 'off'}"
|
249
|
+
end
|
250
|
+
|
251
|
+
def config_color
|
252
|
+
bind = Bio::Shell.cache[:binding]
|
253
|
+
flag = ! @config[:color]
|
254
|
+
@config[:color] = flag
|
255
|
+
if flag
|
256
|
+
IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR
|
257
|
+
eval("conf.prompt_mode = :BIORUBY_COLOR", bind)
|
258
|
+
else
|
259
|
+
IRB.conf[:PROMPT_MODE] = :BIORUBY
|
260
|
+
eval("conf.prompt_mode = :BIORUBY", bind)
|
261
|
+
end
|
262
|
+
end
|
263
|
+
|
264
|
+
def config_pager(cmd = nil)
|
265
|
+
@config[:pager] = cmd
|
266
|
+
end
|
267
|
+
|
268
|
+
def config_splash
|
269
|
+
flag = ! @config[:splash]
|
270
|
+
@config[:splash] = flag
|
271
|
+
STDERR.puts "Splash #{flag ? 'on' : 'off'}"
|
272
|
+
opening_splash
|
273
|
+
end
|
274
|
+
|
275
|
+
def config_message(str = nil)
|
276
|
+
str ||= MESSAGE
|
277
|
+
@config[:message] = str
|
278
|
+
opening_splash
|
279
|
+
end
|
280
|
+
|
281
|
+
### plugin
|
282
|
+
|
283
|
+
def load_plugin
|
284
|
+
load_plugin_dir(plugin_dir)
|
285
|
+
end
|
286
|
+
|
287
|
+
def load_plugin_dir(dir)
|
288
|
+
if File.directory?(dir)
|
289
|
+
Dir.glob("#{dir}/*.rb").sort.each do |file|
|
290
|
+
STDERR.print "Loading plugin (#{file}) ... "
|
291
|
+
load file
|
292
|
+
STDERR.puts "done"
|
293
|
+
end
|
294
|
+
end
|
295
|
+
end
|
296
|
+
|
297
|
+
### object
|
298
|
+
|
299
|
+
def check_marshal
|
300
|
+
if @config[:marshal] and @config[:marshal] != MARSHAL
|
301
|
+
raise "Marshal version mismatch"
|
302
|
+
end
|
303
|
+
end
|
304
|
+
|
305
|
+
def load_object
|
306
|
+
begin
|
307
|
+
check_marshal
|
308
|
+
load_object_file(object_file)
|
309
|
+
rescue
|
310
|
+
warn "Error: Load aborted : #{$!}"
|
311
|
+
end
|
312
|
+
end
|
313
|
+
|
314
|
+
def load_object_file(file)
|
315
|
+
if File.exists?(file)
|
316
|
+
STDERR.print "Loading object (#{file}) ... "
|
317
|
+
begin
|
318
|
+
bind = Bio::Shell.cache[:binding]
|
319
|
+
hash = Marshal.load(File.read(file))
|
320
|
+
hash.each do |k, v|
|
321
|
+
begin
|
322
|
+
Thread.current[:restore_value] = v
|
323
|
+
eval("#{k} = Thread.current[:restore_value]", bind)
|
324
|
+
rescue
|
325
|
+
STDERR.puts "Warning: object '#{k}' couldn't be loaded : #{$!}"
|
326
|
+
end
|
327
|
+
end
|
328
|
+
rescue
|
329
|
+
warn "Error: Failed to load (#{file}) : #{$!}"
|
330
|
+
end
|
331
|
+
STDERR.puts "done"
|
332
|
+
end
|
333
|
+
end
|
334
|
+
|
335
|
+
def save_object
|
336
|
+
save_object_file(object_file)
|
337
|
+
end
|
338
|
+
|
339
|
+
def save_object_file(file)
|
340
|
+
begin
|
341
|
+
STDERR.print "Saving object (#{file}) ... "
|
342
|
+
File.rename(file, "#{file}.old") if File.exist?(file)
|
343
|
+
File.open(file, "w") do |f|
|
344
|
+
bind = Bio::Shell.cache[:binding]
|
345
|
+
list = eval("local_variables", bind)
|
346
|
+
list -= ["_"]
|
347
|
+
hash = {}
|
348
|
+
list.each do |elem|
|
349
|
+
value = eval(elem, bind)
|
350
|
+
if value
|
351
|
+
begin
|
352
|
+
Marshal.dump(value)
|
353
|
+
hash[elem] = value
|
354
|
+
rescue
|
355
|
+
# value could not be dumped.
|
356
|
+
end
|
357
|
+
end
|
358
|
+
end
|
359
|
+
Marshal.dump(hash, f)
|
360
|
+
@config[:marshal] = MARSHAL
|
361
|
+
end
|
362
|
+
STDERR.puts "done"
|
363
|
+
rescue
|
364
|
+
File.rename("#{file}.old", file) if File.exist?("#{file}.old")
|
365
|
+
warn "Error: Failed to save (#{file}) : #{$!}"
|
366
|
+
end
|
367
|
+
end
|
368
|
+
|
369
|
+
### history
|
370
|
+
|
371
|
+
def open_history
|
372
|
+
@cache[:histfile] = File.open(history_file, "a")
|
373
|
+
@cache[:histfile].sync = true
|
374
|
+
end
|
375
|
+
|
376
|
+
def store_history(line)
|
377
|
+
Bio::Shell.cache[:histfile].puts "# #{Time.now}"
|
378
|
+
Bio::Shell.cache[:histfile].puts line
|
379
|
+
end
|
380
|
+
|
381
|
+
def close_history
|
382
|
+
if @cache[:histfile]
|
383
|
+
STDERR.print "Saving history (#{history_file}) ... "
|
384
|
+
@cache[:histfile].close
|
385
|
+
STDERR.puts "done"
|
386
|
+
end
|
387
|
+
end
|
388
|
+
|
389
|
+
def load_history
|
390
|
+
if @cache[:readline]
|
391
|
+
load_history_file(history_file)
|
392
|
+
end
|
393
|
+
end
|
394
|
+
|
395
|
+
def load_history_file(file)
|
396
|
+
if File.exists?(file)
|
397
|
+
STDERR.print "Loading history (#{file}) ... "
|
398
|
+
File.open(file).each do |line|
|
399
|
+
unless line[/^# /]
|
400
|
+
Readline::HISTORY.push line.chomp
|
401
|
+
end
|
402
|
+
end
|
403
|
+
STDERR.puts "done"
|
404
|
+
end
|
405
|
+
end
|
406
|
+
|
407
|
+
# not used (use open_history/close_history instead)
|
408
|
+
def save_history
|
409
|
+
if @cache[:readline]
|
410
|
+
save_history_file(history_file)
|
411
|
+
end
|
412
|
+
end
|
413
|
+
|
414
|
+
def save_history_file(file)
|
415
|
+
begin
|
416
|
+
STDERR.print "Saving history (#{file}) ... "
|
417
|
+
File.open(file, "w") do |f|
|
418
|
+
f.puts Readline::HISTORY.to_a
|
419
|
+
end
|
420
|
+
STDERR.puts "done"
|
421
|
+
rescue
|
422
|
+
warn "Error: Failed to save (#{file}) : #{$!}"
|
423
|
+
end
|
424
|
+
end
|
425
|
+
|
426
|
+
### script
|
427
|
+
|
428
|
+
def script(mode = nil)
|
429
|
+
case mode
|
430
|
+
when :begin, "begin", :start, "start"
|
431
|
+
@cache[:script] = true
|
432
|
+
script_begin
|
433
|
+
when :end, "end", :stop, "stop"
|
434
|
+
@cache[:script] = false
|
435
|
+
script_end
|
436
|
+
save_script
|
437
|
+
else
|
438
|
+
if @cache[:script]
|
439
|
+
@cache[:script] = false
|
440
|
+
script_end
|
441
|
+
save_script
|
442
|
+
else
|
443
|
+
@cache[:script] = true
|
444
|
+
script_begin
|
445
|
+
end
|
446
|
+
end
|
447
|
+
end
|
448
|
+
|
449
|
+
def script_begin
|
450
|
+
STDERR.puts "-- 8< -- 8< -- 8< -- Script -- 8< -- 8< -- 8< --"
|
451
|
+
@script_begin = Readline::HISTORY.size
|
452
|
+
end
|
453
|
+
|
454
|
+
def script_end
|
455
|
+
STDERR.puts "-- >8 -- >8 -- >8 -- Script -- >8 -- >8 -- >8 --"
|
456
|
+
@script_end = Readline::HISTORY.size - 2
|
457
|
+
end
|
458
|
+
|
459
|
+
def save_script
|
460
|
+
if @script_begin and @script_end and @script_begin <= @script_end
|
461
|
+
if File.exists?(script_file)
|
462
|
+
message = "Overwrite script file (#{script_file})? [y/n] "
|
463
|
+
else
|
464
|
+
message = "Save script file (#{script_file})? [y/n] "
|
465
|
+
end
|
466
|
+
if ask_yes_or_no(message)
|
467
|
+
save_script_file(script_file)
|
468
|
+
else
|
469
|
+
STDERR.puts " ... save aborted."
|
470
|
+
end
|
471
|
+
elsif @script_begin and @script_end and @script_begin - @script_end == 1
|
472
|
+
STDERR.puts " ... script aborted."
|
473
|
+
else
|
474
|
+
STDERR.puts "Error: Script range #{@script_begin}..#{@script_end} is invalid"
|
475
|
+
end
|
476
|
+
end
|
477
|
+
|
478
|
+
def save_script_file(file)
|
479
|
+
begin
|
480
|
+
STDERR.print "Saving script (#{file}) ... "
|
481
|
+
File.open(file, "w") do |f|
|
482
|
+
f.puts "#!/usr/bin/env bioruby"
|
483
|
+
f.puts
|
484
|
+
f.puts Readline::HISTORY.to_a[@script_begin..@script_end]
|
485
|
+
f.puts
|
486
|
+
end
|
487
|
+
STDERR.puts "done"
|
488
|
+
rescue
|
489
|
+
@script_begin = nil
|
490
|
+
warn "Error: Failed to save (#{file}) : #{$!}"
|
491
|
+
end
|
492
|
+
end
|
493
|
+
|
494
|
+
### splash
|
495
|
+
|
496
|
+
def splash_message
|
497
|
+
@config[:message] ||= MESSAGE
|
498
|
+
@config[:message].to_s.split(//).join(" ")
|
499
|
+
end
|
500
|
+
|
501
|
+
def splash_message_color
|
502
|
+
str = splash_message
|
503
|
+
ruby = colors[:ruby]
|
504
|
+
none = colors[:none]
|
505
|
+
return str.sub(/R u b y/) { "#{ruby}R u b y#{none}" }
|
506
|
+
end
|
507
|
+
|
508
|
+
def splash_message_action(message = nil)
|
509
|
+
s = message || splash_message
|
510
|
+
l = s.length
|
511
|
+
x = " "
|
512
|
+
0.step(l,2) do |i|
|
513
|
+
l1 = l-i; l2 = l1/2; l4 = l2/2
|
514
|
+
STDERR.print "#{s[0,i]}#{x*l1}#{s[i,1]}\r"
|
515
|
+
sleep(0.001)
|
516
|
+
STDERR.print "#{s[0,i]}#{x*l2}#{s[i,1]}#{x*(l1-l2)}\r"
|
517
|
+
sleep(0.002)
|
518
|
+
STDERR.print "#{s[0,i]}#{x*l4}#{s[i,1]}#{x*(l2-l4)}\r"
|
519
|
+
sleep(0.004)
|
520
|
+
STDERR.print "#{s[0,i+1]}#{x*l4}\r"
|
521
|
+
sleep(0.008)
|
522
|
+
end
|
523
|
+
end
|
524
|
+
|
525
|
+
def splash_message_action_color(message = nil)
|
526
|
+
s = message || splash_message
|
527
|
+
l = s.length
|
528
|
+
c = colors
|
529
|
+
x = " "
|
530
|
+
0.step(l,2) do |i|
|
531
|
+
l1 = l-i; l2 = l1/2; l4 = l2/2
|
532
|
+
STDERR.print "#{c[:n]}#{s[0,i]}#{x*l1}#{c[:y]}#{s[i,1]}\r"
|
533
|
+
sleep(0.001)
|
534
|
+
STDERR.print "#{c[:n]}#{s[0,i]}#{x*l2}#{c[:g]}#{s[i,1]}#{x*(l1-l2)}\r"
|
535
|
+
sleep(0.002)
|
536
|
+
STDERR.print "#{c[:n]}#{s[0,i]}#{x*l4}#{c[:r]}#{s[i,1]}#{x*(l2-l4)}\r"
|
537
|
+
sleep(0.004)
|
538
|
+
STDERR.print "#{c[:n]}#{s[0,i+1]}#{x*l4}\r"
|
539
|
+
sleep(0.008)
|
540
|
+
end
|
541
|
+
end
|
542
|
+
|
543
|
+
def opening_splash
|
544
|
+
STDERR.puts
|
545
|
+
if @config[:splash]
|
546
|
+
if @config[:color]
|
547
|
+
splash_message_action_color
|
548
|
+
else
|
549
|
+
splash_message_action
|
550
|
+
end
|
551
|
+
end
|
552
|
+
if @config[:color]
|
553
|
+
STDERR.print splash_message_color
|
554
|
+
else
|
555
|
+
STDERR.print splash_message
|
556
|
+
end
|
557
|
+
STDERR.puts
|
558
|
+
STDERR.puts
|
559
|
+
STDERR.print " Version : BioRuby #{Bio::BIORUBY_VERSION.join(".")}"
|
560
|
+
STDERR.print " / Ruby #{RUBY_VERSION}"
|
561
|
+
STDERR.puts
|
562
|
+
STDERR.puts
|
563
|
+
end
|
564
|
+
|
565
|
+
def closing_splash
|
566
|
+
STDERR.puts
|
567
|
+
STDERR.puts
|
568
|
+
if @config[:color]
|
569
|
+
STDERR.print splash_message_color
|
570
|
+
else
|
571
|
+
STDERR.print splash_message
|
572
|
+
end
|
573
|
+
STDERR.puts
|
574
|
+
STDERR.puts
|
575
|
+
end
|
576
|
+
|
577
|
+
end
|
578
|
+
|