wwood-bioruby 1.2.11

metadata

@@ -0,0 +1,543 @@
+--- !ruby/object:Gem::Specification 
+name: wwood-bioruby
+version: !ruby/object:Gem::Version 
+  version: 1.2.11
+platform: ruby
+authors: 
+- BioRuby project
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2009-01-18 00:00:00 -08:00
+default_executable: 
+dependencies: []
+
+description: BioRuby is a library for bioinformatics (biology + information science).
+email: staff@bioruby.org
+executables: []
+
+extensions: []
+
+extra_rdoc_files: []
+
+files: 
+- VERSION.yml
+- README_DEV.rdoc
+- README.rdoc
+- bin/br_bioflat.rb
+- bin/br_biogetseq.rb
+- bin/br_pmfetch.rb
+- bin/br_biofetch.rb
+- bin/bioruby
+- lib/bio.rb
+- lib/bio
+- lib/bio/reference.rb
+- lib/bio/pathway.rb
+- lib/bio/util
+- lib/bio/util/restriction_enzyme
+- lib/bio/util/restriction_enzyme/single_strand.rb
+- lib/bio/util/restriction_enzyme/string_formatting.rb
+- lib/bio/util/restriction_enzyme/cut_symbol.rb
+- lib/bio/util/restriction_enzyme/analysis_basic.rb
+- lib/bio/util/restriction_enzyme/single_strand
+- lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb
+- lib/bio/util/restriction_enzyme/single_strand_complement.rb
+- lib/bio/util/restriction_enzyme/enzymes.yaml
+- lib/bio/util/restriction_enzyme/double_stranded.rb
+- lib/bio/util/restriction_enzyme/range
+- lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb
+- lib/bio/util/restriction_enzyme/range/sequence_range.rb
+- lib/bio/util/restriction_enzyme/range/cut_range.rb
+- lib/bio/util/restriction_enzyme/range/sequence_range
+- lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb
+- lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb
+- lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb
+- lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb
+- lib/bio/util/restriction_enzyme/range/cut_ranges.rb
+- lib/bio/util/restriction_enzyme/analysis.rb
+- lib/bio/util/restriction_enzyme/double_stranded
+- lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb
+- lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb
+- lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb
+- lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
+- lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb
+- lib/bio/util/sirna.rb
+- lib/bio/util/contingency_table.rb
+- lib/bio/util/color_scheme
+- lib/bio/util/color_scheme/strand.rb
+- lib/bio/util/color_scheme/buried.rb
+- lib/bio/util/color_scheme/turn.rb
+- lib/bio/util/color_scheme/taylor.rb
+- lib/bio/util/color_scheme/nucleotide.rb
+- lib/bio/util/color_scheme/zappo.rb
+- lib/bio/util/color_scheme/helix.rb
+- lib/bio/util/color_scheme/hydropathy.rb
+- lib/bio/util/restriction_enzyme.rb
+- lib/bio/util/color_scheme.rb
+- lib/bio/compat
+- lib/bio/compat/references.rb
+- lib/bio/compat/features.rb
+- lib/bio/io
+- lib/bio/io/ncbisoap.rb
+- lib/bio/io/dbget.rb
+- lib/bio/io/registry.rb
+- lib/bio/io/pubmed.rb
+- lib/bio/io/flatfile
+- lib/bio/io/flatfile/autodetection.rb
+- lib/bio/io/flatfile/bdb.rb
+- lib/bio/io/flatfile/indexer.rb
+- lib/bio/io/flatfile/index.rb
+- lib/bio/io/flatfile/buffer.rb
+- lib/bio/io/flatfile/splitter.rb
+- lib/bio/io/das.rb
+- lib/bio/io/ensembl.rb
+- lib/bio/io/ncbirest.rb
+- lib/bio/io/sql.rb
+- lib/bio/io/soapwsdl.rb
+- lib/bio/io/ddbjxml.rb
+- lib/bio/io/flatfile.rb
+- lib/bio/io/fetch.rb
+- lib/bio/io/hinv.rb
+- lib/bio/io/keggapi.rb
+- lib/bio/io/biosql
+- lib/bio/io/biosql/reference.rb
+- lib/bio/io/biosql/seqfeature.rb
+- lib/bio/io/biosql/taxon_name.rb
+- lib/bio/io/biosql/bioentry_path.rb
+- lib/bio/io/biosql/term_synonym.rb
+- lib/bio/io/biosql/bioentry_qualifier_value.rb
+- lib/bio/io/biosql/seqfeature_dbxref.rb
+- lib/bio/io/biosql/bioentry.rb
+- lib/bio/io/biosql/dbxref_qualifier_value.rb
+- lib/bio/io/biosql/location.rb
+- lib/bio/io/biosql/taxon.rb
+- lib/bio/io/biosql/location_qualifier_value.rb
+- lib/bio/io/biosql/config
+- lib/bio/io/biosql/config/database.yml
+- lib/bio/io/biosql/bioentry_reference.rb
+- lib/bio/io/biosql/bioentry_dbxref.rb
+- lib/bio/io/biosql/term_dbxref.rb
+- lib/bio/io/biosql/seqfeature_relationship.rb
+- lib/bio/io/biosql/ontology.rb
+- lib/bio/io/biosql/seqfeature_qualifier_value.rb
+- lib/bio/io/biosql/bioentry_relationship.rb
+- lib/bio/io/biosql/term_path.rb
+- lib/bio/io/biosql/seqfeature_path.rb
+- lib/bio/io/biosql/term_relationship.rb
+- lib/bio/io/biosql/comment.rb
+- lib/bio/io/biosql/term.rb
+- lib/bio/io/biosql/term_relationship_term.rb
+- lib/bio/io/biosql/biodatabase.rb
+- lib/bio/io/biosql/biosequence.rb
+- lib/bio/io/biosql/dbxref.rb
+- lib/bio/io/higet.rb
+- lib/bio/io/ebisoap.rb
+- lib/bio/io/fastacmd.rb
+- lib/bio/feature.rb
+- lib/bio/location.rb
+- lib/bio/map.rb
+- lib/bio/appl
+- lib/bio/appl/psort
+- lib/bio/appl/psort/report.rb
+- lib/bio/appl/pts1.rb
+- lib/bio/appl/mafft
+- lib/bio/appl/mafft/report.rb
+- lib/bio/appl/sosui
+- lib/bio/appl/sosui/report.rb
+- lib/bio/appl/paml
+- lib/bio/appl/paml/codeml.rb
+- lib/bio/appl/paml/common_report.rb
+- lib/bio/appl/paml/yn00.rb
+- lib/bio/appl/paml/baseml.rb
+- lib/bio/appl/paml/yn00
+- lib/bio/appl/paml/yn00/report.rb
+- lib/bio/appl/paml/common.rb
+- lib/bio/appl/paml/codeml
+- lib/bio/appl/paml/codeml/report.rb
+- lib/bio/appl/paml/codeml/rates.rb
+- lib/bio/appl/paml/baseml
+- lib/bio/appl/paml/baseml/report.rb
+- lib/bio/appl/sim4
+- lib/bio/appl/sim4/report.rb
+- lib/bio/appl/mafft.rb
+- lib/bio/appl/hmmer
+- lib/bio/appl/hmmer/report.rb
+- lib/bio/appl/fasta
+- lib/bio/appl/fasta/format10.rb
+- lib/bio/appl/spidey
+- lib/bio/appl/spidey/report.rb
+- lib/bio/appl/phylip
+- lib/bio/appl/phylip/distance_matrix.rb
+- lib/bio/appl/phylip/alignment.rb
+- lib/bio/appl/targetp
+- lib/bio/appl/targetp/report.rb
+- lib/bio/appl/fasta.rb
+- lib/bio/appl/psort.rb
+- lib/bio/appl/probcons.rb
+- lib/bio/appl/emboss.rb
+- lib/bio/appl/blast.rb
+- lib/bio/appl/hmmer.rb
+- lib/bio/appl/muscle.rb
+- lib/bio/appl/blast
+- lib/bio/appl/blast/ddbj.rb
+- lib/bio/appl/blast/report.rb
+- lib/bio/appl/blast/format8.rb
+- lib/bio/appl/blast/wublast.rb
+- lib/bio/appl/blast/rpsblast.rb
+- lib/bio/appl/blast/ncbioptions.rb
+- lib/bio/appl/blast/rexml.rb
+- lib/bio/appl/blast/remote.rb
+- lib/bio/appl/blast/format0.rb
+- lib/bio/appl/blast/xmlparser.rb
+- lib/bio/appl/blast/genomenet.rb
+- lib/bio/appl/bl2seq
+- lib/bio/appl/bl2seq/report.rb
+- lib/bio/appl/tcoffee.rb
+- lib/bio/appl/tmhmm
+- lib/bio/appl/tmhmm/report.rb
+- lib/bio/appl/blat
+- lib/bio/appl/blat/report.rb
+- lib/bio/appl/iprscan
+- lib/bio/appl/iprscan/report.rb
+- lib/bio/appl/clustalw.rb
+- lib/bio/appl/sim4.rb
+- lib/bio/appl/genscan
+- lib/bio/appl/genscan/report.rb
+- lib/bio/appl/gcg
+- lib/bio/appl/gcg/msf.rb
+- lib/bio/appl/gcg/seq.rb
+- lib/bio/appl/clustalw
+- lib/bio/appl/clustalw/report.rb
+- lib/bio/command.rb
+- lib/bio/sequence
+- lib/bio/sequence/adapter.rb
+- lib/bio/sequence/generic.rb
+- lib/bio/sequence/format_raw.rb
+- lib/bio/sequence/dblink.rb
+- lib/bio/sequence/format.rb
+- lib/bio/sequence/aa.rb
+- lib/bio/sequence/common.rb
+- lib/bio/sequence/compat.rb
+- lib/bio/sequence/na.rb
+- lib/bio/data
+- lib/bio/data/aa.rb
+- lib/bio/data/codontable.rb
+- lib/bio/data/na.rb
+- lib/bio/sequence.rb
+- lib/bio/tree.rb
+- lib/bio/shell.rb
+- lib/bio/shell
+- lib/bio/shell/web.rb
+- lib/bio/shell/demo.rb
+- lib/bio/shell/object.rb
+- lib/bio/shell/interface.rb
+- lib/bio/shell/plugin
+- lib/bio/shell/plugin/das.rb
+- lib/bio/shell/plugin/psort.rb
+- lib/bio/shell/plugin/flatfile.rb
+- lib/bio/shell/plugin/entry.rb
+- lib/bio/shell/plugin/keggapi.rb
+- lib/bio/shell/plugin/emboss.rb
+- lib/bio/shell/plugin/blast.rb
+- lib/bio/shell/plugin/codon.rb
+- lib/bio/shell/plugin/obda.rb
+- lib/bio/shell/plugin/midi.rb
+- lib/bio/shell/plugin/soap.rb
+- lib/bio/shell/plugin/seq.rb
+- lib/bio/shell/script.rb
+- lib/bio/shell/setup.rb
+- lib/bio/shell/core.rb
+- lib/bio/shell/irb.rb
+- lib/bio/shell/rails
+- lib/bio/shell/rails/vendor
+- lib/bio/shell/rails/vendor/plugins
+- lib/bio/shell/rails/vendor/plugins/bioruby
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_controller.rb
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.css
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml
+- lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif
+- lib/bio/db.rb
+- lib/bio/db
+- lib/bio/db/nexus.rb
+- lib/bio/db/fantom.rb
+- lib/bio/db/pdb
+- lib/bio/db/pdb/utils.rb
+- lib/bio/db/pdb/residue.rb
+- lib/bio/db/pdb/chain.rb
+- lib/bio/db/pdb/atom.rb
+- lib/bio/db/pdb/chemicalcomponent.rb
+- lib/bio/db/pdb/pdb.rb
+- lib/bio/db/pdb/model.rb
+- lib/bio/db/kegg
+- lib/bio/db/kegg/orthology.rb
+- lib/bio/db/kegg/enzyme.rb
+- lib/bio/db/kegg/drug.rb
+- lib/bio/db/kegg/compound.rb
+- lib/bio/db/kegg/kgml.rb
+- lib/bio/db/kegg/reaction.rb
+- lib/bio/db/kegg/glycan.rb
+- lib/bio/db/kegg/genes.rb
+- lib/bio/db/kegg/taxonomy.rb
+- lib/bio/db/kegg/expression.rb
+- lib/bio/db/kegg/genome.rb
+- lib/bio/db/kegg/keggtab.rb
+- lib/bio/db/kegg/brite.rb
+- lib/bio/db/embl
+- lib/bio/db/embl/swissprot.rb
+- lib/bio/db/embl/embl_to_biosequence.rb
+- lib/bio/db/embl/common.rb
+- lib/bio/db/embl/sptr.rb
+- lib/bio/db/embl/format_embl.rb
+- lib/bio/db/embl/uniprot.rb
+- lib/bio/db/embl/embl.rb
+- lib/bio/db/embl/trembl.rb
+- lib/bio/db/prosite.rb
+- lib/bio/db/nbrf.rb
+- lib/bio/db/url.rb
+- lib/bio/db/go.rb
+- lib/bio/db/fasta
+- lib/bio/db/fasta/fasta_to_biosequence.rb
+- lib/bio/db/fasta/format_fasta.rb
+- lib/bio/db/fasta/defline.rb
+- lib/bio/db/medline.rb
+- lib/bio/db/fasta.rb
+- lib/bio/db/rebase.rb
+- lib/bio/db/aaindex.rb
+- lib/bio/db/litdb.rb
+- lib/bio/db/newick.rb
+- lib/bio/db/gff.rb
+- lib/bio/db/biosql
+- lib/bio/db/biosql/sequence.rb
+- lib/bio/db/biosql/biosql_to_biosequence.rb
+- lib/bio/db/pdb.rb
+- lib/bio/db/transfac.rb
+- lib/bio/db/soft.rb
+- lib/bio/db/genbank
+- lib/bio/db/genbank/genpept.rb
+- lib/bio/db/genbank/ddbj.rb
+- lib/bio/db/genbank/genbank_to_biosequence.rb
+- lib/bio/db/genbank/common.rb
+- lib/bio/db/genbank/refseq.rb
+- lib/bio/db/genbank/genbank.rb
+- lib/bio/db/genbank/format_genbank.rb
+- lib/bio/db/lasergene.rb
+- lib/bio/alignment.rb
+- test/functional
+- test/functional/bio
+- test/functional/bio/test_command.rb
+- test/functional/bio/io
+- test/functional/bio/io/test_soapwsdl.rb
+- test/functional/bio/io/test_ensembl.rb
+- test/functional/bio/appl
+- test/functional/bio/appl/test_pts1.rb
+- test/functional/bio/sequence
+- test/functional/bio/sequence/test_output_embl.rb
+- test/runner.rb
+- test/unit
+- test/unit/bio
+- test/unit/bio/test_feature.rb
+- test/unit/bio/test_pathway.rb
+- test/unit/bio/test_alignment.rb
+- test/unit/bio/util
+- test/unit/bio/util/test_restriction_enzyme.rb
+- test/unit/bio/util/test_color_scheme.rb
+- test/unit/bio/util/restriction_enzyme
+- test/unit/bio/util/restriction_enzyme/test_analysis.rb
+- test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb
+- test/unit/bio/util/restriction_enzyme/test_double_stranded.rb
+- test/unit/bio/util/restriction_enzyme/analysis
+- test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb
+- test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb
+- test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb
+- test/unit/bio/util/restriction_enzyme/single_strand
+- test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb
+- test/unit/bio/util/restriction_enzyme/test_string_formatting.rb
+- test/unit/bio/util/restriction_enzyme/test_single_strand.rb
+- test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb
+- test/unit/bio/util/restriction_enzyme/double_stranded
+- test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb
+- test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb
+- test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb
+- test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb
+- test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb
+- test/unit/bio/util/test_contingency_table.rb
+- test/unit/bio/util/test_sirna.rb
+- test/unit/bio/test_command.rb
+- test/unit/bio/io
+- test/unit/bio/io/test_flatfile.rb
+- test/unit/bio/io/flatfile
+- test/unit/bio/io/flatfile/test_autodetection.rb
+- test/unit/bio/io/flatfile/test_splitter.rb
+- test/unit/bio/io/flatfile/test_buffer.rb
+- test/unit/bio/io/test_soapwsdl.rb
+- test/unit/bio/io/test_ensembl.rb
+- test/unit/bio/io/test_fastacmd.rb
+- test/unit/bio/io/test_ddbjxml.rb
+- test/unit/bio/test_sequence.rb
+- test/unit/bio/test_reference.rb
+- test/unit/bio/appl
+- test/unit/bio/appl/test_psort.rb
+- test/unit/bio/appl/mafft
+- test/unit/bio/appl/mafft/test_report.rb
+- test/unit/bio/appl/sosui
+- test/unit/bio/appl/sosui/test_report.rb
+- test/unit/bio/appl/paml
+- test/unit/bio/appl/paml/test_codeml.rb
+- test/unit/bio/appl/paml/codeml
+- test/unit/bio/appl/paml/codeml/test_report.rb
+- test/unit/bio/appl/paml/codeml/test_rates.rb
+- test/unit/bio/appl/test_fasta.rb
+- test/unit/bio/appl/hmmer
+- test/unit/bio/appl/hmmer/test_report.rb
+- test/unit/bio/appl/targetp
+- test/unit/bio/appl/targetp/test_report.rb
+- test/unit/bio/appl/test_blast.rb
+- test/unit/bio/appl/blast
+- test/unit/bio/appl/blast/test_report.rb
+- test/unit/bio/appl/blast/test_ncbioptions.rb
+- test/unit/bio/appl/blast/test_rpsblast.rb
+- test/unit/bio/appl/bl2seq
+- test/unit/bio/appl/bl2seq/test_report.rb
+- test/unit/bio/appl/tmhmm
+- test/unit/bio/appl/tmhmm/test_report.rb
+- test/unit/bio/appl/iprscan
+- test/unit/bio/appl/iprscan/test_report.rb
+- test/unit/bio/appl/genscan
+- test/unit/bio/appl/genscan/test_report.rb
+- test/unit/bio/appl/test_pts1.rb
+- test/unit/bio/test_location.rb
+- test/unit/bio/test_shell.rb
+- test/unit/bio/sequence
+- test/unit/bio/sequence/test_na.rb
+- test/unit/bio/sequence/test_aa.rb
+- test/unit/bio/sequence/test_common.rb
+- test/unit/bio/sequence/test_compat.rb
+- test/unit/bio/sequence/test_dblink.rb
+- test/unit/bio/data
+- test/unit/bio/data/test_na.rb
+- test/unit/bio/data/test_aa.rb
+- test/unit/bio/data/test_codontable.rb
+- test/unit/bio/test_tree.rb
+- test/unit/bio/shell
+- test/unit/bio/shell/plugin
+- test/unit/bio/shell/plugin/test_seq.rb
+- test/unit/bio/test_db.rb
+- test/unit/bio/db
+- test/unit/bio/db/test_prosite.rb
+- test/unit/bio/db/pdb
+- test/unit/bio/db/pdb/test_pdb.rb
+- test/unit/bio/db/kegg
+- test/unit/bio/db/kegg/test_genes.rb
+- test/unit/bio/db/embl
+- test/unit/bio/db/embl/test_embl_rel89.rb
+- test/unit/bio/db/embl/test_embl.rb
+- test/unit/bio/db/embl/test_uniprot.rb
+- test/unit/bio/db/embl/test_sptr.rb
+- test/unit/bio/db/embl/test_common.rb
+- test/unit/bio/db/embl/test_embl_to_bioseq.rb
+- test/unit/bio/db/test_soft.rb
+- test/unit/bio/db/test_fasta.rb
+- test/unit/bio/db/test_medline.rb
+- test/unit/bio/db/test_newick.rb
+- test/unit/bio/db/test_aaindex.rb
+- test/unit/bio/db/test_gff.rb
+- test/unit/bio/db/test_nexus.rb
+- test/unit/bio/db/test_rebase.rb
+- test/unit/bio/db/test_url.rb
+- test/unit/bio/db/test_lasergene.rb
+- test/unit/bio/test_map.rb
+- test/data
+- test/data/aaindex
+- test/data/aaindex/PRAM900102
+- test/data/aaindex/DAYM780301
+- test/data/refseq
+- test/data/refseq/nm_126355.entret
+- test/data/paml
+- test/data/paml/codeml
+- test/data/paml/codeml/control_file.txt
+- test/data/paml/codeml/rates
+- test/data/paml/codeml/output.txt
+- test/data/command
+- test/data/command/echoarg2.bat
+- test/data/embl
+- test/data/embl/AB090716.embl.rel89
+- test/data/embl/AB090716.embl
+- test/data/TMHMM
+- test/data/TMHMM/sample.report
+- test/data/fasta
+- test/data/fasta/example1.txt
+- test/data/fasta/example2.txt
+- test/data/uniprot
+- test/data/uniprot/p53_human.uniprot
+- test/data/HMMER
+- test/data/HMMER/hmmpfam.out
+- test/data/HMMER/hmmsearch.out
+- test/data/prosite
+- test/data/prosite/prosite.dat
+- test/data/SOSUI
+- test/data/SOSUI/sample.report
+- test/data/rpsblast
+- test/data/rpsblast/misc.rpsblast
+- test/data/blast
+- test/data/blast/blastp-multi.m7
+- test/data/blast/b0002.faa.m7
+- test/data/blast/b0002.faa.m8
+- test/data/blast/b0002.faa.m0
+- test/data/blast/2.2.15.blastp.m7
+- test/data/blast/b0002.faa
+- test/data/bl2seq
+- test/data/bl2seq/cd8a_cd8b_blastp.bl2seq
+- test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq
+- test/data/soft
+- test/data/soft/GDS100_partial.soft
+- test/data/soft/GSE3457_family_partial.soft
+- test/data/iprscan
+- test/data/iprscan/merged.raw
+- test/data/iprscan/merged.txt
+- test/data/genscan
+- test/data/genscan/sample.report
+has_rdoc: false
+homepage: http://bioruby.org
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+  version: 
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.2.0
+signing_key: 
+specification_version: 2
+summary: Bioinformatics library
+test_files: []
+