wwood-bioruby 1.2.11
Sign up to get free protection for your applications and to get access to all the features.
- 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
- 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 +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
- 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/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
@@ -0,0 +1,27 @@
|
|
1
|
+
<div id="log_<%= @number %>" class="log">
|
2
|
+
<div class="input">
|
3
|
+
Input: [<%= link_to_remote @number, :url => {:action => "reload_script", :number => @number} %>]
|
4
|
+
<pre class="script">
|
5
|
+
<%=h @script %>
|
6
|
+
</pre>
|
7
|
+
<div class="output">
|
8
|
+
Result:
|
9
|
+
[<%= link_to_remote "methods", :url => {:action => "list_methods", :number => @number} %>]
|
10
|
+
[<%= link_to_remote "classes", :url => {:action => "list_classes", :number => @number} %>]
|
11
|
+
[<%= link_to_remote "modules", :url => {:action => "list_modules", :number => @number} %>]
|
12
|
+
<div id="methods_<%= @number %>" class="methods"></div>
|
13
|
+
<div id="classes_<%= @number %>" class="classes"></div>
|
14
|
+
<div id="modules_<%= @number %>" class="modules"></div>
|
15
|
+
<pre class="result">
|
16
|
+
<%=h @result %>
|
17
|
+
</pre>
|
18
|
+
<% if @output %>
|
19
|
+
Output:
|
20
|
+
<pre class="output">
|
21
|
+
<%=h @output %>
|
22
|
+
</pre>
|
23
|
+
<% end %>
|
24
|
+
</div>
|
25
|
+
</div>
|
26
|
+
</div>
|
27
|
+
|
Binary file
|
Binary file
|
Binary file
|
@@ -0,0 +1,368 @@
|
|
1
|
+
/* body */
|
2
|
+
|
3
|
+
body {
|
4
|
+
margin: 0;
|
5
|
+
color: #555555;
|
6
|
+
background: url("/images/bioruby/bg.gif") repeat-y center;
|
7
|
+
font-family: "trebuchet ms", verdana, arial, helvetica, sans-serif;
|
8
|
+
font-size: 12px;
|
9
|
+
}
|
10
|
+
|
11
|
+
div#content {
|
12
|
+
width: 750px;
|
13
|
+
height: auto;
|
14
|
+
margin: 0 auto 0 auto;
|
15
|
+
text-align: left;
|
16
|
+
}
|
17
|
+
|
18
|
+
/* title */
|
19
|
+
|
20
|
+
div#title {
|
21
|
+
width: 550px;
|
22
|
+
padding-right: 200px;
|
23
|
+
margin-bottom: 20px;
|
24
|
+
text-align: left;
|
25
|
+
background: url("/images/bioruby/gem.png") no-repeat left bottom;
|
26
|
+
}
|
27
|
+
|
28
|
+
div#title .titletop {
|
29
|
+
color: #736451;
|
30
|
+
font-size: 30px;
|
31
|
+
font-weight: normal;
|
32
|
+
text-align: left;
|
33
|
+
text-indent: 70px;
|
34
|
+
margin: 0;
|
35
|
+
padding: 0;
|
36
|
+
padding-top: 20px;
|
37
|
+
margin-bottom: 10px;
|
38
|
+
}
|
39
|
+
|
40
|
+
div#title .titlesub {
|
41
|
+
color: #000000;
|
42
|
+
font-size: 15px;
|
43
|
+
font-weight: normal;
|
44
|
+
text-align: left;
|
45
|
+
text-indent: 70px;
|
46
|
+
margin: 0;
|
47
|
+
padding: 0;
|
48
|
+
border-bottom: 1px solid #eeeeee;
|
49
|
+
}
|
50
|
+
|
51
|
+
/* main */
|
52
|
+
|
53
|
+
div#main {
|
54
|
+
width: 550px;
|
55
|
+
background-color: #ffffff;
|
56
|
+
padding-top: 0px;
|
57
|
+
padding-left: 10px;
|
58
|
+
}
|
59
|
+
|
60
|
+
div#notice {
|
61
|
+
background-color: #fcc;
|
62
|
+
border: 1px solid #f00;
|
63
|
+
}
|
64
|
+
|
65
|
+
div#notice p {
|
66
|
+
margin: 0;
|
67
|
+
padding: 10px;
|
68
|
+
}
|
69
|
+
|
70
|
+
pre {
|
71
|
+
color: #6e8377;
|
72
|
+
background-color: #eaedeb;
|
73
|
+
border-color: #6e8377;
|
74
|
+
border-style: dashed;
|
75
|
+
border-width: 1px;
|
76
|
+
padding: 5px;
|
77
|
+
width: 500px;
|
78
|
+
overflow: auto;
|
79
|
+
}
|
80
|
+
|
81
|
+
div.log {
|
82
|
+
width: 500px;
|
83
|
+
margin-top: 15px;
|
84
|
+
padding-top: 5px;
|
85
|
+
border-top: 1px dotted #333333;
|
86
|
+
}
|
87
|
+
|
88
|
+
div.log div.input pre.script {
|
89
|
+
background-color: #ffffeb;
|
90
|
+
border-style: solid;
|
91
|
+
}
|
92
|
+
|
93
|
+
div.log div.output div.methods {
|
94
|
+
padding: 5px;
|
95
|
+
background-color: #ffffdd;
|
96
|
+
border: 1px solid #ffcc00;
|
97
|
+
}
|
98
|
+
|
99
|
+
div.log div.output div.classes {
|
100
|
+
padding: 5px;
|
101
|
+
background-color: #ccffcc;
|
102
|
+
border: 1px solid #00ff00;
|
103
|
+
}
|
104
|
+
|
105
|
+
div.log div.output div.modules {
|
106
|
+
padding: 5px;
|
107
|
+
background-color: #ffcccc;
|
108
|
+
border: 1px solid #ff0000;
|
109
|
+
}
|
110
|
+
|
111
|
+
div.log div.output pre.result {
|
112
|
+
border-style: dashed;
|
113
|
+
}
|
114
|
+
|
115
|
+
div.log div.output pre.output {
|
116
|
+
border-style: dashed;
|
117
|
+
}
|
118
|
+
|
119
|
+
div.log hr.log {
|
120
|
+
border-style: dotted none none none;
|
121
|
+
border-top-width: 1px;
|
122
|
+
border-color: #6e8377;
|
123
|
+
width: 200px;
|
124
|
+
height: 1px;
|
125
|
+
}
|
126
|
+
|
127
|
+
/* side */
|
128
|
+
|
129
|
+
div#side {
|
130
|
+
width: 150px;
|
131
|
+
float: right;
|
132
|
+
margin-top: 20px;
|
133
|
+
text-align: left;
|
134
|
+
font-size: 12px;
|
135
|
+
color: #e44268;
|
136
|
+
}
|
137
|
+
|
138
|
+
div#side div.title {
|
139
|
+
font-weight: normal;
|
140
|
+
color: #e44268;
|
141
|
+
text-align: left;
|
142
|
+
border-width: 0px 0px 1px 0px;
|
143
|
+
border-bottom: 1px solid #e44268;
|
144
|
+
}
|
145
|
+
|
146
|
+
div#side a:link {
|
147
|
+
color: #ffffff;
|
148
|
+
text-decoration: none;
|
149
|
+
}
|
150
|
+
|
151
|
+
div#side a:visited {
|
152
|
+
color: #ffffff;
|
153
|
+
text-decoration: none;
|
154
|
+
}
|
155
|
+
|
156
|
+
div#side a:hover {
|
157
|
+
color: #cccccc;
|
158
|
+
text-decoration: underline;
|
159
|
+
}
|
160
|
+
|
161
|
+
div#side ol,ul {
|
162
|
+
margin: 10px;
|
163
|
+
padding-left: 10px;
|
164
|
+
}
|
165
|
+
|
166
|
+
div#side li {
|
167
|
+
color: #e44268;
|
168
|
+
}
|
169
|
+
|
170
|
+
div#side img {
|
171
|
+
padding: 5px;
|
172
|
+
/* centering */
|
173
|
+
display: block;
|
174
|
+
margin-left: auto;
|
175
|
+
margin-right: auto;
|
176
|
+
border: 0px;
|
177
|
+
}
|
178
|
+
|
179
|
+
/* history */
|
180
|
+
|
181
|
+
div#history {
|
182
|
+
width: 500px;
|
183
|
+
}
|
184
|
+
|
185
|
+
div#history div.histtime {
|
186
|
+
background-color: #eaedeb;
|
187
|
+
padding: 5px;
|
188
|
+
}
|
189
|
+
|
190
|
+
div#history div.histline {
|
191
|
+
background-color: #ffffeb;
|
192
|
+
padding: 5px;
|
193
|
+
font-family: monospace;
|
194
|
+
white-space: pre;
|
195
|
+
}
|
196
|
+
|
197
|
+
/* command */
|
198
|
+
|
199
|
+
div#command {
|
200
|
+
width: 500px;
|
201
|
+
}
|
202
|
+
|
203
|
+
/* image */
|
204
|
+
|
205
|
+
img {
|
206
|
+
}
|
207
|
+
|
208
|
+
/* em */
|
209
|
+
|
210
|
+
em {
|
211
|
+
color: #6e8377;
|
212
|
+
font-style: normal;
|
213
|
+
}
|
214
|
+
|
215
|
+
/* link */
|
216
|
+
|
217
|
+
a {
|
218
|
+
text-decoration: none;
|
219
|
+
}
|
220
|
+
|
221
|
+
a:link {
|
222
|
+
color: #669933;
|
223
|
+
}
|
224
|
+
|
225
|
+
a:visited {
|
226
|
+
color: #669933;
|
227
|
+
}
|
228
|
+
|
229
|
+
a:hover {
|
230
|
+
text-decoration: underline;
|
231
|
+
}
|
232
|
+
|
233
|
+
/* header */
|
234
|
+
|
235
|
+
h1 {
|
236
|
+
font-size: 180%;
|
237
|
+
color: #ffffff;
|
238
|
+
background-color: #6e8377;
|
239
|
+
line-height: 64px;
|
240
|
+
text-align: left;
|
241
|
+
padding-left: 20px;
|
242
|
+
}
|
243
|
+
|
244
|
+
h2 {
|
245
|
+
font-size: 160%;
|
246
|
+
color: #6e8377;
|
247
|
+
border-color: #b9c3be;
|
248
|
+
border-style: dashed;
|
249
|
+
border-width: 0px 0px 1px 0px;
|
250
|
+
}
|
251
|
+
|
252
|
+
h3 {
|
253
|
+
font-size: 140%;
|
254
|
+
color: #6e8377;
|
255
|
+
border-color: #b9c3be;
|
256
|
+
border-style: dotted;
|
257
|
+
border-width: 0px 0px 1px 0px;
|
258
|
+
}
|
259
|
+
|
260
|
+
h4 {
|
261
|
+
font-size: 130%;
|
262
|
+
color: #6e8377;
|
263
|
+
border-color: #b9c3be;
|
264
|
+
border-style: solid;
|
265
|
+
border-width: 0px 0px 1px 0px;
|
266
|
+
}
|
267
|
+
|
268
|
+
h5 {
|
269
|
+
font-size: 120%;
|
270
|
+
color: #6e8377;
|
271
|
+
}
|
272
|
+
|
273
|
+
h6 {
|
274
|
+
font-size: 110%;
|
275
|
+
color: #6e8377;
|
276
|
+
}
|
277
|
+
|
278
|
+
/* list */
|
279
|
+
|
280
|
+
dt {
|
281
|
+
color: #6e8377;
|
282
|
+
border-color: #b9c3be;
|
283
|
+
border-style: dashed;
|
284
|
+
border-width: 1px;
|
285
|
+
padding: 5px;
|
286
|
+
}
|
287
|
+
|
288
|
+
ul {
|
289
|
+
color: #6e8377;
|
290
|
+
}
|
291
|
+
|
292
|
+
/* table */
|
293
|
+
|
294
|
+
table {
|
295
|
+
border: 1px solid #cccccc;
|
296
|
+
border-collapse: collapse;
|
297
|
+
}
|
298
|
+
|
299
|
+
th {
|
300
|
+
vertical-align: top;
|
301
|
+
padding: 5px;
|
302
|
+
}
|
303
|
+
|
304
|
+
td {
|
305
|
+
vertical-align: top;
|
306
|
+
padding: 5px;
|
307
|
+
}
|
308
|
+
|
309
|
+
div#method_list table {
|
310
|
+
border: none;
|
311
|
+
}
|
312
|
+
|
313
|
+
|
314
|
+
/* form */
|
315
|
+
|
316
|
+
input {
|
317
|
+
background-color: #FFFFFF;
|
318
|
+
padding: 2px;
|
319
|
+
font-size: 10px;
|
320
|
+
color: #666666;
|
321
|
+
border: 1px solid #611022;
|
322
|
+
margin-bottom: 2px;
|
323
|
+
}
|
324
|
+
|
325
|
+
input[type=submit] {
|
326
|
+
background-color: #FFFFFF;
|
327
|
+
padding: 2px;
|
328
|
+
font-size: 10px;
|
329
|
+
color: #ffffff;
|
330
|
+
border: 1px solid #611022;
|
331
|
+
background-color: #E44268;
|
332
|
+
margin-bottom: 2px;
|
333
|
+
}
|
334
|
+
|
335
|
+
/* textarea */
|
336
|
+
|
337
|
+
textarea {
|
338
|
+
background-color: #eaedeb;
|
339
|
+
font-family: monospace;
|
340
|
+
font-size: 12px;
|
341
|
+
overflow: auto;
|
342
|
+
width: 500px;
|
343
|
+
padding: 5px;
|
344
|
+
}
|
345
|
+
|
346
|
+
|
347
|
+
/* blockquote */
|
348
|
+
|
349
|
+
blockquote {
|
350
|
+
color: #6e8377;
|
351
|
+
background-color: #eaedeb;
|
352
|
+
border-color: #6e8377;
|
353
|
+
border-style: dashed;
|
354
|
+
border-width: 1px;
|
355
|
+
}
|
356
|
+
|
357
|
+
/* media */
|
358
|
+
|
359
|
+
@media print {
|
360
|
+
div#main { margin-left: 0px; }
|
361
|
+
div#side { display: none; }
|
362
|
+
}
|
363
|
+
|
364
|
+
@media screen {
|
365
|
+
div#main { margin-left: 0px; }
|
366
|
+
div#side { display: block; }
|
367
|
+
}
|
368
|
+
|
@@ -0,0 +1,47 @@
|
|
1
|
+
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
2
|
+
<html xmlns="http://www.w3.org/1999/xhtml">
|
3
|
+
<head>
|
4
|
+
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
5
|
+
<title>BioRuby shell on Rails</title>
|
6
|
+
<%= stylesheet_link_tag "bioruby.css" %>
|
7
|
+
<%= javascript_include_tag :defaults %>
|
8
|
+
</head>
|
9
|
+
|
10
|
+
<body>
|
11
|
+
|
12
|
+
<div id="content">
|
13
|
+
|
14
|
+
<div id="side">
|
15
|
+
<div class="title">Project</div>
|
16
|
+
<ul>
|
17
|
+
<li><%= link_to "#{File.basename(project_workdir)}", "file://#{project_workdir}" %>
|
18
|
+
</ul>
|
19
|
+
|
20
|
+
<div class="title">Functions</div>
|
21
|
+
<ul>
|
22
|
+
<li><%= link_to "Console", :action => "index" %></li>
|
23
|
+
<li><%= link_to "History", :action => "history" %></li>
|
24
|
+
<li><%= link_to "Commands", :action => "commands" %></li>
|
25
|
+
</ul>
|
26
|
+
|
27
|
+
<div class="title">Local variables</div>
|
28
|
+
<%= render :partial => "variables" %>
|
29
|
+
|
30
|
+
<br>
|
31
|
+
<a href="http://bioruby.org/"><img src="/images/bioruby/link.gif" border=0></a>
|
32
|
+
</div><!-- side -->
|
33
|
+
|
34
|
+
<div id="title">
|
35
|
+
<p class="titletop">BioRuby shell on Rails</p>
|
36
|
+
<p class="titlesub">Web interface for the BioRuby library</p>
|
37
|
+
</div><!-- title -->
|
38
|
+
|
39
|
+
<div id="main">
|
40
|
+
<%= yield %>
|
41
|
+
</div><!-- main -->
|
42
|
+
|
43
|
+
</div><!-- content -->
|
44
|
+
|
45
|
+
</body>
|
46
|
+
|
47
|
+
</html>
|