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
data/ChangeLog
ADDED
@@ -0,0 +1,2046 @@
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2008-07-30 BioHackathon2008 participants from BioRuby project
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* Branch 'biohackathon2008' is merged.
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See doc/Changes-1.3.rd for incompatible changes.
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* lib/bio/sequence.rb, lib/bio/sequence/
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* lib/bio/db/embl/
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* lib/bio/db/genbank/
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* lib/bio/db/fasta.rb, lib/bio/db/fasta/
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A new method #to_biosequence is added to Bio::EMBL, Bio::GenBank
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and Bio::FastaFormat. Bio::FastaFormat#to_seq is now an alias of
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the #to_biosequence method.
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Bio::Sequence#output is added to output formatted text.
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Supported formats are: EMBL, GenBank, Fasta, or raw.
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Written by Naohisa Goto and Jan Aerts.
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* lib/bio/db/biosql/
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* lib/bio/io/sql.rb, lib/bio/io/biosql/
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New BioSQL implementation by Raoul Jean Pierre Bonnal.
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* lib/bio/reference.rb
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* lib/bio/feature.rb
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Bio::References and Bio::Features are obsoleted.
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For more information, see doc/Changes-1.3.rd.
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* (Many changes are not listed here. See git log for details.)
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2008-07-30 Naohisa Goto <ng@bioruby.org>
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* lib/bio/db/gff.rb, test/unit/bio/db/test_gff.rb
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Branch 'test-gff3' in git://github.com/ngoto/bioruby is merged.
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Fixed gff3 attribute bug, and many improvements are added.
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See doc/Changes-1.3.rd for incompatible changes.
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Thanks to Ben Woodcroft who reported the bug and contributed codes.
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2008-07-29 Naohisa Goto <ng@bioruby.org>
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* lib/bio/appl/blast/format0.rb
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Bug fix: fixed ScanError when bit score is in exponential notation
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such as 1.234e+5. Regular expressions for numerics including
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exponential notations are changed to get correct values.
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2008-07-18 Naohisa Goto <ng@bioruby.org>
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* lib/bio/appl/hmmer.rb
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Bug fix: ArgumentError caused by misspelling of a variable name.
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2008-06-23 Jan Aerts <jan.aerts@gmail.com>
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* README.rdoc
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* README_DEV.rdoc
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* gemspec.rb
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Renamed README files to RDoc gets parsed on github website.
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(commit 34b7693f74de2358759e955d8ce36cfe15e64b54)
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Edited README.rdoc and README_DEV.rdoc to reflect move from CVS
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to git.
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(commit a61b16163d3ca74f3f7c8d8e8f03f5f8c68dee60)
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2008-06-13 Naohisa Goto <ng@bioruby.org>
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* lib/bio/reference.rb
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* test/unit/bio/test_reference.rb
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* New method Bio::Reference#pubmed_url added (renamed the url method
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in CVS revision 1.25).
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* Bio::Reference#endnote is changed not to overwrite url if url is
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already given by user.
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* Improvement of Bio::Reference#bibtex method. (Idea to improve
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bibtex method is originally made by Pjotr Prins.)
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* test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb
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"require 'bio/sequence'" is needed to run the tests in this file.
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(commit 735e3563b723645afa65f0e4213a7c92152f68ec)
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2008-05-19 Pjotr Prins <pjotr.prins@wur.nl>
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* sample/fastasort.rb
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Simple example for sorting a flatfile
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(commit 677ac7c0707860f0478e75f72f23faa05b29dc6d)
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* doc/Tutorial.rd
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* sample/fastagrep.rb
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* sample/fastasort.rb
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Piping FASTA files (examples and doc)
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(commit ecd5e04477246dcf6cac84a6fbd21fb59efa3cf0)
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2008-05-14 Naohisa Goto <ng@bioruby.org>
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* lib/bio/appl/blast/format0.rb
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Bug fix: Possibly because of the output format changes of PHI-BLAST,
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Bio::Blast::Default::Report::Iteration#eff_space (and the shortcut
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method in the Report class) failed for PHI-BLAST (blastpgp) results,
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and Iteration#pattern and #pattern_positions (and the
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shortcut methods in the Report class) returned incorrect values.
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2008-05-12 Naohisa Goto <ng@bioruby.org>
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* lib/bio/appl/blast/xmlparser.rb, lib/bio/appl/blast/rexml.rb
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Bug fix: unit test sometime fails due to improper treatment of some
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Blast parameters and difference between rexml and xmlparser.
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To fix the bug, types of some parameters may be changed, e.g.
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Bio::Blast::Report#expect is changed to return Float or nil.
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* lib/bio/appl/blast/format0.rb
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Bug fix: Bio::Blast::Default::Report#eff_space returns wrong value
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("Effective length of database"). It should return the value of
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"Effective search space".
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* test/unit/bio/appl/blast/test_xmlparser.rb
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Bug fix: tests in test/unit/bio/appl/blast/test_report.rb were
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ignored because of conflicts of the names of test classes.
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Class name in test_xmlparser.rb is changed to fix the bug.
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2008-04-23 Naohisa Goto <ng@bioruby.org>
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* lib/bio/db/embl/common.rb
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Bug fix: Bio::EMBL#references failed to parse journal name,
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volume, issue, pages, and year. In addition, it might failed
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to parse PubMed ID.
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(commit c715f51729b115309a78cf29fdce7fef992da875)
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2008-04-18 Naohisa Goto <ng@bioruby.org>
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* lib/bio/db/embl/sptr.rb
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Bug fix: Bio::SPTR#references raises NoMethodError since
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lib/bio/db/embl/sptr.rb CVS version 1.34.
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(commit 1b3e484e19c9c547cecfe53858a646b525685e0d)
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2008-04-15 Naohisa Goto <ng@bioruby.org>
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* lib/bio/appl/blast/rpsblast.rb
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Newly added RPS-Blast default (-m 0) output parser.
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2008-04-01 Naohisa Goto <ng@bioruby.org>
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* lib/bio/appl/blast/format0.rb
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Fixed a bug: Failed to parse database name in some cases.
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Thanks to Tomoaki Nishiyama who reported the bug and sent patches
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([BioRuby-ja] BLAST format0 parser fails header parsing output
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of specific databases).
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* lib/bio/db/pdb/chain.rb, lib/bio/db/pdb/pdb.rb
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Fixed bugs: Bio::PDB::Chain#aaseq failed for nucleotide chain;
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Failed to parse chains for some entries (e.g. 1B2M).
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Thanks to Semin Lee who reported the bugs and sent patches
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([BioRuby] Bio::PDB parsing problem (1B2M)).
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2008-02-19 Toshiaki Katayama <k@bioruby.org>
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* lib/bio/io/ncbirest.rb
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* lib/bio/io/pubmed.rb
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NCBI E-Utilities (REST) functionality is separated to ncbirest.rb
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and pubmed.rb is changed to utilize the Bio::NCBI::REST class for
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esearch and efetch. You can now search and retrieve any database
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in any format that NCBI supports by E-Utilities through the
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Bio::NCBI::REST interface (currently, only esearch and efetch methods
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are implemented).
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(commit 0677bb69044cf6cfba453420bc1bbeb422f691c1)
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(commit f60e9f8153efacff0c97d12fb5c0830ebeb02edd)
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(commit 6e4670ab5e67ca596788f4c26a95a9687d36ce84)
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2008-02-13 Pjotr Prins <pjotr.prins@wur.nl>
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* doc/Tutorial.rd
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(commit d7ee01d86d6982f6b8aa19eba9adac95bebb08e8)
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2008-02-12 Naohisa Goto <ng@bioruby.org>
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* lib/bio/appl/blast/format0.rb
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Fixed bugs: Failed to parse query length for long query
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(>= 10000 letters) as comma is inserted for digit separator
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by blastall; Failed to parse e-value for some BLASTX results.
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Thanks to Shuji Shigenobu who reported the bugs and sent patches.
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2008-02-11 Pjotr Prins <pjotr.prins@wur.nl>
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* doc/Tutorial.rd
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Expanding on the Tutorial
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(bdc1d14f497909041fa761f659a74d98702a335a)
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Minor adjustments to Tutorial
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(72b5f4f0667a3a0c44ca31b0ab8228381e37919c)
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2008-02-06 Pjotr Prins <pjotr.prins@wur.nl>
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* sample/na2aa.rb
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Simple example to translate any NA to AA fasta
|
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(commit 433f974219cf04342935c1760464af24a5696c49)
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|
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2008-02-05 Pjotr Prins <pjotr.prins@wur.nl>
|
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+
|
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* sample/gb2fasta.rb
|
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|
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Fixed broken require in gb2fasta example
|
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(commit b55daed0d6cff2e45155be01ef2a946925c972cf)
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|
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2008-02-05 Pjotr Prins <pjotr.prins@wur.nl>
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* doc/Tutorial.rd
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Minor tweak to Tutorial.rd
|
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(commit 75416d780f99de24498a47fd22703d74f9a22329)
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2008-02-03 Pjotr Prins <pjotr.prins@wur.nl>
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* doc/Tutorial.rd
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More doctests in Tutorial.rd
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(commit 39d182bb67977956c0f22631ac596d65ccce74ff)
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2008-02-02 Pjotr Prins <pjotr.prins@wur.nl>
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* doc/Tutorial.rd
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Tabs in the Tutorial broke the rd parser - the Wiki will be fixed
|
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now.
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(commit 49078a5dea4f16f44add1882c60bf75df67ea19b)
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Updating tutorial.
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(commit f2f2005c3964f37e2d65afef0d52e63950d6bcb7)
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(commit d2b05581953712d0ac67ba0de1aa43853ed4e27f)
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|
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2008-02-02 Toshiaki Katayama <k@bioruby.org>
|
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|
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* lib/bio/shell/rails/vendor/plugins/
|
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|
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The 'generators' directory is moved under the 'bioruby' subdirectory
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so that 'bioruby --rails' command can work with Rails 2.x series
|
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in addition to the Rails 1.2.x series.
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|
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2008-01-30 Mitsuteru Nakao <n@bioruby.org>
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|
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* lib/bio/appl/blast.rb
|
256
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|
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Fixed the bug at building the blastall command line options ('-m 0').
|
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(commit 61443d177847825505103488573186dfc4e7568e)
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|
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2008-01-10 Naohisa Goto <ng@bioruby.org>
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|
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* lib/bio/appl/emboss.rb
|
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|
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Added a method Bio::EMBOSS.run(program, arguments...)
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and Bio::EMBOSS.new is obsoleted.
|
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(commit fa04d97b073aefe05edc34a84498ba0a57ff98d2)
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|
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2008-01-10 Toshiaki Katayama <k@bioruby.org>
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|
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* lib/bio/io/hinv.rb
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Bio::Hinv to access the H-invitational DB (http://h-invitational.jp/)
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web service in REST mode is added.
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+
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+
2007-12-30 Toshiaki Katayama <k@bioruby.org>
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+
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* BioRuby 1.2.1 released
|
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+
|
279
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+
This version is not Ruby 1.9 (released few days ago) compliant yet.
|
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+
|
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+
2007-12-28 Naohisa Goto <ng@bioruby.org>
|
282
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+
|
283
|
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* lib/bio/appl/blast/report/format0.rb
|
284
|
+
|
285
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+
Fixed parse error when compisition-based statistics were enabled.
|
286
|
+
In addition, Bio::Blast::Default::Report#references and
|
287
|
+
Bio::Blast::Default::Report::HSP#stat_method methods are added.
|
288
|
+
In NCBI BLAST 2.2.17, default option of composition-based
|
289
|
+
statistics for blastp or tblastn are changed to be enabled
|
290
|
+
by default.
|
291
|
+
|
292
|
+
* lib/bio/appl/blast/report/wublast.rb
|
293
|
+
|
294
|
+
Changed to follow the above changes in format0.rb.
|
295
|
+
|
296
|
+
* lib/bio/sequence/common.rb
|
297
|
+
|
298
|
+
Ruby 1.9 compliant: in window_search method, a local variable name
|
299
|
+
outside the iterator loop is changed not to be shadowed by the
|
300
|
+
iterator variable.
|
301
|
+
|
302
|
+
* lib/bio/db/pdb/pdb.rb
|
303
|
+
|
304
|
+
Ruby 1.9 compliant: changed to avoid "RuntimeError: implicit
|
305
|
+
argument passing of super from method defined by define_method()
|
306
|
+
is not supported. Specify all arguments explicitly." error.
|
307
|
+
|
308
|
+
Ruby 1.9 compliant: Bio::PDB::Record.get_record_class and
|
309
|
+
Bio::PDB::Record.create_definition_hash (Note: they should only
|
310
|
+
be internally used by PDB parser and users should not call them)
|
311
|
+
are changed to follow the change of Module#constants which
|
312
|
+
returns an array of Symbol instead of String.
|
313
|
+
|
314
|
+
2007-12-26 Naohisa Goto <ng@bioruby.org>
|
315
|
+
|
316
|
+
* lib/bio/alignment.rb
|
317
|
+
|
318
|
+
Ruby 1.9 compliant: in EnumerableExtension#each_window and
|
319
|
+
OriginalAlignment#index methods, local variable names outside the
|
320
|
+
iterator loops are changed not to be shadowed by iterator
|
321
|
+
variables.
|
322
|
+
|
323
|
+
Warning messages for uninitialized instance variables of
|
324
|
+
@gap_regexp, @gap_char, @missing_char, and @seqclass
|
325
|
+
are suppressed.
|
326
|
+
|
327
|
+
* test/unit/bio/test_alignment.rb
|
328
|
+
|
329
|
+
Ruby 1.9 compliant: Ruby 1.9 compliant: The last comma in Array.[]
|
330
|
+
is no longer allowed. (For example,
|
331
|
+
class A < Array; end; A[ 1, 2, 3, ]
|
332
|
+
raises syntax error in Ruby 1.9.)
|
333
|
+
|
334
|
+
2007-12-21 Toshiaki Katayama <k@bioruby.org>
|
335
|
+
|
336
|
+
* lib/bio/db/medline.rb
|
337
|
+
|
338
|
+
Added doi and pii methods to extract DOI and PII number from AID field
|
339
|
+
|
340
|
+
2007-12-18 Naohisa Goto <ng@bioruby.org>
|
341
|
+
|
342
|
+
* lib/bio/db/pdb/pdb.rb
|
343
|
+
|
344
|
+
Bio::PDB#inspect is added to prevent memory exhaust problem.
|
345
|
+
([BioRuby] Parse big PDB use up all memory)
|
346
|
+
|
347
|
+
* lib/bio/db/pdb/model.rb
|
348
|
+
|
349
|
+
Bio::PDB::Model#inspect is added.
|
350
|
+
|
351
|
+
* lib/bio/db/pdb/chain.rb
|
352
|
+
|
353
|
+
Bio::PDB::Chain#inspect is added.
|
354
|
+
|
355
|
+
* lib/bio/db/pdb/residue.rb
|
356
|
+
|
357
|
+
Bio::PDB::Residue#inspect is added.
|
358
|
+
This also affects Bio::PDB::Heterogen#inspect.
|
359
|
+
|
360
|
+
2007-12-15 Toshiaki Katayama <k@bioruby.org>
|
361
|
+
|
362
|
+
* BioRuby 1.2.0 released
|
363
|
+
|
364
|
+
* BioRuby shell is improved
|
365
|
+
* file save functionality is fixed
|
366
|
+
* deprecated require_gem is changed to gem to suppress warnings
|
367
|
+
* deprecated end_form_tag is rewrited to suppress warnings
|
368
|
+
* images for Rails shell are separated to the bioruby directory
|
369
|
+
* spinner is shown during the evaluation
|
370
|
+
* background image in the textarea is removed for the visibility
|
371
|
+
* Bio::Blast is fixed to parse -m 8 formatted result correctly
|
372
|
+
* Bio::PubMed is rewrited to enhance its functionality
|
373
|
+
* e.g. 'rettype' => 'count' and 'retmode' => 'xml' are available
|
374
|
+
* Bio::FlatFile is improved to accept recent MEDLINE format
|
375
|
+
* Bio::KEGG::COMPOUND is enhanced to utilize REMARK field
|
376
|
+
* Bio::KEGG::API is fixed to skip filter when the value is Fixnum
|
377
|
+
* A number of minor bug fixes
|
378
|
+
|
379
|
+
2007-12-12 Naohisa Goto <ng@bioruby.org>
|
380
|
+
|
381
|
+
* lib/bio/db/newick.rb:
|
382
|
+
|
383
|
+
Changed to be compliant with the Gary Olsen's Interpretation of
|
384
|
+
the "Newick's 8:45" Tree Format Standard.
|
385
|
+
|
386
|
+
* test/unit/bio/db/test_newick.rb
|
387
|
+
|
388
|
+
More tests are added.
|
389
|
+
|
390
|
+
* lib/bio/io/flatfile/indexer.rb
|
391
|
+
|
392
|
+
Fixed a misspelling in Bio::FlatFileIndex.formatstring2class.
|
393
|
+
|
394
|
+
2007-11-28 Toshiaki Katayama <k@bioruby.org>
|
395
|
+
|
396
|
+
* lib/bio/io/pubmed.rb:
|
397
|
+
|
398
|
+
Fixed search, query methods (but use of esearch and efetch is
|
399
|
+
strongly recommended).
|
400
|
+
|
401
|
+
efetch method is enhanced to accept any PubMed search options
|
402
|
+
as a hash (to retrieve in XML format etc.)
|
403
|
+
|
404
|
+
Changed to wait 3 seconds among each access by default to be
|
405
|
+
compliant with the NCBI terms (Make no more than one request
|
406
|
+
every 3 seconds).
|
407
|
+
|
408
|
+
All Bio::PubMed.* class methods are changed to instance methods
|
409
|
+
(interface as the class methods are remained for the backward
|
410
|
+
compatibility).
|
411
|
+
|
412
|
+
2007-07-19 Toshiaki Katayama <k@bioruby.org>
|
413
|
+
|
414
|
+
* BioRuby 1.1.0 released
|
415
|
+
|
416
|
+
2007-07-17 Toshiaki Katayama <k@bioruby.org>
|
417
|
+
|
418
|
+
* lib/bio/io/das.rb
|
419
|
+
|
420
|
+
Fixed that mapmaster method to return correct value (mapmaseter's
|
421
|
+
URL). This bug is reported and fixed by Dave Thorne.
|
422
|
+
|
423
|
+
2007-07-16 Naohisa Goto <ng@bioruby.org>
|
424
|
+
|
425
|
+
* lib/bio/mafft/report.rb
|
426
|
+
|
427
|
+
For generic multi-fasta formatted sequence alignment,
|
428
|
+
Bio::Alignment::MultiFastaFormat is newly added based on
|
429
|
+
Bio::MAFFT::Report class, and Bio::MAFFT::Report is
|
430
|
+
changed to inherit the new class.
|
431
|
+
Tests are added in test/unit/bio/appl/mafft/test_report.rb.
|
432
|
+
|
433
|
+
* lib/bio/alignment.rb
|
434
|
+
|
435
|
+
New modules and classes Bio::Alignment::FactoryTemplate::* are added.
|
436
|
+
They are used by following three new classes.
|
437
|
+
|
438
|
+
* lib/bio/appl/muscle.rb
|
439
|
+
* lib/bio/appl/probcons.rb
|
440
|
+
* lib/bio/appl/tcoffee.rb
|
441
|
+
|
442
|
+
New classess Bio::Muscle, Bio::Probcons, and Bio::Tcoffee are added
|
443
|
+
for MUSCLE, ProbCons, and T-Coffee multiple alignment programs.
|
444
|
+
Contributed by Jeffrey Blakeslee and colleagues.
|
445
|
+
|
446
|
+
* lib/bio/appl/clustalw.rb
|
447
|
+
* lib/bio/appl/mafft.rb
|
448
|
+
|
449
|
+
Interfaces of Bio::ClustalW and Bio::MAFFT are added/modified
|
450
|
+
to follow Bio::Alignment::FactoryTemplate (but not yet changed to
|
451
|
+
use it).
|
452
|
+
|
453
|
+
2007-07-09 Toshiaki Katayama <k@bioruby.org>
|
454
|
+
|
455
|
+
* BioRuby shell on Rails has new CSS theme
|
456
|
+
|
457
|
+
Completely new design for BioRuby shell on Rails translated from
|
458
|
+
the 'DibdoltRed' theme on www.openwebdesign.org which is created by
|
459
|
+
Darjan Panic and Brian Green as a public domain work!
|
460
|
+
|
461
|
+
2007-07-09 Toshiaki Katayama <k@bioruby.org>
|
462
|
+
|
463
|
+
* lib/bio/db/kegg/taxonomy.rb
|
464
|
+
|
465
|
+
Newly added KEGG taxonomy file parser which treats taxonomic tree
|
466
|
+
structure of the KEGG organisms. The file is available at
|
467
|
+
ftp://ftp.genome.jp/pub/kegg/genes/taxonomy
|
468
|
+
and is a replacement of the previously used keggtab file (obsoleted).
|
469
|
+
|
470
|
+
* lib/bio/db/kegg/keggtab.rb
|
471
|
+
|
472
|
+
Bio::KEGG::Keggtab is obsoleted as the file is no longer provided.
|
473
|
+
Use Bio::KEGG::Taxonomy (lib/bio/db/kegg/taxonomy.rb) instead.
|
474
|
+
|
475
|
+
* lib/bio/shell/plugin/soap.rb
|
476
|
+
|
477
|
+
Newly added web service plugins for BioRuby shell which supports
|
478
|
+
NCBI SOAP, EBI SOAP and DDBJ XML in addition to the KEGG API.
|
479
|
+
|
480
|
+
2007-07-09 Naohisa Goto <ng@bioruby.org>
|
481
|
+
|
482
|
+
* lib/bio/db/pdb/pdb.rb
|
483
|
+
|
484
|
+
Pdb_LString.new is changed not to raise error for nil.
|
485
|
+
|
486
|
+
Fixed a bug when below records does not exist in a PDB entry:
|
487
|
+
REMARK (remark), JRNL (jrnl), HELIX (helix),
|
488
|
+
TURN (turn), SHEET (sheet), SSBOND (ssbond), SEQRES (seqres),
|
489
|
+
DBREF (dbref), KEYWDS (keywords), AUTHOR (authors),
|
490
|
+
HEADER (entry_id, accession, classification),
|
491
|
+
TITLE (definition), and REVDAT (version) records (methods).
|
492
|
+
|
493
|
+
Incompatible change: Bio::PDB#record is changed to return
|
494
|
+
an empty array for nonexistent record.
|
495
|
+
|
496
|
+
(reported by Mikael Borg)
|
497
|
+
|
498
|
+
2007-07-09 Naohisa Goto <ng@bioruby.org>
|
499
|
+
|
500
|
+
* lib/bio/io/flatfile.rb
|
501
|
+
|
502
|
+
Bio::FlatFile.foreach is added (which is suggested by IO.foreach).
|
503
|
+
|
504
|
+
2007-06-28 Toshiaki Katayama <k@bioruby.org>
|
505
|
+
|
506
|
+
* lib/bio/shell/setup.rb, core.rb
|
507
|
+
|
508
|
+
Changed not to use Dir.chdir by caching full path of the save
|
509
|
+
directory at a start up time, so that user can freely change
|
510
|
+
the work directory without affecting object/history saving
|
511
|
+
functionality.
|
512
|
+
|
513
|
+
Bio::Shell.cache[:savedir] stores the session saving directory
|
514
|
+
(session means shell/session/{config,history,object} files),
|
515
|
+
Bio::Shell.cache[:workdir] stores the working directory at a start
|
516
|
+
up time (can be same directory with the :savedir) and both are
|
517
|
+
converted and stored as full path allowing user to use Dir.chdir
|
518
|
+
in the shell session).
|
519
|
+
|
520
|
+
If --rails (-r) option is applied, 'bioruby' command will run in
|
521
|
+
the Rails server mode, and the server will start in the :savedir.
|
522
|
+
|
523
|
+
(A) IRB mode
|
524
|
+
|
525
|
+
1. run in the current directory and the session will be saved
|
526
|
+
in the ~/.bioruby directory
|
527
|
+
|
528
|
+
% bioruby
|
529
|
+
|
530
|
+
2. run in the current directory and the session will be saved
|
531
|
+
in the foo/bar directory
|
532
|
+
|
533
|
+
% bioruby foo/bar
|
534
|
+
|
535
|
+
3. run in the current directory and the session will be saved
|
536
|
+
in the /tmp/foo/bar directory
|
537
|
+
|
538
|
+
% bioruby /tmp/foo/bar
|
539
|
+
|
540
|
+
(B) Rails mode
|
541
|
+
|
542
|
+
4. run in the ~/.bioruby directory and the session will also be saved
|
543
|
+
in the ~/.bioruby directory
|
544
|
+
|
545
|
+
% bioruby -r
|
546
|
+
|
547
|
+
5. run in the foo/bar directory and the session will also be saved
|
548
|
+
in the foo/bar directory
|
549
|
+
|
550
|
+
% bioruby -r foo/bar
|
551
|
+
|
552
|
+
6. run in the /tmp/foo/bar directory and the session will also be
|
553
|
+
saved in the /tmp/foo/bar directory
|
554
|
+
|
555
|
+
% bioruby -r /tmp/foo/bar
|
556
|
+
|
557
|
+
(C) Script mode
|
558
|
+
|
559
|
+
7. run in the current directory using the session saved
|
560
|
+
in the ~/.bioruby directory
|
561
|
+
|
562
|
+
% bioruby ~/.bioruby/shell/script.rb
|
563
|
+
|
564
|
+
8. run in the current directory using the session saved
|
565
|
+
in the foo/bar directory
|
566
|
+
|
567
|
+
% bioruby foo/bar/shell/script.rb
|
568
|
+
|
569
|
+
9. run in the current directory using the session saved
|
570
|
+
in the /tmp/foo/bar directory
|
571
|
+
|
572
|
+
% bioruby /tmp/foo/bar/shell/script.rb
|
573
|
+
|
574
|
+
2007-06-21 Toshiaki Katayama <k@bioruby.org>
|
575
|
+
|
576
|
+
* lib/bio/shell/setup.rb
|
577
|
+
|
578
|
+
If no directory is specified to the bioruby command,
|
579
|
+
use ~/.bioruby directory as the default save directory
|
580
|
+
instead of the current directory, as suggested by Jun Sese.
|
581
|
+
|
582
|
+
User can use 'bioruby' command without botherd by directories
|
583
|
+
and files previously created by the 'bioruby' command
|
584
|
+
in the current directory even when not needed.
|
585
|
+
|
586
|
+
2007-05-19 Toshiaki Katayama <k@bioruby.org>
|
587
|
+
|
588
|
+
* lib/bio/appl/fasta.rb
|
589
|
+
|
590
|
+
Bug fixed that exec_local fails to exec when @ktup is nil.
|
591
|
+
This problem is reported and fixed by Fredrik Johansson.
|
592
|
+
|
593
|
+
* lib/bio/db/gff.rb
|
594
|
+
|
595
|
+
parser_attributes method in GFF3 class is modified to use
|
596
|
+
'=' char as a separator instead of ' ' (which is used in
|
597
|
+
GFF2 spec).
|
598
|
+
|
599
|
+
2007-04-06 Toshiaki Katayama <k@bioruby.org>
|
600
|
+
|
601
|
+
* COPYING, COPYING.LIB are removed
|
602
|
+
|
603
|
+
BioRuby is now distributed under the same terms as Ruby.
|
604
|
+
|
605
|
+
On behalf of the BioRuby developer, I have asked all authors of
|
606
|
+
the BioRuby code to change BioRuby's license from LGPL to Ruby's.
|
607
|
+
And we have finished to change license of all modules in the BioRuby
|
608
|
+
library. This means that Ruby user can freely use BioRuby library
|
609
|
+
without being annoyed by licensing issues.
|
610
|
+
|
611
|
+
* lib/bio/db/kegg/ko.rb is renamed to lib/bio/db/kegg/ortholog.rb
|
612
|
+
|
613
|
+
KEGG KO database is renamed to KEGG ORTHOLOG database, thus we
|
614
|
+
follow the change. Bio::KEGG::KO is renamed to Bio::KEGG::ORTHOLOG.
|
615
|
+
|
616
|
+
Bio::KEGG::ORTHOLOG#genes, dblinks methods are rewrited to use
|
617
|
+
lines_fetch method.
|
618
|
+
|
619
|
+
* lib/bio/data/aa.rb
|
620
|
+
|
621
|
+
to_re method is changed that the generated regexp to include
|
622
|
+
ambiguous amino acid itself - replacement of amino acid X should
|
623
|
+
include X itself.
|
624
|
+
|
625
|
+
2007-04-05 Trevor Wennblom <trevor@corevx.com>
|
626
|
+
|
627
|
+
* License headers are completely rewrited to Ruby's.
|
628
|
+
|
629
|
+
2007-04-02 Naohisa Goto <ng@bioruby.org>
|
630
|
+
|
631
|
+
* lib/bio/appl/mafft.rb
|
632
|
+
|
633
|
+
Incompatible change: Bio::MAFFT#output is changed to return
|
634
|
+
a string of multi-fasta formmatted text. To get an array of
|
635
|
+
Bio::FastaFormat objects (as of 1.0 or before), please use
|
636
|
+
report.data instead.
|
637
|
+
|
638
|
+
2007-03-29 Toshiaki Katayama <k@bioruby.org>
|
639
|
+
|
640
|
+
* lib/bio/db/kegg/cell.rb
|
641
|
+
|
642
|
+
Obsoleted as the KEGG CELL database is not publically available
|
643
|
+
any more.
|
644
|
+
|
645
|
+
2007-03-28 Toshiaki Katayama <k@bioruby.org>
|
646
|
+
|
647
|
+
* lib/bio/shell/rails/.../bioruby_controller.rb
|
648
|
+
|
649
|
+
BioRuby shell on Rails access is changed to be limited only from
|
650
|
+
the localhost for security reason (if local_request?).
|
651
|
+
|
652
|
+
* lib/bio/command.rb
|
653
|
+
|
654
|
+
The post_form method is modified to accept URL as a string and
|
655
|
+
extended to accept params as
|
656
|
+
array of string
|
657
|
+
array of hash
|
658
|
+
array of array
|
659
|
+
or
|
660
|
+
string
|
661
|
+
in addition to hash (also can be ommited if not needed - defaults
|
662
|
+
to nil).
|
663
|
+
|
664
|
+
Keys and parameters of params are forced to use to_s for sure.
|
665
|
+
|
666
|
+
* lib/bio/io/ensembl.rb
|
667
|
+
|
668
|
+
Re-designed to allows user to use Bio::Ensembl.new without
|
669
|
+
creating inherited sub class.
|
670
|
+
|
671
|
+
Changed to use Bio::Command.post_form
|
672
|
+
|
673
|
+
* lib/bio/das.rb
|
674
|
+
|
675
|
+
Changed to use Bio::Command
|
676
|
+
|
677
|
+
* lib/bio/shell/plugin/das.rb
|
678
|
+
|
679
|
+
Newly added BioDAS client plugin for BioRuby shell.
|
680
|
+
|
681
|
+
das.list_sequences
|
682
|
+
das.dna
|
683
|
+
das.features
|
684
|
+
|
685
|
+
2007-03-15 Toshiaki Katayama <k@bioruby.org>
|
686
|
+
|
687
|
+
* lib/bio/shell/irb.rb
|
688
|
+
|
689
|
+
Changed to load Rails environment when bioruby shell is invoked
|
690
|
+
in the Rails project directory. This means that user can use
|
691
|
+
'bioruby' command as a better './script/console' which has
|
692
|
+
persistent objects and shared history.
|
693
|
+
|
694
|
+
2007-03-08 Toshiaki Katayama <k@bioruby.org>
|
695
|
+
|
696
|
+
* lib/bio/db/kegg/drug.rb
|
697
|
+
|
698
|
+
Newly added KEGG DRUG database parser.
|
699
|
+
|
700
|
+
* lib/bio/db/kegg/glycan.rb
|
701
|
+
|
702
|
+
Bio::KEGG::GLYCAN#bindings method is removed.
|
703
|
+
Bio::KEGG::GLYCAN#comment, remarks methods are added.
|
704
|
+
Bio::KEGG::GLYCAN#orthologs and dblinks methods are changed to use
|
705
|
+
lines_fetch method.
|
706
|
+
|
707
|
+
* lib/bio/kegg/compound.rb
|
708
|
+
|
709
|
+
Bio::KEGG::COMPOUND#glycans method is added
|
710
|
+
Bio::KEGG::COMPOUND#names method is changed to return an array
|
711
|
+
of stripped strings.
|
712
|
+
|
713
|
+
* lib/bio/db/kegg/genes.rb
|
714
|
+
|
715
|
+
Bio::KEGG::GENES#orthologs method is added.
|
716
|
+
|
717
|
+
2007-03-27 Naohisa Goto <ng@bioruby.org>
|
718
|
+
|
719
|
+
* lib/bio/command.rb
|
720
|
+
|
721
|
+
Bio::Command.call_command_fork and query_command_fork methods
|
722
|
+
are changed to handle all Ruby exceptions in the child process.
|
723
|
+
|
724
|
+
* lib/bio/io/flatfile.rb
|
725
|
+
|
726
|
+
UniProt format autodetection was changed to follow the change of
|
727
|
+
UniProtKB release 9.0 of 31-Oct-2006.
|
728
|
+
|
729
|
+
2007-02-12 Naohisa Goto <ng@bioruby.org>
|
730
|
+
|
731
|
+
* lib/bio/io/flatfile.rb
|
732
|
+
|
733
|
+
Exception class UnknownDataFormatError is added.
|
734
|
+
It will be raised before reading data from IO when data format
|
735
|
+
hasn't been specified due to failure of file format autodetection.
|
736
|
+
|
737
|
+
2007-02-12 Toshiaki Katayama <k@bioruby.org>
|
738
|
+
|
739
|
+
* lib/bio/io/flatfile.rb
|
740
|
+
|
741
|
+
Added support for KEGG EGENES.
|
742
|
+
|
743
|
+
2007-02-02 Trevor Wennblom <trevor@corevx.com>
|
744
|
+
|
745
|
+
* lib/bio/util/restriction_enzyme*
|
746
|
+
|
747
|
+
Bio::RestrictionEnzyme stabilized.
|
748
|
+
|
749
|
+
2007-02-02 Trevor Wennblom <trevor@corevx.com>
|
750
|
+
|
751
|
+
* lib/bio/db/lasergene.rb
|
752
|
+
|
753
|
+
Bio::Lasergene Interface for DNAStar Lasergene sequence file format
|
754
|
+
|
755
|
+
2007-02-02 Trevor Wennblom <trevor@corevx.com>
|
756
|
+
|
757
|
+
* lib/bio/db/soft.rb
|
758
|
+
|
759
|
+
Bio::SOFT for reading SOFT formatted NCBI GEO files.
|
760
|
+
|
761
|
+
2007-01-16 Toshiaki Katayama <k@bioruby.org>
|
762
|
+
|
763
|
+
* BioRuby shell on Rails new features and fixes
|
764
|
+
|
765
|
+
New features:
|
766
|
+
* Input [#] is linked to action for filling textarea from history
|
767
|
+
* [methods] is separated into columns for readability
|
768
|
+
|
769
|
+
Fixes and improvements:
|
770
|
+
* HIDE_VARIABLES is moved from helper to controller to avoid warning
|
771
|
+
"already initialized constant - HIDE_VARIABLES" repeated on reload.
|
772
|
+
* <div id="evaluate"> is renamed to "log_#" with number for future
|
773
|
+
extention.
|
774
|
+
* <div id="log_#"> are inserted in the <div id="logs">
|
775
|
+
|
776
|
+
2007-01-15 Toshiaki Katayama <k@bioruby.org>
|
777
|
+
|
778
|
+
* lib/bio/db.rb
|
779
|
+
|
780
|
+
lines_fetch method (internally used various bio/db/*.rb modules)
|
781
|
+
is rewrited to concatenate indented sub field.
|
782
|
+
|
783
|
+
* lib/bio/db/kegg/compound.rb
|
784
|
+
|
785
|
+
Bio::KEGG::COMPOUND#comment method which returns contents of
|
786
|
+
the COMMENT line is added
|
787
|
+
|
788
|
+
* lib/bio/db/kegg/enzyme.rb
|
789
|
+
|
790
|
+
Bio::KEGG::ENZYME#entry_id is changed to return EC number only.
|
791
|
+
Previous version of entry_id method is renamed to entry method
|
792
|
+
which returns a "EC x.x.x.x Enzyme" style string.
|
793
|
+
|
794
|
+
Bio::KEGG::ENZYME#obsolete? method is added which returns boolean
|
795
|
+
value (true or false) according to the ENTRY line contains
|
796
|
+
a string 'Obsolete' or not.
|
797
|
+
|
798
|
+
Bio::KEGG::ENZYME#all_reac, iubmb_reactions, kegg_reactions methods
|
799
|
+
are added to support newly added ALL_REAC field.
|
800
|
+
|
801
|
+
Bio::KEGG::ENZYME#inhibitors and orthologs methods are added.
|
802
|
+
|
803
|
+
Bio::KEGG::ENZYME#substrates, products, inhibitors, cofactors,
|
804
|
+
pathways, orthologs, diseases, motifs methods are rewrited to
|
805
|
+
utilizes new lines_fetch method in db.rb to process continuous
|
806
|
+
sub field.
|
807
|
+
|
808
|
+
* lib/bio/db/kegg/genome.rb
|
809
|
+
|
810
|
+
Bio::KEGG::GENOME#scaffolds, gc, genomemap methods are obsoleted.
|
811
|
+
Bio::KEGG::GENOME#distance, data_source, original_db methods are
|
812
|
+
added.
|
813
|
+
|
814
|
+
2006-12-24 Toshiaki Katayama <k@bioruby.org>
|
815
|
+
|
816
|
+
* bin/bioruby, lib/bio/shell/, lib/bio/shell/rails/
|
817
|
+
(lib/bio/shell/rails/vendor/plugins/generators/)
|
818
|
+
|
819
|
+
Web functionallity of the BioRuby shell is completely rewrited
|
820
|
+
to utilize generator of the Ruby on Rails. This means we don't
|
821
|
+
need to have a copy of the rails installation in our code base
|
822
|
+
any more. The shell now run in threads so user does not need
|
823
|
+
to run 2 processes as before (drb and webrick). Most importantly,
|
824
|
+
the shell is extended to have textarea to input any code and
|
825
|
+
the evaluated result is returned with AJAX having various neat
|
826
|
+
visual effects.
|
827
|
+
|
828
|
+
* lib/bio.rb
|
829
|
+
|
830
|
+
Extended to have Bio.command where command can be any BioRuby
|
831
|
+
shell methods.
|
832
|
+
ex. puts Bio.getseq("atgc" * 10).randomize.translate
|
833
|
+
|
834
|
+
* lib/bio/shell/plugin/entry.rb, seq.rb
|
835
|
+
|
836
|
+
seq, ent, obj commands are renamed to getseq, getent, getobj
|
837
|
+
respectively. This getseq is also changed to return Bio::Sequence
|
838
|
+
with @moltype = Bio::Sequence::NA object instead of Bio::Sequence::NA
|
839
|
+
object.
|
840
|
+
|
841
|
+
* lib/bio/db/kegg/kgml.rb
|
842
|
+
|
843
|
+
Some method names are changed to avoid confusion:
|
844
|
+
* entry_type is renamed to category (<entry type="">)
|
845
|
+
* map is renamed to pathway (<entry map="">)
|
846
|
+
|
847
|
+
2006-12-19 Christian Zmasek <czmasek@burnham.org>
|
848
|
+
|
849
|
+
* lib/bio/db/nexus.rb
|
850
|
+
|
851
|
+
Bio::Nexus is newly developed during the Phyloinformatics hackathon.
|
852
|
+
|
853
|
+
2006-12-16 Toshiaki Katayama <k@birouby.org>
|
854
|
+
|
855
|
+
* lib/bio/io/sql.rb
|
856
|
+
|
857
|
+
Updated to follow recent BioSQL schema contributed by
|
858
|
+
Raoul Jean Pierre Bonnal.
|
859
|
+
|
860
|
+
2006-12-15 Mitsuteru Nakao <n@bioruby.org>
|
861
|
+
|
862
|
+
* lib/bio/appl/iprscan/report.rb
|
863
|
+
|
864
|
+
Bio::Iprscan::Report for InterProScan output is newly added.
|
865
|
+
2006-12-15 Naohisa Goto <ng@bioruby.org>
|
866
|
+
|
867
|
+
* lib/bio/appl/mafft/report.rb
|
868
|
+
|
869
|
+
Bio::MAFFT::Report#initialize is changed to get a string of
|
870
|
+
multi-fasta formmatted text instead of Array.
|
871
|
+
|
872
|
+
2006-12-14 Naohisa Goto <ng@bioruby.org>
|
873
|
+
|
874
|
+
* lib/bio/appl/phylip/alignment.rb
|
875
|
+
|
876
|
+
Phylip format multiple sequence alignment parser class
|
877
|
+
Bio::Phylip::PhylipFormat is newly added.
|
878
|
+
|
879
|
+
* lib/bio/appl/phylip/distance_matrix.rb
|
880
|
+
|
881
|
+
Bio::Phylip::DistanceMatrix, a parser for phylip distance matrix
|
882
|
+
(generated by dnadist/protdist/restdist programs) is newly added.
|
883
|
+
|
884
|
+
* lib/bio/appl/gcg/msf.rb, lib/bio/appl/gcg/seq.rb
|
885
|
+
|
886
|
+
Bio::GCG::Msf in lib/bio/appl/gcg/msf.rb for GCG MSF multiple
|
887
|
+
sequence alignment format parser, and Bio::GCG::Seq in
|
888
|
+
lib/bio/appl/gcg/seq.rb for GCG sequence format parser are
|
889
|
+
newly added.
|
890
|
+
|
891
|
+
* lib/bio/alignment.rb
|
892
|
+
|
893
|
+
Output of Phylip interleaved/non-interleaved format (.phy),
|
894
|
+
Molphy alignment format (.mol), and GCG MSF format (.msf)
|
895
|
+
are supported. Bio::Alignment::ClustalWFormatter is removed
|
896
|
+
and methods in the module are renamed and moved to
|
897
|
+
Bio::Alignment::Output.
|
898
|
+
|
899
|
+
* lib/bio/appl/clustalw.rb, lib/bio/appl/mafft.rb, lib/bio/appl/sim4.rb
|
900
|
+
|
901
|
+
Changed to use Bio::Command instead of Open3.popen3.
|
902
|
+
|
903
|
+
2006-12-13 Naohisa Goto <ng@bioruby.org>
|
904
|
+
|
905
|
+
* lib/bio/tree.rb, lib/bio/db/newick.rb
|
906
|
+
|
907
|
+
Bio::PhylogeneticTree is renamed to Bio::Tree, and
|
908
|
+
lib/bio/phylogenetictree.rb is renamed to lib/bio/tree.rb.
|
909
|
+
NHX (New Hampshire eXtended) parser/writer support are added.
|
910
|
+
|
911
|
+
2006-12-13 Toshiaki Katayama <k@bioruby.org>
|
912
|
+
|
913
|
+
* doc/Desing.rd.ja, doc/TODO.rd.ja, doc/BioRuby.rd.ja are obsoletd.
|
914
|
+
|
915
|
+
2006-10-05 Naohisa Goto <ng@bioruby.org>
|
916
|
+
|
917
|
+
* lib/bio/db/newick.rb
|
918
|
+
|
919
|
+
Bio::Newick for Newick standard phylogenetic tree parser is
|
920
|
+
newly added (contributed by Daniel Amelang).
|
921
|
+
|
922
|
+
* lib/bio/phylogenetictree.rb
|
923
|
+
|
924
|
+
Bio::PhylogeneticTree for phylogenetic tree data structure
|
925
|
+
is newly added.
|
926
|
+
|
927
|
+
2006-09-19 Toshiaki Katayama <k@bioruby.org>
|
928
|
+
|
929
|
+
* lib/bio/io/soapwsdl.rb
|
930
|
+
* lib/bio/io/ebisoap.rb
|
931
|
+
* lib/bio/io/ncbisoap.rb
|
932
|
+
|
933
|
+
Newly added web service modules.
|
934
|
+
|
935
|
+
* lib/bio/db/kegg/kgml.rb
|
936
|
+
|
937
|
+
Accessor for the <component> attribute is added.
|
938
|
+
|
939
|
+
* lib/bio/shell/plugin/codon.rb
|
940
|
+
|
941
|
+
Support for Pyrrolysine and Selenocysteine are added in the
|
942
|
+
BioRuby shell.
|
943
|
+
|
944
|
+
* lib/bio/sshell/plugin/seq.rb
|
945
|
+
|
946
|
+
sixtrans, skip, step methods are added in the BioRuby shell.
|
947
|
+
bioruby> seqtrans(seq)
|
948
|
+
|
949
|
+
bioruby> seq.step(window_size) {|subseq|
|
950
|
+
# do something on subseq
|
951
|
+
}
|
952
|
+
|
953
|
+
bioruby> seq.skip(window_sizep, step_size) {|subseq|
|
954
|
+
# do something on subseq
|
955
|
+
}
|
956
|
+
|
957
|
+
2006-07-26 Toshiaki Katayama <k@bioruby.org>
|
958
|
+
|
959
|
+
* lib/bio/data/aa.rb
|
960
|
+
|
961
|
+
Amino acids J (Xle: I/L), O (Pyl: pyrrolysine) and X (unknown)
|
962
|
+
are added (now we have consumed 26 alphabets!).
|
963
|
+
|
964
|
+
* lib/bio/io/fastacmd.rb
|
965
|
+
|
966
|
+
Fixed that new version of fastacmd (in BLAST package) changed
|
967
|
+
the option from '-D T' to '-D 1', contributed by the author
|
968
|
+
of this module Shuji Shigenobu.
|
969
|
+
|
970
|
+
* lib/bio/shell/plugin/psort.rb
|
971
|
+
|
972
|
+
Newly added BioRuby shell plugin for PSORT
|
973
|
+
|
974
|
+
* lib/bio/shell/plugin/blast.rb
|
975
|
+
|
976
|
+
Newly added BioRuby shell plugin for BLAST search against KEGG GENES
|
977
|
+
|
978
|
+
* lib/bio/db/prosite.rb
|
979
|
+
|
980
|
+
PROSITE#re instance method is added to translate PATTERN of
|
981
|
+
the entry to Regexp using PROSITE.pa2re class method.
|
982
|
+
|
983
|
+
* lib/bio/db/kegg/genes.rb
|
984
|
+
|
985
|
+
Bio::KEGG::GENES#keggclass method is renamed to pathway
|
986
|
+
Bio::KEGG::GENES#splinks method is removed
|
987
|
+
Bio::KEGG::GENES#motifs method is added
|
988
|
+
these reflect changes made in the original KEGG GENES database.
|
989
|
+
|
990
|
+
Bio::KEGG::GENES#locations method is added to return Bio::Locations
|
991
|
+
Bio::KEGG::GENES#codon_usage is renamed cu_list (returns as Array)
|
992
|
+
Bio::KEGG::GENES#cu is renamed to codon_usage (returns as Hash)
|
993
|
+
Bio::KEGG::GENES#aalen, nalen methods are changed to return
|
994
|
+
the number written in the entry (use seq.length to obtain calculated
|
995
|
+
number as before).
|
996
|
+
|
997
|
+
* lib/bio/db/kegg/kgml.rb
|
998
|
+
|
999
|
+
Names of some accessors have been changed (including bug fixes)
|
1000
|
+
and instance variable @dom is obsoleted. Here's a list of
|
1001
|
+
incompatible attribute names with KGML tags by this change:
|
1002
|
+
<entry>
|
1003
|
+
:id -> :entry_id
|
1004
|
+
:type -> :entry_type
|
1005
|
+
names()
|
1006
|
+
<graphics>
|
1007
|
+
:name -> :label
|
1008
|
+
:type -> :shape
|
1009
|
+
<relation>
|
1010
|
+
:entry1 -> :node1
|
1011
|
+
:entry2 -> :node2
|
1012
|
+
:type -> :rel
|
1013
|
+
<subtype>
|
1014
|
+
edge()
|
1015
|
+
<reaction>
|
1016
|
+
:name -> :entry_id
|
1017
|
+
:type -> :direction
|
1018
|
+
|
1019
|
+
* lib/bio/io/das.rb
|
1020
|
+
|
1021
|
+
Bug fixed that the value of segment.stop was overwritten by
|
1022
|
+
segment.orientation.
|
1023
|
+
|
1024
|
+
2006-07-14 Naohisa Goto <ng@bioruby.org>
|
1025
|
+
|
1026
|
+
* lib/bio/command.rb
|
1027
|
+
|
1028
|
+
Bio::Command::Tools and Bio::Command::NetTools are combined
|
1029
|
+
and re-constructed into a new Bio::Command module.
|
1030
|
+
|
1031
|
+
lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
|
1032
|
+
lib/bio/appl/emboss.rb, lib/bio/appl/psort.rb,
|
1033
|
+
lib/bio/appl/hmmer.rb, lib/bio/db/fantom.rb,
|
1034
|
+
lib/bio/io/fastacmd.rb, lib/bio/io/fetch.rb,
|
1035
|
+
lib/bio/io/keggapi.rb, lib/bio/io/pubmed.rb, and
|
1036
|
+
lib/bio/io/registry.rb are changed to use the new Bio::Command
|
1037
|
+
instead of old Bio::Command or Net::HTTP.
|
1038
|
+
|
1039
|
+
2006-06-29 Naohisa Goto <ng@bioruby.org>
|
1040
|
+
|
1041
|
+
* lib/bio/appl/blat/report.rb
|
1042
|
+
|
1043
|
+
Bio::BLAT::Report::Hit#milli_bad, #percent_identity, #protein?,
|
1044
|
+
#score, and #psl_version methods/attributes are newly added,
|
1045
|
+
and psl files without headers are supported (discussed in
|
1046
|
+
bioruby-ja ML).
|
1047
|
+
|
1048
|
+
2006-06-27 Naohisa Goto <ng@bioruby.org>
|
1049
|
+
|
1050
|
+
* lib/bio/sequence/na.rb
|
1051
|
+
|
1052
|
+
Bio::Sequence::NA#gc_content, #at_content, #gc_skew, #at_skew
|
1053
|
+
are newly added. Bio::Sequence::NA#gc_percent are changed
|
1054
|
+
not to raise ZeroDivisionError and returns 0 when given sequence
|
1055
|
+
is empty.
|
1056
|
+
|
1057
|
+
* lib/bio/db/pdb/pdb.rb
|
1058
|
+
|
1059
|
+
Bio::PDB::ATOM#name, #resName, #iCode, #chaarge, #segID, and
|
1060
|
+
#element are changed to strip whitespaces when initializing.
|
1061
|
+
Bio::PDB::HETATM is also subject to the above changes.
|
1062
|
+
(suggested by Mikael Borg)
|
1063
|
+
|
1064
|
+
2006-06-12 Naohisa Goto <ng@bioruby.org>
|
1065
|
+
|
1066
|
+
* lib/bio/io/flatfile.rb
|
1067
|
+
|
1068
|
+
Bug fix: Bio::FlatFile.open(klass, filename) didn't work.
|
1069
|
+
|
1070
|
+
2006-05-30 Toshiaki Katayama <k@bioruby.org>
|
1071
|
+
|
1072
|
+
* lib/bio/io/soapwsdl.rb
|
1073
|
+
|
1074
|
+
Generic list_methods method which extracts web service methods
|
1075
|
+
defined in the WSDL file is added.
|
1076
|
+
|
1077
|
+
2006-05-02 Mitsuteru Nakao <n@bioruby.org>
|
1078
|
+
|
1079
|
+
* lib/bio/appl/pts1.rb
|
1080
|
+
|
1081
|
+
Bio::PTS1 first commit.
|
1082
|
+
|
1083
|
+
2006-04-30 Naohisa Goto <ng@bioruby.org>
|
1084
|
+
|
1085
|
+
* lib/bio/appl/blast/format0.rb
|
1086
|
+
|
1087
|
+
Bug fix: parse error for hits whose database sequence names
|
1088
|
+
contain 'Score', and subsequent hits after them would lost
|
1089
|
+
(reported by Tomoaki NISHIYAMA).
|
1090
|
+
|
1091
|
+
2006-04-14 Mitsuteru Nakao <n@bioruby.org>
|
1092
|
+
|
1093
|
+
* lib/bio/io/ensembl.rb
|
1094
|
+
|
1095
|
+
Bio::Ensembl first commit. It is a client class for Ensembl Genome
|
1096
|
+
Browser.
|
1097
|
+
|
1098
|
+
2006-03-22 Naohisa Goto <ng@bioruby.org>
|
1099
|
+
|
1100
|
+
* lib/bio/io/flatfile.rb
|
1101
|
+
|
1102
|
+
Bug fix: Bio::FlatFile raises error for pipes, ARGF, etc.
|
1103
|
+
The bug also affects bio/appl/mafft.rb, bio/appl/clustalw.rb,
|
1104
|
+
bio/appl/blast.rb, bio/io/fastacmd.rb, and so on.
|
1105
|
+
|
1106
|
+
Bio::FlatFile#entry_start_pos and #entry_ended_pos are
|
1107
|
+
changed to be enabled only when Bio::FlatFile#entry_pos_flag
|
1108
|
+
is true.
|
1109
|
+
|
1110
|
+
2006-02-27 Toshiaki Katayama <k@bioruby.org>
|
1111
|
+
|
1112
|
+
* BioRuby 1.0.0 released
|
1113
|
+
|
1114
|
+
2006-02-10 Toshiaki Katayama <k@bioruby.org>
|
1115
|
+
|
1116
|
+
* BioRuby shell is changed to use session/ directory under the current
|
1117
|
+
or specified directory to store the session information instead of
|
1118
|
+
./.bioruby directory.
|
1119
|
+
|
1120
|
+
2006-02-05 Toshiaki Katayama <k@bioruby.org>
|
1121
|
+
|
1122
|
+
* License to be changed to Ruby's (not yet completed).
|
1123
|
+
|
1124
|
+
2006-02-01 Trevor Wennblom <trevor@corevx.com>
|
1125
|
+
|
1126
|
+
* Bio::RestrictionEnzyme first commit for comments.
|
1127
|
+
* See lib/bio/util/restriction_enzyme.rb and
|
1128
|
+
test/unit/bio/util/restriction_enzyme
|
1129
|
+
|
1130
|
+
2006-01-28 Toshiaki Katayama <k@bioruby.org>
|
1131
|
+
|
1132
|
+
* lib/bio/appl/emboss.rb
|
1133
|
+
|
1134
|
+
EMBOSS USA format is now accepted via seqret/entret commands
|
1135
|
+
and also utilized in the BioRuby shell (lib/bio/shell.rb,
|
1136
|
+
plugin/entry.rb, plugin/emboss.rb).
|
1137
|
+
|
1138
|
+
* lib/bio/io/brdb.rb is removed - unused Bio::BRDB (BioRuby DB)
|
1139
|
+
|
1140
|
+
2006-01-23 Toshiaki Katayama <k@bioruby.org>
|
1141
|
+
|
1142
|
+
* lib/bio/sequence.rb
|
1143
|
+
|
1144
|
+
Bio::Sequence is refactored to be a container class for
|
1145
|
+
any sequence annotations. Functionality is separared into
|
1146
|
+
several files under the lib/bio/sequence/ direcotry as
|
1147
|
+
common.rb, compat.rb, aa.rb, na.rb, format.rb
|
1148
|
+
|
1149
|
+
2006-01-20 Toshiaki Katayama <k@bioruby.org>
|
1150
|
+
|
1151
|
+
* BioRuby 0.7.1 is released.
|
1152
|
+
|
1153
|
+
2006-01-12 Toshiaki Katayama <k@bioruby.org>
|
1154
|
+
|
1155
|
+
* lib/bio/db.ra: fixed a bug of the tag_cut method introduced in 0.7.0
|
1156
|
+
(reported by Alex Gutteridge)
|
1157
|
+
|
1158
|
+
2006-01-04 Naohisa Goto <ng@bioruby.org>
|
1159
|
+
|
1160
|
+
* Bio::PDB is refactored. See doc/Changes-0.7 for more details.
|
1161
|
+
|
1162
|
+
2005-12-19 Toshiaki Katayama <k@bioruby.org>
|
1163
|
+
|
1164
|
+
* BioRuby 0.7.0 is released.
|
1165
|
+
|
1166
|
+
See doc/Changes-0.7.rd file for major and incompatible changes.
|
1167
|
+
|
1168
|
+
2005-12-19 Naohisa Goto <ng@bioruby.org>
|
1169
|
+
|
1170
|
+
* lib/bio/db/pdb.rb, lib/bio/db/pdb/pdb.rb, lib/bio/db/pdb/*.rb
|
1171
|
+
* Many changes have been made.
|
1172
|
+
* Bio::PDB::FieldDef is removed and Bio::PDB::Record is completely
|
1173
|
+
changed. Now, Record is changed from hash to Struct, and
|
1174
|
+
method_missing is no longer used.
|
1175
|
+
* In the "MODEL" record, model_serial is changed to serial.
|
1176
|
+
* In any records, record_type is changed to record_name.
|
1177
|
+
* In most records contains real numbers, changed to return
|
1178
|
+
float values instead of strings.
|
1179
|
+
* Pdb_AChar, Pdb_Atom, Pdb_Character, Pdb_Continuation,
|
1180
|
+
Pdb_Date, Pdb_IDcode, Pdb_Integer, Pdb_LString, Pdb_List,
|
1181
|
+
Pdb_Real, Pdb_Residue_name, Pdb_SList, Pdb_Specification_list,
|
1182
|
+
Pdb_String, Pdb_StringRJ and Pdb_SymOP are moved under
|
1183
|
+
Bio::PDB::DataType.
|
1184
|
+
* There are more and more changes to be written...
|
1185
|
+
|
1186
|
+
* lib/bio/db/pdb/atom.rb
|
1187
|
+
* Bio::PDB::Atom is removed.
|
1188
|
+
Instead, please use Bio::PDB::Record::ATOM and
|
1189
|
+
Bio::PDB::Record::HETATM.
|
1190
|
+
|
1191
|
+
2005-12-02 Naohisa Goto <ng:bioruby.org>
|
1192
|
+
|
1193
|
+
* lib/bio/alignment.rb
|
1194
|
+
* Old Bio::Alignment class is renamed to
|
1195
|
+
Bio::Alignment::OriginalAlignment.
|
1196
|
+
Now, new Bio::Alignment is a module. However,
|
1197
|
+
you don't mind so much because most of the class methods
|
1198
|
+
previously existed are defined to delegate to the new
|
1199
|
+
Bio::Alignment::OriginalAlignment class,
|
1200
|
+
for keeping backward compatibility.
|
1201
|
+
* New classes and modules are introduced. Please refer RDoc.
|
1202
|
+
* each_site and some methods changed to return Bio::Alignment::Site,
|
1203
|
+
which inherits Array (previously returned Array).
|
1204
|
+
* consensus_iupac now returns only standard bases
|
1205
|
+
'a', 'c', 'g', 't', 'm', 'r', 'w', 's', 'y', 'k', 'v',
|
1206
|
+
'h', 'd', 'b', 'n', or nil (in SiteMethods#consensus_iupac) or
|
1207
|
+
'?' (or missing_char, in EnumerableExtension#consensus_iupac).
|
1208
|
+
Note that consensus_iupac now does not return u and invalid
|
1209
|
+
letters not defined in IUPAC standard even if all bases
|
1210
|
+
are equal.
|
1211
|
+
* There are more and more changes to be written...
|
1212
|
+
|
1213
|
+
2005-11-05 Toshiaki Katayama <k@bioruby.org>
|
1214
|
+
|
1215
|
+
* lib/bio/sequence.rb
|
1216
|
+
|
1217
|
+
Bio::Sequence.auto(str) method is added which auto detect the
|
1218
|
+
molecular type of the string and then returns the
|
1219
|
+
Bio::Sequence::NA or Bio::Sequence::AA object.
|
1220
|
+
|
1221
|
+
Bio::Sequence#blast and Bio::Sequence#fasta methods are removed.
|
1222
|
+
|
1223
|
+
* lib/bio/shell/plugin/codon.rb
|
1224
|
+
|
1225
|
+
Newly added plugin to treat codon table.
|
1226
|
+
ColoredCodonTable is ported from the codontable.rb
|
1227
|
+
|
1228
|
+
2005-11-01 Toshiaki Katayama <k@bioruby.org>
|
1229
|
+
|
1230
|
+
* bin/bioruby, lib/bio/shell/
|
1231
|
+
|
1232
|
+
All methods are changed to private methods to avoid adding them
|
1233
|
+
in top level binding, which caused many unexpected behaviors,
|
1234
|
+
as adviced by Koichi Sasada.
|
1235
|
+
|
1236
|
+
The MIDI plugin is now able to select musical scales.
|
1237
|
+
|
1238
|
+
2005-10-23 Toshiaki Katayama <k@bioruby.org>
|
1239
|
+
|
1240
|
+
* lib/bio/util/color_scheme
|
1241
|
+
|
1242
|
+
Newly contributed Bio::ColorScheme
|
1243
|
+
|
1244
|
+
* lib/bio/db/kegg/kgml.rb
|
1245
|
+
|
1246
|
+
Newly added KEGG KGML parser.
|
1247
|
+
|
1248
|
+
2005-10-05 Toshiaki Katayama <k@bioruby.org>
|
1249
|
+
|
1250
|
+
* lib/bio/shell/plugin/midi.rb
|
1251
|
+
|
1252
|
+
Sequcne to MIDI plugin is contributed by Natsuhiro Ichinose
|
1253
|
+
|
1254
|
+
2005-09-25 Toshiaki Katayama <k@bioruby.org>
|
1255
|
+
|
1256
|
+
* README.DEV
|
1257
|
+
|
1258
|
+
Newly added guideline document for the contributors.
|
1259
|
+
|
1260
|
+
* README
|
1261
|
+
|
1262
|
+
Updated and added instructions on RubyGems.
|
1263
|
+
|
1264
|
+
2005-09-23 Toshiaki Katayama <k@bioruby.org>
|
1265
|
+
|
1266
|
+
* bin/bioruby, lib/bio/shell.rb, lib/bio/shell/core.rb,
|
1267
|
+
lib/bio/shell/session.rb, lib/bio/shell/plugin/seq.rb,
|
1268
|
+
lib/bio/shell/flatfile.rb, lib/bio/shell/obda.rb
|
1269
|
+
|
1270
|
+
Newly added BioRuby shell, the command line user interface.
|
1271
|
+
Try 'bioruby' command in your terminal.
|
1272
|
+
|
1273
|
+
* doc/Changes-0.7.rd
|
1274
|
+
|
1275
|
+
Newly added document describing incompatible and important
|
1276
|
+
changes between the BioRuby 0.6 and 0.7 versions.
|
1277
|
+
|
1278
|
+
* lib/bio/sequence.rb
|
1279
|
+
|
1280
|
+
Bio::Sequence.guess, Bio::Sequence#guess methods are added
|
1281
|
+
which guess the sequence type by following fomula (default
|
1282
|
+
value for the threshold is 0.9).
|
1283
|
+
|
1284
|
+
number of ATGC
|
1285
|
+
--------------------------------------- > threshold
|
1286
|
+
number of other chars - number of N
|
1287
|
+
|
1288
|
+
2005-09-10 Naohisa Goto <ng@bioruby.org>
|
1289
|
+
|
1290
|
+
* lib/bio.rb, lib/bio/appl/blast.rb, lib/bio/appl/blast/format0.rb,
|
1291
|
+
lib/bio/appl/blast/report.rb, lib/bio/appl/clustalw.rb,
|
1292
|
+
lib/bio/appl/fasta.rb, lib/bio/appl/fasta/format10.rb,
|
1293
|
+
lib/bio/appl/hmmer.rb, lib/bio/appl/hmmer/report.rb,
|
1294
|
+
lib/bio/appl/mafft.rb, lib/bio/appl/psort.rb,
|
1295
|
+
lib/bio/appl/psort/report.rb, lib/bio/appl/sim4.rb,
|
1296
|
+
lib/bio/db/genbank/ddbj.rb, lib/bio/io/flatfile/bdb.rb,
|
1297
|
+
lib/bio/io/flatfile/index.rb, lib/bio/io/flatfile/indexer.rb
|
1298
|
+
|
1299
|
+
fixed autoload problem
|
1300
|
+
|
1301
|
+
* lib/bio/appl/blast.rb, lib/bio/appl/blast/report.rb
|
1302
|
+
|
1303
|
+
Bio::Blast.reports method was moved from lib/bio/appl/blast/report.rb
|
1304
|
+
to lib/bio/appl/blast.rb for autoload.
|
1305
|
+
|
1306
|
+
2005-08-31 Toshiaki Katayama <k@bioryby.org>
|
1307
|
+
|
1308
|
+
* BioRuby 0.6.4 is released.
|
1309
|
+
|
1310
|
+
* doc/KEGG_API.rd
|
1311
|
+
|
1312
|
+
Newly added English version of the KEGG API manual.
|
1313
|
+
|
1314
|
+
* lib/bio/aa.rb
|
1315
|
+
|
1316
|
+
the 'one2name' method introduced in 0.6.3 is fixed and added 'one'
|
1317
|
+
and 'three' methods as aliases for 'to_1' and 'to_3' methods.
|
1318
|
+
|
1319
|
+
2005-08-31 Naohisa Goto <ng@bioruby.org>
|
1320
|
+
|
1321
|
+
* removed unused file lib/bio/appl/factory.rb
|
1322
|
+
(the functionality had been integrated into lib/bio/command.rb)
|
1323
|
+
|
1324
|
+
* doc/Tutorial.rd
|
1325
|
+
|
1326
|
+
Newly added an English translation of the Japanese tutorial.
|
1327
|
+
|
1328
|
+
2005-08-16 Naohisa Goto <ng@bioruby.org>
|
1329
|
+
|
1330
|
+
* lib/bio/command.rb
|
1331
|
+
|
1332
|
+
Newly added Bio::Command::Tools module.
|
1333
|
+
Bio::Command::Tools is a collection of useful methods
|
1334
|
+
for execution of external commands.
|
1335
|
+
|
1336
|
+
* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb,
|
1337
|
+
lib/bio/appl/hmmer.rb, lib/bio/io/fastacmd.rb
|
1338
|
+
|
1339
|
+
For security reason, shell special characters are escaped.
|
1340
|
+
|
1341
|
+
* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb, lib/bio/appl/hmmer.rb
|
1342
|
+
|
1343
|
+
Options are stored with an array (@options).
|
1344
|
+
#options and #opions= methods are added.
|
1345
|
+
|
1346
|
+
* lib/bio/appl/blast.rb, lib/bio/appl/fasta.rb
|
1347
|
+
|
1348
|
+
Bio::Blast.remote and Bio::Fasta.remote is fixed to work
|
1349
|
+
with the recent change of the GenomeNet.
|
1350
|
+
|
1351
|
+
2005-08-11 Toshiaki Katayama <k@bioruby.org>
|
1352
|
+
|
1353
|
+
* Sequence#to_re method to have compatibility with 0.6.2 for RNA
|
1354
|
+
|
1355
|
+
* Fixed Bio::Fastacmd#fetch to work
|
1356
|
+
|
1357
|
+
* Bio::Fastacmd and Bio::Bl2seq classes (introduced in 0.6.3) are
|
1358
|
+
renamed to Bio::Blast::Fastacmd, Bio::Blast::Bl2seq respectively.
|
1359
|
+
|
1360
|
+
2005-08-09 Toshiaki Katayama <k@bioruby.org>
|
1361
|
+
|
1362
|
+
* BioRuby 0.6.3 is released.
|
1363
|
+
|
1364
|
+
This version would be the final release to support Ruby 1.6 series
|
1365
|
+
(as long as no serious bug is found:).
|
1366
|
+
|
1367
|
+
* lib/bio/util/sirna.rb:
|
1368
|
+
|
1369
|
+
Newly added method for desing of siRNA, contributed by
|
1370
|
+
Itoshi Nikaido. The lib/bio/util/ directory if reserved
|
1371
|
+
for bioinfomatics algorithms implemented by pure Ruby.
|
1372
|
+
|
1373
|
+
* lib/bio/io/fastacmd.rb:
|
1374
|
+
|
1375
|
+
Newly added wrapper for NCBI fastacmd program, contributed by
|
1376
|
+
Shinji Shigenobu.
|
1377
|
+
|
1378
|
+
* lib/bio/appl/hmmer/report.rb:
|
1379
|
+
|
1380
|
+
Bug fixed by Masashi Fujita when the position of sequence
|
1381
|
+
rarely becomes '-' instead of digits.
|
1382
|
+
|
1383
|
+
2005-08-08 Mitsuteru Nakao <n@bioruby.org>
|
1384
|
+
|
1385
|
+
* lib/bio/db/embl/sptr.rb:
|
1386
|
+
|
1387
|
+
Added Bio::SPTR#protein_name and Bio::SPTR#synoyms methods.
|
1388
|
+
contributed by Luca Pireddu.
|
1389
|
+
|
1390
|
+
Changed Bio::SPTR#gn, Bio::SPTR#gene_name and
|
1391
|
+
Bio::SPTR#gene_names methods. contributed by Luca Pireddu.
|
1392
|
+
|
1393
|
+
2005-08-08 Naohisa Goto <ng@bioruby.org>
|
1394
|
+
|
1395
|
+
* lib/bio/appl/bl2seq/report.rb:
|
1396
|
+
|
1397
|
+
Newly added bl2seq (BLAST 2 sequences) output parser.
|
1398
|
+
|
1399
|
+
* lib/bio/appl/blast/format0.rb:
|
1400
|
+
|
1401
|
+
Added `self.class::` before F0dbstat.new for bl2seq/report.rb
|
1402
|
+
|
1403
|
+
2005-08-07 Toshiaki Katayama <k@bioruby.org>
|
1404
|
+
|
1405
|
+
* lib/bio/sequence.rb, lib/bio/data/na.rb, lib/bio/data/aa.rb:
|
1406
|
+
|
1407
|
+
Bio::NucleicAcid, Bio::AminoAcid classes are refactored to have
|
1408
|
+
Data module, and this module is included and extended to make
|
1409
|
+
all methods as both of instance methods and class methods.
|
1410
|
+
|
1411
|
+
Bio::Sequence::NA and AA classes are rewrited (molecular_weight,
|
1412
|
+
to_re methods) to use Bio::NucleicAcid.
|
1413
|
+
|
1414
|
+
Bio::Sequence::NA#molecular_weight method is fixed to subtract
|
1415
|
+
two hydrogens per each base.
|
1416
|
+
|
1417
|
+
* lib/bio/db/medline.rb: publication_type (pt) method is added.
|
1418
|
+
|
1419
|
+
2005-08-07 Naohisa Goto <ng@bioruby.org>
|
1420
|
+
|
1421
|
+
* lib/bio/db/genbank/common.rb:
|
1422
|
+
|
1423
|
+
Avoid NoMethodError (private method `chomp` called for nil:NilClass)
|
1424
|
+
when parsing features of
|
1425
|
+
|
1426
|
+
ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/
|
1427
|
+
Salmonella_typhimurium_LT2/AE006468.gbk
|
1428
|
+
|
1429
|
+
2005-07-11 Toshiaki Katayama <k@bioruby.org>
|
1430
|
+
|
1431
|
+
* bin/br_pmfetch.rb:
|
1432
|
+
|
1433
|
+
Added sort by page option (--sort page)
|
1434
|
+
|
1435
|
+
* lib/io/higet.rb:
|
1436
|
+
|
1437
|
+
Newly added Bio::HGC::HiGet class for HiGet SOAP service.
|
1438
|
+
|
1439
|
+
2005-06-28 Toshiaki Katayama <k@bioruby.org>
|
1440
|
+
|
1441
|
+
* gemspec.rb: newly added RubyGems spec file.
|
1442
|
+
|
1443
|
+
2005-06-21 Naohisa Goto <ng@bioruby.org>
|
1444
|
+
|
1445
|
+
* lib/bio/appl/blast/report.rb:
|
1446
|
+
|
1447
|
+
Newly added support for reading BLAST -m 7 result files
|
1448
|
+
through Bio::FlatFile by adding
|
1449
|
+
DELIMITER = "</BlastOutput>\n" to Bio::Blast::Report class.
|
1450
|
+
(Note that tab-delimited format (-m 8 and -m 9) are not yet
|
1451
|
+
supported by Bio::FlatFile)
|
1452
|
+
|
1453
|
+
* lib/bio/io/flatfile.rb:
|
1454
|
+
|
1455
|
+
Added file format autodetection of BLAST XML format.
|
1456
|
+
|
1457
|
+
2005-06-20 Naohisa Goto <ng@bioruby.org>
|
1458
|
+
|
1459
|
+
* lib/bio/appl/blast/format0.rb: added 'to_s' to store original entry
|
1460
|
+
|
1461
|
+
2005-04-04 Mitsuteru Nakao <n@bioruby.org>
|
1462
|
+
|
1463
|
+
* lib/bio/db/go.rb:
|
1464
|
+
|
1465
|
+
Newly added Bio::GO::External2go class for parsing external2go file.
|
1466
|
+
|
1467
|
+
2005-03-10 Naohisa Goto <ng@bioruby.org>
|
1468
|
+
|
1469
|
+
* lib/bio/io/flatfile.rb:
|
1470
|
+
|
1471
|
+
Added file format autodetection of Spidey (Bio::Spidey::Report).
|
1472
|
+
|
1473
|
+
2005-03-10 Naohisa Goto <ng@bioruby.org>
|
1474
|
+
|
1475
|
+
* lib/bio/io/flatfile.rb:
|
1476
|
+
|
1477
|
+
Added file format autodetection for Bio::KEGG::KO,
|
1478
|
+
Bio::KEGG::GLYCAN, Bio::KEGG::REACTION, Bio::Blat::Report
|
1479
|
+
and Bio::Sim4::Report.
|
1480
|
+
|
1481
|
+
In order to distinguish Bio::KEGG::REACTION and
|
1482
|
+
Bio::KEGG::COMPOUND, autodetection regexp. of
|
1483
|
+
Bio::KEGG::COMPOUND were modified.
|
1484
|
+
|
1485
|
+
2005-02-09 KATAYAMA Toshiaki <k@bioruby.org>
|
1486
|
+
|
1487
|
+
* lib/bio/db/kegg/genes.rb:
|
1488
|
+
|
1489
|
+
Added cu method which returns codon usage in Hash for the
|
1490
|
+
convenience (codon_usage method returns in Array or Fixnum).
|
1491
|
+
|
1492
|
+
2004-12-13 KATAYAMA Toshiaki <k@bioruby.org>
|
1493
|
+
|
1494
|
+
* BioRuby 0.6.2 released.
|
1495
|
+
|
1496
|
+
* test/all_tests.rb:
|
1497
|
+
|
1498
|
+
Unit tests for some classes are newly incorporated by
|
1499
|
+
Moses Hohman. You can try it by 'ruby install.rb test'
|
1500
|
+
|
1501
|
+
* lib/bio/appl/spidey/report.rb:
|
1502
|
+
|
1503
|
+
Newly added Spidey result parser class.
|
1504
|
+
|
1505
|
+
* lib/bio/appl/blat/report.rb:
|
1506
|
+
|
1507
|
+
Newly added BLAT result parser class.
|
1508
|
+
|
1509
|
+
* fixes and improvements:
|
1510
|
+
* lib/bio/appl/blast/blast/format0.rb
|
1511
|
+
* minor fix for the Blast default format parser
|
1512
|
+
* lib/bio/alignment.rb
|
1513
|
+
* Alignment class
|
1514
|
+
* lib/bio/db/prosite.rb
|
1515
|
+
* bug reported by Rolv Seehuus is fixed
|
1516
|
+
* some methods are added
|
1517
|
+
|
1518
|
+
2004-10-25 KATAYAMA Toshiaki <k@bioruby.org>
|
1519
|
+
|
1520
|
+
* lib/bio/db/{compound.rb,reaction.rb,glycan.rb}:
|
1521
|
+
|
1522
|
+
Newly added parser for KEGG REACTION and KEGG GLYCAN database
|
1523
|
+
entries, fix for KEGG COMPOUND parser to support the new format.
|
1524
|
+
|
1525
|
+
2004-10-09 GOTO Naohisa <ng@bioruby.org>
|
1526
|
+
|
1527
|
+
* lib/bio/appl/sim4.rb
|
1528
|
+
|
1529
|
+
Newly added sim4 wrapper class.
|
1530
|
+
This is test version, specs would be changed frequently.
|
1531
|
+
|
1532
|
+
* lib/bio/appl/sim4/report.rb
|
1533
|
+
|
1534
|
+
Newly added sim4 result parser class.
|
1535
|
+
|
1536
|
+
2004-08-25 KATAYAMA Toshiaki <k@bioruby.org>
|
1537
|
+
|
1538
|
+
* BioRuby 0.6.1 released.
|
1539
|
+
* fix for the packaging miss of 0.6.0
|
1540
|
+
* bin/*.rb are renamed to bin/br_*.rb (similar to the BioPerl's
|
1541
|
+
convention: bp_*.pl)
|
1542
|
+
|
1543
|
+
2004-08-24 KATAYAMA Toshiaki <k@bioruby.org>
|
1544
|
+
|
1545
|
+
* BioRuby 0.6.0 released.
|
1546
|
+
* many fixes for Ruby 1.8
|
1547
|
+
* updated for genome.ad.jp -> genome.jp transition
|
1548
|
+
|
1549
|
+
* lib/bio/db/pdb.rb
|
1550
|
+
|
1551
|
+
Newly added parser for PDB contributed by Alex Gutteridge (EBI).
|
1552
|
+
|
1553
|
+
* lib/bio/data/codontable.rb
|
1554
|
+
|
1555
|
+
Bio::CodonTable is rewrited to be a class instead of static variable.
|
1556
|
+
Now it can hold table definition, start codons, stop codons and
|
1557
|
+
added methods to detect start/stop codons and reverse translation.
|
1558
|
+
|
1559
|
+
Also includes sample code to show codon table in ANSI colored
|
1560
|
+
ascii art, have fun.
|
1561
|
+
|
1562
|
+
* lib/bio/sequence.rb
|
1563
|
+
|
1564
|
+
Bio::Sequence::NA#translate is rewrited to accept an user defined
|
1565
|
+
codon table as a Bio::CodonTable object and any character can be
|
1566
|
+
specified for the unknown codon. This method runs about 30% faster
|
1567
|
+
than ever before.
|
1568
|
+
|
1569
|
+
Bio::Sequence::AA#to_re method is added for the symmetry.
|
1570
|
+
|
1571
|
+
Bio::Seq will be changed to hold generic rich sequence features.
|
1572
|
+
This means Bio::Seq is no longer an alias of Bio::Sequence but
|
1573
|
+
is a sequence object model, something like contents of a GenBank
|
1574
|
+
entry, common in BioPerl, BioJava etc.
|
1575
|
+
|
1576
|
+
* lib/bio/io/soapwsdl.rb
|
1577
|
+
|
1578
|
+
Newly added common interface for SOAP/WSDL in BioRuby
|
1579
|
+
used by keggapi.rb, ddbjxml.rb.
|
1580
|
+
|
1581
|
+
* lib/bio/io/keggapi.rb
|
1582
|
+
|
1583
|
+
Completely rewrited to support KEGG API v3.0
|
1584
|
+
|
1585
|
+
* lib/bio/io/esoap.rb
|
1586
|
+
|
1587
|
+
Newly added client library for Entrez Utilities SOAP interface.
|
1588
|
+
|
1589
|
+
* lib/bio/db/genbank, lib/bio/db/embl
|
1590
|
+
|
1591
|
+
Refactored to use common.rb as a common module.
|
1592
|
+
|
1593
|
+
* bin/pmfetch.rb
|
1594
|
+
|
1595
|
+
Newly added command to search PubMed.
|
1596
|
+
|
1597
|
+
* bin/biofetch.rb, flatfile.rb, biogetseq.rb
|
1598
|
+
|
1599
|
+
Renamed to have .rb suffix.
|
1600
|
+
|
1601
|
+
* sample/biofetch.rb
|
1602
|
+
|
1603
|
+
Rewrited to use KEGG API instead of DBGET
|
1604
|
+
|
1605
|
+
|
1606
|
+
2003-10-13 KATAYAMA Toshiaki <k@bioruby.org>
|
1607
|
+
|
1608
|
+
* BioRuby 0.5.3 released.
|
1609
|
+
|
1610
|
+
Fixed bugs in Blast XML parsers: xmlparser.rb is fixed not to
|
1611
|
+
omit the string after ' and " in sequence definitions,
|
1612
|
+
rexml.rb is fixed not to raise NoMethodError as "undefined
|
1613
|
+
method `each_element_with_text' for nil:NilClass".
|
1614
|
+
|
1615
|
+
2003-10-07 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
|
1616
|
+
|
1617
|
+
* lib/bio/db/nbrf.rb
|
1618
|
+
|
1619
|
+
Newly added NBRF/PIR flatfile sequence format class.
|
1620
|
+
|
1621
|
+
2003-09-30 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
|
1622
|
+
|
1623
|
+
* lib/bio/db/pdb.rb
|
1624
|
+
|
1625
|
+
Newly added PDB database flatfile format class.
|
1626
|
+
This is pre-alpha version, specs shall be changed frequently.
|
1627
|
+
|
1628
|
+
2003-08-22 KATAYAMA Toshiaki <k@bioruby.org>
|
1629
|
+
|
1630
|
+
* BioRuby 0.5.2 released.
|
1631
|
+
|
1632
|
+
Fixed to be loaded in Ruby 1.8.0 without warnings.
|
1633
|
+
|
1634
|
+
* doc/KEGG_API.rd.ja
|
1635
|
+
|
1636
|
+
Newly added a Japanese document on the KEGG API.
|
1637
|
+
|
1638
|
+
2003-08-12 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
|
1639
|
+
|
1640
|
+
* lib/bio/appl/blast/format0.rb
|
1641
|
+
|
1642
|
+
Newly added NCBI BLAST default (-m 0) output parser,
|
1643
|
+
which may be 5-10x faster than BioPerl's parser.
|
1644
|
+
This is alpha version, specs may be frequently changed.
|
1645
|
+
PHI-BLAST support is still incomplete.
|
1646
|
+
Ruby 1.8 recommended. In ruby 1.6, you need strscan.
|
1647
|
+
|
1648
|
+
* lib/bio/appl/blast/wublast.rb
|
1649
|
+
|
1650
|
+
Newly added WU-BLAST default output parser.
|
1651
|
+
This is alpha version, specs may be frequently changed.
|
1652
|
+
Support for parameters and statistics are still incomplete.
|
1653
|
+
Ruby 1.8 recommended. In ruby 1.6, you need strscan.
|
1654
|
+
|
1655
|
+
2003-07-25 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp>
|
1656
|
+
|
1657
|
+
* lib/bio/alignment.rb:
|
1658
|
+
|
1659
|
+
Newly added multiple sequence alignment class.
|
1660
|
+
|
1661
|
+
* lib/bio/appl/alignfactory.rb:
|
1662
|
+
|
1663
|
+
Newly added template class for multiple alignment software.
|
1664
|
+
|
1665
|
+
* lib/bio/appl/clustalw.rb:
|
1666
|
+
|
1667
|
+
Newly added CLUSTAL W wrapper.
|
1668
|
+
<http://www.ebk.ac.uk/clustalw/>
|
1669
|
+
<ftp://ftp.ebk.ac.uk/pub/software/unix/clustalw/>
|
1670
|
+
|
1671
|
+
* lib/bio/appl/clustalw/report.rb:
|
1672
|
+
|
1673
|
+
Newly added CLUSTAL W result data (*.aln file) parser.
|
1674
|
+
|
1675
|
+
* lib/bio/appl/mafft.rb, lib/bio/appl/mafft/report.rb:
|
1676
|
+
|
1677
|
+
Newly added MAFFT wrapper and report parser.
|
1678
|
+
(MAFFT is a multiple sequence alignment program based on FFT.)
|
1679
|
+
<http://www.biophys.kyoto-u.ac.jp/~katoh/programs/align/mafft/>
|
1680
|
+
|
1681
|
+
2003-07-16 KATAYAMA Toshiaki <k@bioruby.org>
|
1682
|
+
|
1683
|
+
* BioRuby version 0.5.1 released.
|
1684
|
+
|
1685
|
+
* lib/bio/sequence.rb: some methods (using 'rna?' internally) were
|
1686
|
+
temporally unusable by the changes in 0.5.0 is fixed.
|
1687
|
+
|
1688
|
+
* lib/bio/io/flatfile.rb: autodetection failure of the fasta entry
|
1689
|
+
without sequence is fixed. FlatFile.auto method is added.
|
1690
|
+
|
1691
|
+
* lib/bio/db.rb: sugtag2array fixed. DB.open now accepts IO/ARGF.
|
1692
|
+
|
1693
|
+
* lib/bio/db/embl.rb: references method is added.
|
1694
|
+
|
1695
|
+
|
1696
|
+
2003-06-25 KATAYAMA Toshiaki <k@bioruby.org>
|
1697
|
+
|
1698
|
+
* BioRuby version 0.5.0 released.
|
1699
|
+
|
1700
|
+
* lib/bio/appl/blast/report.rb:
|
1701
|
+
|
1702
|
+
Refactored from xmlparser.rb, rexml.rb, and format8.rb files.
|
1703
|
+
Formats are auto detected and parsers are automatically
|
1704
|
+
selected by checking whether XMLParser or REXML are installed.
|
1705
|
+
You can call simply as
|
1706
|
+
Bio::Blast::Report.new(blastoutput)
|
1707
|
+
or you can choose parsers/format explicitly by
|
1708
|
+
Bio::Blast::Report.xmlparser(format7blastoutput)
|
1709
|
+
Bio::Blast::Report.rexml(fomat7blastoutput)
|
1710
|
+
Bio::Blast::Report.tab(format8blastoutput)
|
1711
|
+
You can also use newly added class method reports for multiple
|
1712
|
+
xml blast output.
|
1713
|
+
Bio::Blast.reports(output) # output can be IO or String
|
1714
|
+
|
1715
|
+
* lib/bio/appl/fasta/report.rb:
|
1716
|
+
|
1717
|
+
Refactored from format10.rb, format6.rb and sample/* files.
|
1718
|
+
|
1719
|
+
* lib/bio/appl/hmmer/report.rb:
|
1720
|
+
|
1721
|
+
Bug fix and clean up.
|
1722
|
+
|
1723
|
+
* bin/biogetseq:
|
1724
|
+
|
1725
|
+
Newly added OBDA (BioRegistry) entry retrieval command.
|
1726
|
+
|
1727
|
+
* etc/bioinformatics/seqdatabase.ini, lib/bio/io/registry.rb:
|
1728
|
+
Updated for new OBDA spec (Singapore version).
|
1729
|
+
Including config file versioning and changes in tag names,
|
1730
|
+
support for OBDA_SEARCH_PATH environmental variable.
|
1731
|
+
|
1732
|
+
* lib/bio/io/keggapi.rb:
|
1733
|
+
|
1734
|
+
Newly added KEGG API client library.
|
1735
|
+
<http://www.genome.ad.jp/kegg/soap/>
|
1736
|
+
|
1737
|
+
* lib/bio/io/ddbjxml.rb:
|
1738
|
+
|
1739
|
+
Newly added DDBJ XML client library (test needed).
|
1740
|
+
<http://xml.nig.ac.jp/>
|
1741
|
+
|
1742
|
+
* lib/bio/io/das.rb:
|
1743
|
+
|
1744
|
+
Newly added BioDAS client library.
|
1745
|
+
|
1746
|
+
* lib/bio/db/gff.rb:
|
1747
|
+
|
1748
|
+
Newly added GFF format parser/store library.
|
1749
|
+
|
1750
|
+
* lib/bio/appl/tmhmm/report.rb:
|
1751
|
+
|
1752
|
+
Newly added TMHMM report parser.
|
1753
|
+
<http://www.cbs.dtu.dk/services/TMHMM/>
|
1754
|
+
|
1755
|
+
* lib/bio/appl/targetp/report.rb:
|
1756
|
+
|
1757
|
+
Newly added TargetP report parser.
|
1758
|
+
<http://www.cbs.dtu.dk/services/TargetP/>
|
1759
|
+
|
1760
|
+
* lib/bio/appl/sosui/report.rb:
|
1761
|
+
|
1762
|
+
Newly added SOSUI report parser.
|
1763
|
+
<http://sosui.proteome.bio.tuat.ac.jp/cgi-bin/sosui.cgi>
|
1764
|
+
|
1765
|
+
* lib/bio/appl/psort/report.rb:
|
1766
|
+
|
1767
|
+
Newly added PSORT report parser.
|
1768
|
+
<http://www.psort.org/>, <http://psort.ims.u-tokyo.ac.jp/>
|
1769
|
+
|
1770
|
+
* lib/bio/appl/genscan/report.rb:
|
1771
|
+
|
1772
|
+
Newly added GENSCAN report parser.
|
1773
|
+
<http://genes.mit.edu/GENSCAN.html>
|
1774
|
+
|
1775
|
+
* lib/bio/db/prosite.rb: bug fix in ps2re method.
|
1776
|
+
|
1777
|
+
* lib/bio/db/fantom.rb:
|
1778
|
+
|
1779
|
+
Newly added FANTOM database parser (XML).
|
1780
|
+
<http://fantom2.gsc.riken.go.jp/>
|
1781
|
+
|
1782
|
+
* lib/bio/db/go.rb:
|
1783
|
+
|
1784
|
+
Newly added GO parser.
|
1785
|
+
<http://www.geneontology.org/>
|
1786
|
+
|
1787
|
+
* lib/bio/feature.rb:
|
1788
|
+
|
1789
|
+
'each' method now accepts an argument to select specific feature.
|
1790
|
+
|
1791
|
+
* lib/bio/db/fasta.rb: definition=, data= to change comment line.
|
1792
|
+
|
1793
|
+
* lib/bio/db/genbank.rb:
|
1794
|
+
|
1795
|
+
References and features now accept a block. 'acc_version' method
|
1796
|
+
is added to return the Accsession.Version string.
|
1797
|
+
'accession' method now returns Accession part of the acc_version.
|
1798
|
+
'version' method now returns Version part of the acc_version as
|
1799
|
+
an integer.
|
1800
|
+
|
1801
|
+
* lib/bio/db/keggtab.rb:
|
1802
|
+
|
1803
|
+
Rewrited for bug fix and clean up (note: some methods renamed!)
|
1804
|
+
* gsub('abrev', 'abbrev') in method names
|
1805
|
+
* db_path_by_keggorg is changed to db_path_by_abbrev
|
1806
|
+
* @bio_root is changed to @bioroot (ENV['BIOROOT'] overrides)
|
1807
|
+
* Bio::KEGG::DBname is changed to Bio::KEGG::Keggtab::DB
|
1808
|
+
* @database is added (a hash with its key db_abbreb)
|
1809
|
+
* database, name, path methods added with its argument db_abbreb
|
1810
|
+
|
1811
|
+
* lib/bio/io/flatfile.rb:
|
1812
|
+
|
1813
|
+
Enumerable mix-in is included.
|
1814
|
+
|
1815
|
+
* lib/bio/io/flatfile/indexer.rb:
|
1816
|
+
|
1817
|
+
Indexing of the FASTA format file is now supported with various
|
1818
|
+
type of definition line.
|
1819
|
+
|
1820
|
+
* bin/dbget:
|
1821
|
+
|
1822
|
+
Removed (moved under sample directory because the port of the
|
1823
|
+
dbget server is now closed).
|
1824
|
+
|
1825
|
+
* install.rb:
|
1826
|
+
|
1827
|
+
Changed to use setup 3.1.4 to avoid installing CVS/ directory.
|
1828
|
+
|
1829
|
+
* sample/goslim.rb:
|
1830
|
+
|
1831
|
+
Added a sample to generate histogram from GO slim.
|
1832
|
+
|
1833
|
+
* sample/tdiary.rb:
|
1834
|
+
|
1835
|
+
Added for tDiary <http://www.tdiary.org/> users. have fun. :)
|
1836
|
+
|
1837
|
+
2003-01-28 KATAYAMA Toshiaki <k@bioruby.org>
|
1838
|
+
|
1839
|
+
* BioRuby version 0.4.0 released.
|
1840
|
+
* bin/bioflat:
|
1841
|
+
* newly added for the BioFlat indexing
|
1842
|
+
* lib/bio/io/flatfile.rb, flatfile/{indexer.rb,index.rb,bdb.rb}:
|
1843
|
+
* flatfile indexing is supported by N. Goto
|
1844
|
+
* lib/bio/db/genbank.rb: changed to contain common methods only
|
1845
|
+
* lib/bio/db/genbank/genbank.rb
|
1846
|
+
* lib/bio/db/genbank/genpept.rb
|
1847
|
+
* lib/bio/db/genbank/refseq.rb
|
1848
|
+
* lib/bio/db/genbank/ddbj.rb
|
1849
|
+
* lib/bio/db/embl.rb: changed to contain common methods only
|
1850
|
+
* lib/bio/db/embl/embl.rb
|
1851
|
+
* lib/bio/db/embl/sptr.rb
|
1852
|
+
* lib/bio/db/embl/swissprot.rb
|
1853
|
+
* lib/bio/db/embl/trembl.rb
|
1854
|
+
* lib/bio/appl/emboss.rb:
|
1855
|
+
* added - just a generic wrapper, no specific parsers yet.
|
1856
|
+
* lib/bio/appl/hmmer.rb:
|
1857
|
+
* added - execution wrapper
|
1858
|
+
* lib/bio/appl/hmmer/report.rb:
|
1859
|
+
* added - parsers for hmmsearch, hmmpfam contributed by H. Suga
|
1860
|
+
* lib/bio/db.rb: open method added for easy use of flatfile.
|
1861
|
+
* lib/bio/db/kegg/genes.rb:
|
1862
|
+
* fixed bug in codon_usage method in the case of long sequence >999
|
1863
|
+
* eclinks, splinks, pathways, gbposition, chromosome methods added
|
1864
|
+
* lib/bio/db/aaindex.rb:
|
1865
|
+
* adapted for the new AAindex2 format (release >= 6.0).
|
1866
|
+
* lib/bio/db/fasta.rb: entry_id is changed to return first word only
|
1867
|
+
* lib/bio/data/na.rb, aa.rb, keggorg.rb:
|
1868
|
+
* moved under class NucleicAcid, AminoAcid, KEGG (!)
|
1869
|
+
* in the test codes, DBGET is replaced by BioFetch
|
1870
|
+
|
1871
|
+
2002-08-30 Yoshinori K. Okuji <okuji@enbug.org>
|
1872
|
+
|
1873
|
+
* lib/bio/matrix.rb: Removed.
|
1874
|
+
* lib/bio/db/aaindex.rb: Require matrix instead of bio/matrix.
|
1875
|
+
* lib/bio/db/transfac.rb: Likewise.
|
1876
|
+
* lib/bio/pathway.rb: Likewise.
|
1877
|
+
(Pathway#dump_matrix): Don't use Matrix#dump.
|
1878
|
+
|
1879
|
+
2002-07-30 KATAYAMA Toshiaki <k@bioruby.org>
|
1880
|
+
|
1881
|
+
* BioRuby version 0.3.9 released.
|
1882
|
+
* lib/bio/location.rb:
|
1883
|
+
* Locations#length (size) methods added (contributed by N. Goto)
|
1884
|
+
* Locations#relative method added (contributed by N. Goto)
|
1885
|
+
* Locations#absolute method is renamed from offset
|
1886
|
+
* Locations#offset, offset_aa methods removed
|
1887
|
+
* use absolute/relative(n, :aa) for _aa
|
1888
|
+
* Locations#[], range methods added
|
1889
|
+
* Location#range method added
|
1890
|
+
* lib/bio/db/embl.rb:
|
1891
|
+
* fix accession method.
|
1892
|
+
* lib/bio/db/genpept.rb:
|
1893
|
+
* temporally added - in the next release, we will make refactoring.
|
1894
|
+
* lib/bio/reference.rb:
|
1895
|
+
* in bibtex and bibitem format, "PMIDnum" is changed to "PMID:num".
|
1896
|
+
* lib/bio/io/pubmed.rb:
|
1897
|
+
* esearch, efetch methods are added.
|
1898
|
+
* lib/bio/db/aaindex.rb:
|
1899
|
+
* fix serious bug in the index method to support negative values.
|
1900
|
+
* lib/bio/db.rb:
|
1901
|
+
* fix fetch method to cut tag without fail.
|
1902
|
+
* lib/bio/extend.rb:
|
1903
|
+
* added first_line_only option for the prefix in fill method.
|
1904
|
+
* doc/Tutorial.rd.ja:
|
1905
|
+
* added docs on BibTeX etc.
|
1906
|
+
|
1907
|
+
2002-06-26 KATAYAMA Toshiaki <k@bioruby.org>
|
1908
|
+
|
1909
|
+
* BioRuby version 0.3.8 released.
|
1910
|
+
* lib/bio/sequence.rb:
|
1911
|
+
* normalize! method added for clean up the object itself.
|
1912
|
+
* 'to_seq' method was renamed to 'seq' (!)
|
1913
|
+
* to_xxxx should be used when the class of the object changes.
|
1914
|
+
* lib/bio/appl/blast/xmparser.rb:
|
1915
|
+
* each_iteration, each_hit, each, hits, statistics, message methods
|
1916
|
+
are added in Report class.
|
1917
|
+
* statistics, message methods are added in Iteration class.
|
1918
|
+
* methods compatible with Fasta::Report::Hit are added in Hit class.
|
1919
|
+
* lib/bio/appl/blast/rexml.rb:
|
1920
|
+
* many APIs were changed to follow the xmlparser.rb's. (!)
|
1921
|
+
* lib/bio/appl/{blast.rb,fasta.rb]:
|
1922
|
+
* class method parser() is added for loading specified Report class.
|
1923
|
+
* etc/bioinformatics/seqdatabase.ini: added for OBDA (!)
|
1924
|
+
* sample setup for BioRegistry - Open Bio Sequence Database Access.
|
1925
|
+
* lib/bio/extend.rb: added (!)
|
1926
|
+
* This module adds some functionarity to the existing classes and
|
1927
|
+
not loaded by default. User should require specifically if needed.
|
1928
|
+
* lib/bio/util/*: removed and merged into lib/bio/extend.rb (!)
|
1929
|
+
* lib/bio/id.rb: removed (!)
|
1930
|
+
* lib/bio/db/{embl.rb,sptr.rb,transfac.rb}: added entry_id
|
1931
|
+
* lib/bio/data/keggorg.rb: updated
|
1932
|
+
* sample/genes2* sample/genome2*: updated
|
1933
|
+
* doc/Tutrial.rd.ja: updated
|
1934
|
+
|
1935
|
+
2002-06-19 KATAYAMA Toshiaki <k@bioruby.org>
|
1936
|
+
|
1937
|
+
* BioRuby version 0.3.7 released.
|
1938
|
+
* lib/bio/sequence.rb: Sequence inherits String again (!)
|
1939
|
+
* lib/bio/db.rb, db/embl.rb, db/sptr.rb: moved EMBL specific methods
|
1940
|
+
|
1941
|
+
2002-06-18 KATAYAMA Toshiaki <k@bioruby.org>
|
1942
|
+
|
1943
|
+
* lib/bio/feature.rb: Bio::Feature#[] method added
|
1944
|
+
* doc/Tutrial.rd.ja: changed to use Feature class
|
1945
|
+
|
1946
|
+
2002-05-28 KATAYAMA Toshiaki <k@bioruby.org>
|
1947
|
+
|
1948
|
+
* lib/bio/appl/fasta.rb: parser separated, API renewal (!)
|
1949
|
+
* lib/bio/appl/fasta/format10.rb: moved from fasta.rb
|
1950
|
+
|
1951
|
+
* lib/bio/appl/blast.rb: parser separated, API renewal (!)
|
1952
|
+
* lib/bio/appl/blast/format8.rb: newly added
|
1953
|
+
* lib/bio/appl/blast/rexml.rb: newly added
|
1954
|
+
* lib/bio/appl/blast/xmlparser.rb: moved from blast.rb
|
1955
|
+
|
1956
|
+
2002-05-16 KATAYAMA Toshiaki <k@bioruby.org>
|
1957
|
+
|
1958
|
+
* lib/bio/sequence.rb: added alias 'Seq' for class Sequence
|
1959
|
+
* lib/bio/db/fasta.rb: entry method added
|
1960
|
+
|
1961
|
+
2002-05-15 KATAYAMA Toshiaki <k@bioruby.org>
|
1962
|
+
|
1963
|
+
* lib/bio/io/dbget.rb: bug fixed for pfam (was wrongly skip # lines)
|
1964
|
+
* lib/bio/location.rb: offset method added, eased range check
|
1965
|
+
|
1966
|
+
2002-04-26 KATAYAMA Toshiaki <k@bioruby.org>
|
1967
|
+
|
1968
|
+
* sample/biofetch.rb: new 'info=' option added
|
1969
|
+
|
1970
|
+
2002-04-22 KATAYAMA Toshiaki <k@bioruby.org>
|
1971
|
+
|
1972
|
+
* lib/bio/appl/fasta.rb: follow changes made at fasta.genome.ad.jp
|
1973
|
+
* sample/gb2tab.rb: fixed to use authors.inspect for reference
|
1974
|
+
|
1975
|
+
2002-04-15 KATAYAMA Toshiaki <k@bioruby.org>
|
1976
|
+
|
1977
|
+
* sample/gb2fasta.rb: changed to follow new genbank.rb spec.
|
1978
|
+
* sample/gt2fasta.rb: changed to follow new genbank.rb spec.
|
1979
|
+
* sample/gbtab2mysql.rb: added for loading tab delimited data.
|
1980
|
+
|
1981
|
+
2002/04/08
|
1982
|
+
* version 0.3.6 released -k
|
1983
|
+
* fixed inconsistency among db.rb, genbank.rb, genome.rb -k
|
1984
|
+
* lib/bio/db/genbank.rb : serious bug fixed in locus method -k
|
1985
|
+
* lib/bio/feature.rb : method name 'type' has changed -k
|
1986
|
+
|
1987
|
+
2002/03/27
|
1988
|
+
* sample/gb2tab.rb changed to follow new genbank.rb w/ new schema -k
|
1989
|
+
|
1990
|
+
2002/03/26
|
1991
|
+
* sample/gb2tab.rb use ruby instead of perl in the example -o
|
1992
|
+
* sample/gb2fasta.rb updated -o
|
1993
|
+
|
1994
|
+
2002/03/11
|
1995
|
+
* version 0.3.5 released -k
|
1996
|
+
|
1997
|
+
2002/03/04
|
1998
|
+
* lib/bio/sequence.rb to_a, to_ary methods renamed to names, codes -k
|
1999
|
+
* sample/biofetch.rb added for BioFetch server -k
|
2000
|
+
* bin/biofetch added for BioFetch client -k
|
2001
|
+
* lib/bio/io/fetch.rb added for BioFetch library -k
|
2002
|
+
* lib/bio/io/sql.rb added for BioSQL -k
|
2003
|
+
* lib/bio/io/registry.rb added for BioDirectory/Registry -k
|
2004
|
+
* lib/bio/feature.rb added for BioSQL, GenBank, EMBL etc. -k
|
2005
|
+
* lib/bio/db/genbank.rb rewrited to use Features, References -k
|
2006
|
+
* lib/bio/db/{genes,genome}.rb clean up -k
|
2007
|
+
* lib/bio/reference.rb added class References -k
|
2008
|
+
|
2009
|
+
2002/02/05
|
2010
|
+
* changed to use 'cgi' instead of 'cgi-lib' -n,k
|
2011
|
+
|
2012
|
+
2002/01/31
|
2013
|
+
* version 0.3.4 released -k
|
2014
|
+
* lib/bio/db/genbank.rb -k
|
2015
|
+
* fix for multiple 'allele' in the feature key. (thanx Lixin)
|
2016
|
+
|
2017
|
+
2002/01/07
|
2018
|
+
* lib/bio/appl/blast.rb -n
|
2019
|
+
* remote blast support etc.
|
2020
|
+
|
2021
|
+
2001/12/18
|
2022
|
+
* lib/bio/id.rb -k
|
2023
|
+
* newly created
|
2024
|
+
* lib/bio/io/brdb.rb -k
|
2025
|
+
* newly created
|
2026
|
+
* lib/bio/db.rb -k
|
2027
|
+
* template methods are deleted
|
2028
|
+
* detailed docuement added
|
2029
|
+
* lib/bio/sequence.rb -k
|
2030
|
+
* to_fasta, complement, translate fixed (due to the changes made
|
2031
|
+
in 0.3.3)
|
2032
|
+
* Sequence::NA#initialize doesn't replace 'u' with 't' any longer
|
2033
|
+
* gc_percent, complement, translate, to_re, molecular_weight
|
2034
|
+
methods are adapted to this change
|
2035
|
+
* molecular_weight changed to calculate more precisely
|
2036
|
+
* test code added
|
2037
|
+
* lib/bio.rb -k
|
2038
|
+
* rescue for require 'bio/appl/blast' is deleted
|
2039
|
+
|
2040
|
+
2001/12/15
|
2041
|
+
* lib/bio/sequence.rb -o
|
2042
|
+
* Sequence#to_str added
|
2043
|
+
|
2044
|
+
2001/12/15
|
2045
|
+
* version 0.3.3 released -k
|
2046
|
+
|