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bioruby.gemspec
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# 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 = "2.0.6"
s.author = "BioRuby project"
s.email = "[email protected]"
s.homepage = "http://bioruby.org/"
s.license = "Ruby"
s.summary = "Bioinformatics library"
s.description = "BioRuby is a library for bioinformatics (biology + information science)."
s.platform = Gem::Platform::RUBY
s.files = [
".github/workflows/ruby.yml",
".gitignore",
"BSDL",
"COPYING",
"COPYING.ja",
"ChangeLog",
"GPL",
"Gemfile",
"KNOWN_ISSUES.rdoc",
"LEGAL",
"LGPL",
"README.rdoc",
"README_DEV.rdoc",
"RELEASE_NOTES.rdoc",
"Rakefile",
"appveyor.yml",
"bioruby.gemspec",
"bioruby.gemspec.erb",
"doc/ChangeLog-1.4.3",
"doc/ChangeLog-1.5.0",
"doc/ChangeLog-before-1.3.1",
"doc/ChangeLog-before-1.4.2",
"doc/Changes-0.7.rd",
"doc/Changes-1.3.rdoc",
"doc/RELEASE_NOTES-1.4.0.rdoc",
"doc/RELEASE_NOTES-1.4.1.rdoc",
"doc/RELEASE_NOTES-1.4.2.rdoc",
"doc/RELEASE_NOTES-1.4.3.rdoc",
"doc/RELEASE_NOTES-1.5.0.rdoc",
"doc/Tutorial.md",
"doc/Tutorial.rd",
"doc/Tutorial.rd.html",
"doc/Tutorial.rd.ja",
"doc/Tutorial.rd.ja.html",
"doc/Tutorial_ja.md",
"doc/bioruby.css",
"etc/bioinformatics/seqdatabase.ini",
"lib/bio.rb",
"lib/bio/alignment.rb",
"lib/bio/appl/bl2seq/report.rb",
"lib/bio/appl/blast.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/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/meme/mast.rb",
"lib/bio/appl/meme/mast/report.rb",
"lib/bio/appl/meme/motif.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/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/embl/uniprotkb.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/fasta/format_qual.rb",
"lib/bio/db/fasta/qual.rb",
"lib/bio/db/fasta/qual_to_biosequence.rb",
"lib/bio/db/fastq.rb",
"lib/bio/db/fastq/fastq_to_biosequence.rb",
"lib/bio/db/fastq/format_fastq.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/common.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/module.rb",
"lib/bio/db/kegg/orthology.rb",
"lib/bio/db/kegg/pathway.rb",
"lib/bio/db/kegg/reaction.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/sanger_chromatogram/abif.rb",
"lib/bio/db/sanger_chromatogram/chromatogram.rb",
"lib/bio/db/sanger_chromatogram/chromatogram_to_biosequence.rb",
"lib/bio/db/sanger_chromatogram/scf.rb",
"lib/bio/db/soft.rb",
"lib/bio/db/transfac.rb",
"lib/bio/feature.rb",
"lib/bio/io/das.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/hinv.rb",
"lib/bio/io/ncbirest.rb",
"lib/bio/io/pubmed.rb",
"lib/bio/io/registry.rb",
"lib/bio/io/togows.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/sequence/quality_score.rb",
"lib/bio/sequence/sequence_masker.rb",
"lib/bio/tree.rb",
"lib/bio/tree/output.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/dense_int_array.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/sorted_num_array.rb",
"lib/bio/util/restriction_enzyme/string_formatting.rb",
"lib/bio/util/sirna.rb",
"lib/bio/version.rb",
"sample/any2fasta.rb",
"sample/benchmark_clustalw_report.rb",
"sample/biofetch.rb",
"sample/color_scheme_aa.rb",
"sample/color_scheme_na.rb",
"sample/demo_aaindex.rb",
"sample/demo_aminoacid.rb",
"sample/demo_bl2seq_report.rb",
"sample/demo_blast_report.rb",
"sample/demo_codontable.rb",
"sample/demo_das.rb",
"sample/demo_fasta_remote.rb",
"sample/demo_fastaformat.rb",
"sample/demo_genbank.rb",
"sample/demo_genscan_report.rb",
"sample/demo_gff1.rb",
"sample/demo_go.rb",
"sample/demo_hmmer_report.rb",
"sample/demo_kegg_compound.rb",
"sample/demo_kegg_drug.rb",
"sample/demo_kegg_genome.rb",
"sample/demo_kegg_glycan.rb",
"sample/demo_kegg_orthology.rb",
"sample/demo_kegg_reaction.rb",
"sample/demo_litdb.rb",
"sample/demo_locations.rb",
"sample/demo_ncbi_rest.rb",
"sample/demo_nucleicacid.rb",
"sample/demo_pathway.rb",
"sample/demo_prosite.rb",
"sample/demo_psort.rb",
"sample/demo_psort_report.rb",
"sample/demo_pubmed.rb",
"sample/demo_sequence.rb",
"sample/demo_sirna.rb",
"sample/demo_sosui_report.rb",
"sample/demo_targetp_report.rb",
"sample/demo_tmhmm_report.rb",
"sample/enzymes.rb",
"sample/fasta2tab.rb",
"sample/fastagrep.rb",
"sample/fastasort.rb",
"sample/fastq2html.cwl",
"sample/fastq2html.rb",
"sample/fastq2html.testdata.yaml",
"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.cwl",
"sample/na2aa.rb",
"sample/na2aa.testdata.yaml",
"sample/pmfetch.rb",
"sample/pmsearch.rb",
"sample/rev_comp.cwl",
"sample/rev_comp.rb",
"sample/rev_comp.testdata.yaml",
"sample/seqdatabase.ini",
"sample/ssearch2tab.rb",
"sample/tdiary.rb",
"sample/test_restriction_enzyme_long.rb",
"sample/tfastx2tab.rb",
"sample/vs-genes.rb",
"test/bioruby_test_helper.rb",
"test/data/HMMER/hmmpfam.out",
"test/data/HMMER/hmmsearch.out",
"test/data/KEGG/1.1.1.1.enzyme",
"test/data/KEGG/C00025.compound",
"test/data/KEGG/D00063.drug",
"test/data/KEGG/G00024.glycan",
"test/data/KEGG/G01366.glycan",
"test/data/KEGG/K02338.orthology",
"test/data/KEGG/M00118.module",
"test/data/KEGG/R00006.reaction",
"test/data/KEGG/T00005.genome",
"test/data/KEGG/T00070.genome",
"test/data/KEGG/b0529.gene",
"test/data/KEGG/ec00072.pathway",
"test/data/KEGG/hsa00790.pathway",
"test/data/KEGG/ko00312.pathway",
"test/data/KEGG/map00030.pathway",
"test/data/KEGG/map00052.pathway",
"test/data/KEGG/rn00250.pathway",
"test/data/KEGG/test.kgml",
"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/clustalw/example1-seqnos.aln",
"test/data/clustalw/example1.aln",
"test/data/command/echoarg2.bat",
"test/data/command/echoarg2.sh",
"test/data/embl/AB090716.embl",
"test/data/embl/AB090716.embl.rel89",
"test/data/fasta/EFTU_BACSU.fasta",
"test/data/fasta/example1.txt",
"test/data/fasta/example2.txt",
"test/data/fastq/README.txt",
"test/data/fastq/error_diff_ids.fastq",
"test/data/fastq/error_double_qual.fastq",
"test/data/fastq/error_double_seq.fastq",
"test/data/fastq/error_long_qual.fastq",
"test/data/fastq/error_no_qual.fastq",
"test/data/fastq/error_qual_del.fastq",
"test/data/fastq/error_qual_escape.fastq",
"test/data/fastq/error_qual_null.fastq",
"test/data/fastq/error_qual_space.fastq",
"test/data/fastq/error_qual_tab.fastq",
"test/data/fastq/error_qual_unit_sep.fastq",
"test/data/fastq/error_qual_vtab.fastq",
"test/data/fastq/error_short_qual.fastq",
"test/data/fastq/error_spaces.fastq",
"test/data/fastq/error_tabs.fastq",
"test/data/fastq/error_trunc_at_plus.fastq",
"test/data/fastq/error_trunc_at_qual.fastq",
"test/data/fastq/error_trunc_at_seq.fastq",
"test/data/fastq/error_trunc_in_plus.fastq",
"test/data/fastq/error_trunc_in_qual.fastq",
"test/data/fastq/error_trunc_in_seq.fastq",
"test/data/fastq/error_trunc_in_title.fastq",
"test/data/fastq/illumina_full_range_as_illumina.fastq",
"test/data/fastq/illumina_full_range_as_sanger.fastq",
"test/data/fastq/illumina_full_range_as_solexa.fastq",
"test/data/fastq/illumina_full_range_original_illumina.fastq",
"test/data/fastq/longreads_as_illumina.fastq",
"test/data/fastq/longreads_as_sanger.fastq",
"test/data/fastq/longreads_as_solexa.fastq",
"test/data/fastq/longreads_original_sanger.fastq",
"test/data/fastq/misc_dna_as_illumina.fastq",
"test/data/fastq/misc_dna_as_sanger.fastq",
"test/data/fastq/misc_dna_as_solexa.fastq",
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