ngoto-bio 1.2.9.9001

data/bioruby.gemspec

@@ -0,0 +1,463 @@
+# This file is automatically generated from bioruby.gemspec.erb and
+# should NOT be edited by hand.
+# 
+Gem::Specification.new do |s|
+  s.name = 'bio'
+  s.version = "1.2.9.9001"
+
+  s.author = "BioRuby project"
+  s.email = "staff@bioruby.org"
+  s.homepage = "http://bioruby.org/"
+  s.rubyforge_project = "bioruby"
+  s.summary = "Bioinformatics library"
+  s.description = "BioRuby is a library for bioinformatics (biology + information science)."
+
+  s.platform = Gem::Platform::RUBY
+  s.files = [
+    "ChangeLog",
+    "README.rdoc",
+    "README_DEV.rdoc",
+    "Rakefile",
+    "bin/bioruby",
+    "bin/br_biofetch.rb",
+    "bin/br_bioflat.rb",
+    "bin/br_biogetseq.rb",
+    "bin/br_pmfetch.rb",
+    "bioruby.gemspec",
+    "bioruby.gemspec.erb",
+    "doc/Changes-0.7.rd",
+    "doc/Changes-1.3.rdoc",
+    "doc/KEGG_API.rd",
+    "doc/KEGG_API.rd.ja",
+    "doc/Tutorial.rd",
+    "doc/Tutorial.rd.ja",
+    "etc/bioinformatics/seqdatabase.ini",
+    "extconf.rb",
+    "lib/bio.rb",
+    "lib/bio/alignment.rb",
+    "lib/bio/appl/bl2seq/report.rb",
+    "lib/bio/appl/blast.rb",
+    "lib/bio/appl/blast/ddbj.rb",
+    "lib/bio/appl/blast/format0.rb",
+    "lib/bio/appl/blast/format8.rb",
+    "lib/bio/appl/blast/genomenet.rb",
+    "lib/bio/appl/blast/ncbioptions.rb",
+    "lib/bio/appl/blast/remote.rb",
+    "lib/bio/appl/blast/report.rb",
+    "lib/bio/appl/blast/rexml.rb",
+    "lib/bio/appl/blast/rpsblast.rb",
+    "lib/bio/appl/blast/wublast.rb",
+    "lib/bio/appl/blast/xmlparser.rb",
+    "lib/bio/appl/blat/report.rb",
+    "lib/bio/appl/clustalw.rb",
+    "lib/bio/appl/clustalw/report.rb",
+    "lib/bio/appl/emboss.rb",
+    "lib/bio/appl/fasta.rb",
+    "lib/bio/appl/fasta/format10.rb",
+    "lib/bio/appl/gcg/msf.rb",
+    "lib/bio/appl/gcg/seq.rb",
+    "lib/bio/appl/genscan/report.rb",
+    "lib/bio/appl/hmmer.rb",
+    "lib/bio/appl/hmmer/report.rb",
+    "lib/bio/appl/iprscan/report.rb",
+    "lib/bio/appl/mafft.rb",
+    "lib/bio/appl/mafft/report.rb",
+    "lib/bio/appl/muscle.rb",
+    "lib/bio/appl/paml/baseml.rb",
+    "lib/bio/appl/paml/baseml/report.rb",
+    "lib/bio/appl/paml/codeml.rb",
+    "lib/bio/appl/paml/codeml/rates.rb",
+    "lib/bio/appl/paml/codeml/report.rb",
+    "lib/bio/appl/paml/common.rb",
+    "lib/bio/appl/paml/common_report.rb",
+    "lib/bio/appl/paml/yn00.rb",
+    "lib/bio/appl/paml/yn00/report.rb",
+    "lib/bio/appl/phylip/alignment.rb",
+    "lib/bio/appl/phylip/distance_matrix.rb",
+    "lib/bio/appl/probcons.rb",
+    "lib/bio/appl/psort.rb",
+    "lib/bio/appl/psort/report.rb",
+    "lib/bio/appl/pts1.rb",
+    "lib/bio/appl/sim4.rb",
+    "lib/bio/appl/sim4/report.rb",
+    "lib/bio/appl/sosui/report.rb",
+    "lib/bio/appl/spidey/report.rb",
+    "lib/bio/appl/targetp/report.rb",
+    "lib/bio/appl/tcoffee.rb",
+    "lib/bio/appl/tmhmm/report.rb",
+    "lib/bio/command.rb",
+    "lib/bio/compat/features.rb",
+    "lib/bio/compat/references.rb",
+    "lib/bio/data/aa.rb",
+    "lib/bio/data/codontable.rb",
+    "lib/bio/data/na.rb",
+    "lib/bio/db.rb",
+    "lib/bio/db/aaindex.rb",
+    "lib/bio/db/biosql/biosql_to_biosequence.rb",
+    "lib/bio/db/biosql/sequence.rb",
+    "lib/bio/db/embl/common.rb",
+    "lib/bio/db/embl/embl.rb",
+    "lib/bio/db/embl/embl_to_biosequence.rb",
+    "lib/bio/db/embl/format_embl.rb",
+    "lib/bio/db/embl/sptr.rb",
+    "lib/bio/db/embl/swissprot.rb",
+    "lib/bio/db/embl/trembl.rb",
+    "lib/bio/db/embl/uniprot.rb",
+    "lib/bio/db/fantom.rb",
+    "lib/bio/db/fasta.rb",
+    "lib/bio/db/fasta/defline.rb",
+    "lib/bio/db/fasta/fasta_to_biosequence.rb",
+    "lib/bio/db/fasta/format_fasta.rb",
+    "lib/bio/db/genbank/common.rb",
+    "lib/bio/db/genbank/ddbj.rb",
+    "lib/bio/db/genbank/format_genbank.rb",
+    "lib/bio/db/genbank/genbank.rb",
+    "lib/bio/db/genbank/genbank_to_biosequence.rb",
+    "lib/bio/db/genbank/genpept.rb",
+    "lib/bio/db/genbank/refseq.rb",
+    "lib/bio/db/gff.rb",
+    "lib/bio/db/go.rb",
+    "lib/bio/db/kegg/brite.rb",
+    "lib/bio/db/kegg/compound.rb",
+    "lib/bio/db/kegg/drug.rb",
+    "lib/bio/db/kegg/enzyme.rb",
+    "lib/bio/db/kegg/expression.rb",
+    "lib/bio/db/kegg/genes.rb",
+    "lib/bio/db/kegg/genome.rb",
+    "lib/bio/db/kegg/glycan.rb",
+    "lib/bio/db/kegg/keggtab.rb",
+    "lib/bio/db/kegg/kgml.rb",
+    "lib/bio/db/kegg/orthology.rb",
+    "lib/bio/db/kegg/reaction.rb",
+    "lib/bio/db/kegg/taxonomy.rb",
+    "lib/bio/db/lasergene.rb",
+    "lib/bio/db/litdb.rb",
+    "lib/bio/db/medline.rb",
+    "lib/bio/db/nbrf.rb",
+    "lib/bio/db/newick.rb",
+    "lib/bio/db/nexus.rb",
+    "lib/bio/db/pdb.rb",
+    "lib/bio/db/pdb/atom.rb",
+    "lib/bio/db/pdb/chain.rb",
+    "lib/bio/db/pdb/chemicalcomponent.rb",
+    "lib/bio/db/pdb/model.rb",
+    "lib/bio/db/pdb/pdb.rb",
+    "lib/bio/db/pdb/residue.rb",
+    "lib/bio/db/pdb/utils.rb",
+    "lib/bio/db/prosite.rb",
+    "lib/bio/db/rebase.rb",
+    "lib/bio/db/soft.rb",
+    "lib/bio/db/transfac.rb",
+    "lib/bio/feature.rb",
+    "lib/bio/io/biosql/biodatabase.rb",
+    "lib/bio/io/biosql/bioentry.rb",
+    "lib/bio/io/biosql/bioentry_dbxref.rb",
+    "lib/bio/io/biosql/bioentry_path.rb",
+    "lib/bio/io/biosql/bioentry_qualifier_value.rb",
+    "lib/bio/io/biosql/bioentry_reference.rb",
+    "lib/bio/io/biosql/bioentry_relationship.rb",
+    "lib/bio/io/biosql/biosequence.rb",
+    "lib/bio/io/biosql/comment.rb",
+    "lib/bio/io/biosql/config/database.yml",
+    "lib/bio/io/biosql/dbxref.rb",
+    "lib/bio/io/biosql/dbxref_qualifier_value.rb",
+    "lib/bio/io/biosql/location.rb",
+    "lib/bio/io/biosql/location_qualifier_value.rb",
+    "lib/bio/io/biosql/ontology.rb",
+    "lib/bio/io/biosql/reference.rb",
+    "lib/bio/io/biosql/seqfeature.rb",
+    "lib/bio/io/biosql/seqfeature_dbxref.rb",
+    "lib/bio/io/biosql/seqfeature_path.rb",
+    "lib/bio/io/biosql/seqfeature_qualifier_value.rb",
+    "lib/bio/io/biosql/seqfeature_relationship.rb",
+    "lib/bio/io/biosql/taxon.rb",
+    "lib/bio/io/biosql/taxon_name.rb",
+    "lib/bio/io/biosql/term.rb",
+    "lib/bio/io/biosql/term_dbxref.rb",
+    "lib/bio/io/biosql/term_path.rb",
+    "lib/bio/io/biosql/term_relationship.rb",
+    "lib/bio/io/biosql/term_relationship_term.rb",
+    "lib/bio/io/biosql/term_synonym.rb",
+    "lib/bio/io/das.rb",
+    "lib/bio/io/dbget.rb",
+    "lib/bio/io/ddbjxml.rb",
+    "lib/bio/io/ebisoap.rb",
+    "lib/bio/io/ensembl.rb",
+    "lib/bio/io/fastacmd.rb",
+    "lib/bio/io/fetch.rb",
+    "lib/bio/io/flatfile.rb",
+    "lib/bio/io/flatfile/autodetection.rb",
+    "lib/bio/io/flatfile/bdb.rb",
+    "lib/bio/io/flatfile/buffer.rb",
+    "lib/bio/io/flatfile/index.rb",
+    "lib/bio/io/flatfile/indexer.rb",
+    "lib/bio/io/flatfile/splitter.rb",
+    "lib/bio/io/higet.rb",
+    "lib/bio/io/hinv.rb",
+    "lib/bio/io/keggapi.rb",
+    "lib/bio/io/ncbirest.rb",
+    "lib/bio/io/ncbisoap.rb",
+    "lib/bio/io/pubmed.rb",
+    "lib/bio/io/registry.rb",
+    "lib/bio/io/soapwsdl.rb",
+    "lib/bio/io/sql.rb",
+    "lib/bio/location.rb",
+    "lib/bio/map.rb",
+    "lib/bio/pathway.rb",
+    "lib/bio/reference.rb",
+    "lib/bio/sequence.rb",
+    "lib/bio/sequence/aa.rb",
+    "lib/bio/sequence/adapter.rb",
+    "lib/bio/sequence/common.rb",
+    "lib/bio/sequence/compat.rb",
+    "lib/bio/sequence/dblink.rb",
+    "lib/bio/sequence/format.rb",
+    "lib/bio/sequence/format_raw.rb",
+    "lib/bio/sequence/generic.rb",
+    "lib/bio/sequence/na.rb",
+    "lib/bio/shell.rb",
+    "lib/bio/shell/core.rb",
+    "lib/bio/shell/demo.rb",
+    "lib/bio/shell/interface.rb",
+    "lib/bio/shell/irb.rb",
+    "lib/bio/shell/object.rb",
+    "lib/bio/shell/plugin/blast.rb",
+    "lib/bio/shell/plugin/codon.rb",
+    "lib/bio/shell/plugin/das.rb",
+    "lib/bio/shell/plugin/emboss.rb",
+    "lib/bio/shell/plugin/entry.rb",
+    "lib/bio/shell/plugin/flatfile.rb",
+    "lib/bio/shell/plugin/keggapi.rb",
+    "lib/bio/shell/plugin/midi.rb",
+    "lib/bio/shell/plugin/obda.rb",
+    "lib/bio/shell/plugin/psort.rb",
+    "lib/bio/shell/plugin/seq.rb",
+    "lib/bio/shell/plugin/soap.rb",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_classes.rhtml",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_log.rhtml",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_methods.rhtml",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_modules.rhtml",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/_variables.rhtml",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-bg.gif",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-gem.png",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby-link.gif",
+    "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/bioruby_controller.rb",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/bioruby_helper.rb",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/commands.rhtml",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/history.rhtml",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/index.rhtml",
+    "lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/templates/spinner.gif",
+    "lib/bio/shell/script.rb",
+    "lib/bio/shell/setup.rb",
+    "lib/bio/shell/web.rb",
+    "lib/bio/tree.rb",
+    "lib/bio/util/color_scheme.rb",
+    "lib/bio/util/color_scheme/buried.rb",
+    "lib/bio/util/color_scheme/helix.rb",
+    "lib/bio/util/color_scheme/hydropathy.rb",
+    "lib/bio/util/color_scheme/nucleotide.rb",
+    "lib/bio/util/color_scheme/strand.rb",
+    "lib/bio/util/color_scheme/taylor.rb",
+    "lib/bio/util/color_scheme/turn.rb",
+    "lib/bio/util/color_scheme/zappo.rb",
+    "lib/bio/util/contingency_table.rb",
+    "lib/bio/util/restriction_enzyme.rb",
+    "lib/bio/util/restriction_enzyme/analysis.rb",
+    "lib/bio/util/restriction_enzyme/analysis_basic.rb",
+    "lib/bio/util/restriction_enzyme/cut_symbol.rb",
+    "lib/bio/util/restriction_enzyme/double_stranded.rb",
+    "lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb",
+    "lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb",
+    "lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb",
+    "lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb",
+    "lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb",
+    "lib/bio/util/restriction_enzyme/enzymes.yaml",
+    "lib/bio/util/restriction_enzyme/range/cut_range.rb",
+    "lib/bio/util/restriction_enzyme/range/cut_ranges.rb",
+    "lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb",
+    "lib/bio/util/restriction_enzyme/range/sequence_range.rb",
+    "lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb",
+    "lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb",
+    "lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb",
+    "lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb",
+    "lib/bio/util/restriction_enzyme/single_strand.rb",
+    "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/string_formatting.rb",
+    "lib/bio/util/sirna.rb",
+    "rdoc.zsh",
+    "sample/any2fasta.rb",
+    "sample/biofetch.rb",
+    "sample/color_scheme_na.rb",
+    "sample/dbget",
+    "sample/demo_sequence.rb",
+    "sample/enzymes.rb",
+    "sample/fasta2tab.rb",
+    "sample/fastagrep.rb",
+    "sample/fastasort.rb",
+    "sample/fsplit.rb",
+    "sample/gb2fasta.rb",
+    "sample/gb2tab.rb",
+    "sample/gbtab2mysql.rb",
+    "sample/genes2nuc.rb",
+    "sample/genes2pep.rb",
+    "sample/genes2tab.rb",
+    "sample/genome2rb.rb",
+    "sample/genome2tab.rb",
+    "sample/goslim.rb",
+    "sample/gt2fasta.rb",
+    "sample/na2aa.rb",
+    "sample/pmfetch.rb",
+    "sample/pmsearch.rb",
+    "sample/psortplot_html.rb",
+    "sample/ssearch2tab.rb",
+    "sample/tdiary.rb",
+    "sample/tfastx2tab.rb",
+    "sample/vs-genes.rb",
+    "setup.rb",
+    "test/data/HMMER/hmmpfam.out",
+    "test/data/HMMER/hmmsearch.out",
+    "test/data/SOSUI/sample.report",
+    "test/data/TMHMM/sample.report",
+    "test/data/aaindex/DAYM780301",
+    "test/data/aaindex/PRAM900102",
+    "test/data/bl2seq/cd8a_cd8b_blastp.bl2seq",
+    "test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq",
+    "test/data/blast/2.2.15.blastp.m7",
+    "test/data/blast/b0002.faa",
+    "test/data/blast/b0002.faa.m0",
+    "test/data/blast/b0002.faa.m7",
+    "test/data/blast/b0002.faa.m8",
+    "test/data/blast/blastp-multi.m7",
+    "test/data/command/echoarg2.bat",
+    "test/data/embl/AB090716.embl",
+    "test/data/embl/AB090716.embl.rel89",
+    "test/data/fasta/example1.txt",
+    "test/data/fasta/example2.txt",
+    "test/data/genscan/sample.report",
+    "test/data/iprscan/merged.raw",
+    "test/data/iprscan/merged.txt",
+    "test/data/paml/codeml/control_file.txt",
+    "test/data/paml/codeml/output.txt",
+    "test/data/paml/codeml/rates",
+    "test/data/prosite/prosite.dat",
+    "test/data/refseq/nm_126355.entret",
+    "test/data/rpsblast/misc.rpsblast",
+    "test/data/soft/GDS100_partial.soft",
+    "test/data/soft/GSE3457_family_partial.soft",
+    "test/data/uniprot/p53_human.uniprot",
+    "test/functional/bio/appl/test_pts1.rb",
+    "test/functional/bio/io/test_ensembl.rb",
+    "test/functional/bio/io/test_soapwsdl.rb",
+    "test/functional/bio/sequence/test_output_embl.rb",
+    "test/functional/bio/test_command.rb",
+    "test/runner.rb",
+    "test/unit/bio/appl/bl2seq/test_report.rb",
+    "test/unit/bio/appl/blast/test_ncbioptions.rb",
+    "test/unit/bio/appl/blast/test_report.rb",
+    "test/unit/bio/appl/blast/test_rpsblast.rb",
+    "test/unit/bio/appl/genscan/test_report.rb",
+    "test/unit/bio/appl/hmmer/test_report.rb",
+    "test/unit/bio/appl/iprscan/test_report.rb",
+    "test/unit/bio/appl/mafft/test_report.rb",
+    "test/unit/bio/appl/paml/codeml/test_rates.rb",
+    "test/unit/bio/appl/paml/codeml/test_report.rb",
+    "test/unit/bio/appl/paml/test_codeml.rb",
+    "test/unit/bio/appl/sosui/test_report.rb",
+    "test/unit/bio/appl/targetp/test_report.rb",
+    "test/unit/bio/appl/test_blast.rb",
+    "test/unit/bio/appl/test_fasta.rb",
+    "test/unit/bio/appl/test_pts1.rb",
+    "test/unit/bio/appl/tmhmm/test_report.rb",
+    "test/unit/bio/data/test_aa.rb",
+    "test/unit/bio/data/test_codontable.rb",
+    "test/unit/bio/data/test_na.rb",
+    "test/unit/bio/db/embl/test_common.rb",
+    "test/unit/bio/db/embl/test_embl.rb",
+    "test/unit/bio/db/embl/test_embl_rel89.rb",
+    "test/unit/bio/db/embl/test_embl_to_bioseq.rb",
+    "test/unit/bio/db/embl/test_sptr.rb",
+    "test/unit/bio/db/embl/test_uniprot.rb",
+    "test/unit/bio/db/kegg/test_genes.rb",
+    "test/unit/bio/db/pdb/test_pdb.rb",
+    "test/unit/bio/db/test_aaindex.rb",
+    "test/unit/bio/db/test_fasta.rb",
+    "test/unit/bio/db/test_gff.rb",
+    "test/unit/bio/db/test_lasergene.rb",
+    "test/unit/bio/db/test_medline.rb",
+    "test/unit/bio/db/test_newick.rb",
+    "test/unit/bio/db/test_nexus.rb",
+    "test/unit/bio/db/test_prosite.rb",
+    "test/unit/bio/db/test_rebase.rb",
+    "test/unit/bio/db/test_soft.rb",
+    "test/unit/bio/io/flatfile/test_autodetection.rb",
+    "test/unit/bio/io/flatfile/test_buffer.rb",
+    "test/unit/bio/io/flatfile/test_splitter.rb",
+    "test/unit/bio/io/test_ddbjxml.rb",
+    "test/unit/bio/io/test_ensembl.rb",
+    "test/unit/bio/io/test_fastacmd.rb",
+    "test/unit/bio/io/test_flatfile.rb",
+    "test/unit/bio/io/test_soapwsdl.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/sequence/test_na.rb",
+    "test/unit/bio/shell/plugin/test_seq.rb",
+    "test/unit/bio/test_alignment.rb",
+    "test/unit/bio/test_command.rb",
+    "test/unit/bio/test_db.rb",
+    "test/unit/bio/test_feature.rb",
+    "test/unit/bio/test_location.rb",
+    "test/unit/bio/test_map.rb",
+    "test/unit/bio/test_pathway.rb",
+    "test/unit/bio/test_reference.rb",
+    "test/unit/bio/test_sequence.rb",
+    "test/unit/bio/test_shell.rb",
+    "test/unit/bio/test_tree.rb",
+    "test/unit/bio/util/restriction_enzyme/analysis/test_calculated_cuts.rb",
+    "test/unit/bio/util/restriction_enzyme/analysis/test_cut_ranges.rb",
+    "test/unit/bio/util/restriction_enzyme/analysis/test_sequence_range.rb",
+    "test/unit/bio/util/restriction_enzyme/double_stranded/test_aligned_strands.rb",
+    "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_cut_locations_in_enzyme_notation.rb",
+    "test/unit/bio/util/restriction_enzyme/single_strand/test_cut_locations_in_enzyme_notation.rb",
+    "test/unit/bio/util/restriction_enzyme/test_analysis.rb",
+    "test/unit/bio/util/restriction_enzyme/test_cut_symbol.rb",
+    "test/unit/bio/util/restriction_enzyme/test_double_stranded.rb",
+    "test/unit/bio/util/restriction_enzyme/test_single_strand.rb",
+    "test/unit/bio/util/restriction_enzyme/test_single_strand_complement.rb",
+    "test/unit/bio/util/restriction_enzyme/test_string_formatting.rb",
+    "test/unit/bio/util/test_color_scheme.rb",
+    "test/unit/bio/util/test_contingency_table.rb",
+    "test/unit/bio/util/test_restriction_enzyme.rb",
+    "test/unit/bio/util/test_sirna.rb"
+  ]
+
+  s.has_rdoc = true
+  s.extra_rdoc_files = [ 
+    "README.rdoc",
+    "README_DEV.rdoc",
+    "doc/Changes-1.3.rdoc"
+  ]
+  s.rdoc_options << '--main' << 'README.rdoc'
+  s.rdoc_options << '--exclude' << '\.yaml\z'
+
+  s.require_path = 'lib'
+  s.autorequire = 'bio'
+
+  s.bindir = "bin"
+  s.executables = [
+    "bioruby",
+    "br_biofetch.rb",
+    "br_bioflat.rb",
+    "br_biogetseq.rb",
+    "br_pmfetch.rb"
+  ]
+  s.default_executable = "bioruby"
+end

data/bioruby.gemspec.erb

@@ -0,0 +1,79 @@
+Gem::Specification.new do |s|
+  s.name = 'bio'
+  s.version = "1.2.9.9001"
+
+  s.author = "BioRuby project"
+  s.email = "staff@bioruby.org"
+  s.homepage = "http://bioruby.org/"
+  s.rubyforge_project = "bioruby"
+  s.summary = "Bioinformatics library"
+  s.description = "BioRuby is a library for bioinformatics (biology + information science)."
+
+  s.platform = Gem::Platform::RUBY
+  s.files = [
+    <% ###### Below is executed in ERB environment ######
+    # Gets file list from the "git-ls-files" command.
+    files = `git-ls-files 2>/dev/null`.to_s.split(/\r?\n/)
+    files.delete_if { |x| x.empty? }
+    # When git-ls-files isn't available, creates a list from current files.
+    unless $?.success? or files.size <= 0 then
+      files =
+        [ "README.rdoc", "README_DEV.rdoc", "ChangeLog",
+          "Rakefile", "bioruby.gemspec.erb",
+          "bioruby.gemspec", "setup.rb",
+          "extconf.rb", "rdoc.zsh"
+        ] + Dir.glob("{bin,doc,etc,lib,sample,test}/**/*").delete_if do |item|
+              case item
+              when /(\A|\/)CVS(\z|\/)/, /(\A|\/)rdoc(\z|\/)/, /\~\z/
+                true
+              else
+                false
+              end
+            end
+    end
+    files.push "bioruby.gemspec" unless files.include?("bioruby.gemspec")
+    %><%= 
+    files.collect { |x| x.dump }.join(",\n    ")
+       ###### Above is executed in ERB environment ######
+    %>
+  ]
+
+  s.has_rdoc = true
+  s.extra_rdoc_files = [ 
+    <%= ###### Below is executed in ERB environment ######
+        # Files whose suffix are .rdoc are selected.
+        rdoc_files = files.find_all { |item| /\.rdoc\z/ =~ item }
+        # Fail safe settings
+        if rdoc_files.empty? then
+          rdoc_files = [ 'README.rdoc', 'README_DEV.rdoc',
+                         'doc/Changes-1.3.rdoc' ]
+        end
+        rdoc_files.collect { |x| x.dump }.join(",\n    ")
+        ###### Above is executed in ERB environment ######
+    %>
+  ]
+  s.rdoc_options << '--main' << 'README.rdoc'
+  s.rdoc_options << '--exclude' << '\.yaml\z'
+
+  s.require_path = 'lib'
+  s.autorequire = 'bio'
+
+  s.bindir = "bin"
+  s.executables = [
+    <%= ###### Below is executed in ERB environment ######
+        # Files in bin/ directory are selected.
+        exec_files = files.find_all { |item| /\Abin\// =~ item }
+        # Non-executable files are removed from the list.
+        exec_files.delete_if { |item| !File.executable?(item) }
+        # strip "bin/"
+        exec_files.collect! { |item| item.sub(/\Abin\//, '') }
+        # Fail safe settings
+        if exec_files.empty? then
+            exec_files = [ "bioruby", "br_biofetch.rb", "br_biogetseq.rb", "br_bioflat.rb", "br_pmfetch.rb" ]
+        end
+        exec_files.collect { |x| x.dump }.join(",\n    ")
+        ###### Above is executed in ERB environment ######
+    %>
+  ]
+  s.default_executable = "bioruby"
+end