bioruby.gemspec in bio-1.3.1 vs bioruby.gemspec in bio-1.4.0
- old
+ new
@@ -1,11 +1,11 @@
# 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 = "1.3.1"
+ s.version = "1.4.0"
s.author = "BioRuby project"
s.email = "staff@bioruby.org"
s.homepage = "http://bioruby.org/"
s.rubyforge_project = "bioruby"
@@ -21,18 +21,20 @@
"KNOWN_ISSUES.rdoc",
"LEGAL",
"LGPL",
"README.rdoc",
"README_DEV.rdoc",
+ "RELEASE_NOTES.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/ChangeLog-before-1.3.1",
"doc/Changes-0.7.rd",
"doc/Changes-1.3.rdoc",
"doc/KEGG_API.rd",
"doc/KEGG_API.rd.ja",
"doc/Tutorial.rd",
@@ -69,10 +71,13 @@
"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",
@@ -115,20 +120,26 @@
"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/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",
@@ -151,12 +162,20 @@
"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/phyloxml/phyloxml.xsd",
+ "lib/bio/db/phyloxml/phyloxml_elements.rb",
+ "lib/bio/db/phyloxml/phyloxml_parser.rb",
+ "lib/bio/db/phyloxml/phyloxml_writer.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/biosql/ar-biosql.rb",
"lib/bio/io/biosql/biosql.rb",
@@ -197,10 +216,11 @@
"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/shell.rb",
"lib/bio/shell/core.rb",
"lib/bio/shell/demo.rb",
"lib/bio/shell/interface.rb",
"lib/bio/shell/irb.rb",
@@ -278,11 +298,46 @@
"rdoc.zsh",
"sample/any2fasta.rb",
"sample/biofetch.rb",
"sample/color_scheme_na.rb",
"sample/dbget",
+ "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_ddbjxml.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_kegg_taxonomy.rb",
+ "sample/demo_keggapi.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/fsplit.rb",
@@ -300,15 +355,24 @@
"sample/pmfetch.rb",
"sample/pmsearch.rb",
"sample/psortplot_html.rb",
"sample/ssearch2tab.rb",
"sample/tdiary.rb",
+ "sample/test_phyloxml_big.rb",
"sample/tfastx2tab.rb",
"sample/vs-genes.rb",
"setup.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/R00006.reaction",
"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",
@@ -322,20 +386,83 @@
"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/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",
+ "test/data/fastq/misc_dna_original_sanger.fastq",
+ "test/data/fastq/misc_rna_as_illumina.fastq",
+ "test/data/fastq/misc_rna_as_sanger.fastq",
+ "test/data/fastq/misc_rna_as_solexa.fastq",
+ "test/data/fastq/misc_rna_original_sanger.fastq",
+ "test/data/fastq/sanger_full_range_as_illumina.fastq",
+ "test/data/fastq/sanger_full_range_as_sanger.fastq",
+ "test/data/fastq/sanger_full_range_as_solexa.fastq",
+ "test/data/fastq/sanger_full_range_original_sanger.fastq",
+ "test/data/fastq/solexa_full_range_as_illumina.fastq",
+ "test/data/fastq/solexa_full_range_as_sanger.fastq",
+ "test/data/fastq/solexa_full_range_as_solexa.fastq",
+ "test/data/fastq/solexa_full_range_original_solexa.fastq",
+ "test/data/fastq/wrapping_as_illumina.fastq",
+ "test/data/fastq/wrapping_as_sanger.fastq",
+ "test/data/fastq/wrapping_as_solexa.fastq",
+ "test/data/fastq/wrapping_original_sanger.fastq",
"test/data/gcg/pileup-aa.msf",
"test/data/genscan/sample.report",
"test/data/iprscan/merged.raw",
"test/data/iprscan/merged.txt",
+ "test/data/meme/db",
+ "test/data/meme/mast",
+ "test/data/meme/mast.out",
+ "test/data/meme/meme.out",
"test/data/paml/codeml/control_file.txt",
"test/data/paml/codeml/output.txt",
"test/data/paml/codeml/rates",
+ "test/data/phyloxml/apaf.xml",
+ "test/data/phyloxml/bcl_2.xml",
+ "test/data/phyloxml/made_up.xml",
+ "test/data/phyloxml/ncbi_taxonomy_mollusca_short.xml",
+ "test/data/phyloxml/phyloxml_examples.xml",
"test/data/prosite/prosite.dat",
"test/data/refseq/nm_126355.entret",
"test/data/rpsblast/misc.rpsblast",
+ "test/data/sanger_chromatogram/test_chromatogram_abif.ab1",
+ "test/data/sanger_chromatogram/test_chromatogram_scf_v2.scf",
+ "test/data/sanger_chromatogram/test_chromatogram_scf_v3.scf",
"test/data/sim4/complement-A4.sim4",
"test/data/sim4/simple-A4.sim4",
"test/data/sim4/simple2-A4.sim4",
"test/data/soft/GDS100_partial.soft",
"test/data/soft/GSE3457_family_partial.soft",
@@ -355,10 +482,13 @@
"test/unit/bio/appl/gcg/test_msf.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/meme/mast/test_report.rb",
+ "test/unit/bio/appl/meme/test_mast.rb",
+ "test/unit/bio/appl/meme/test_motif.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/sim4/test_report.rb",
"test/unit/bio/appl/sosui/test_report.rb",
@@ -376,20 +506,33 @@
"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/fasta/test_format_qual.rb",
+ "test/unit/bio/db/kegg/test_compound.rb",
+ "test/unit/bio/db/kegg/test_drug.rb",
+ "test/unit/bio/db/kegg/test_enzyme.rb",
"test/unit/bio/db/kegg/test_genes.rb",
+ "test/unit/bio/db/kegg/test_glycan.rb",
+ "test/unit/bio/db/kegg/test_orthology.rb",
+ "test/unit/bio/db/kegg/test_reaction.rb",
"test/unit/bio/db/pdb/test_pdb.rb",
+ "test/unit/bio/db/sanger_chromatogram/test_abif.rb",
+ "test/unit/bio/db/sanger_chromatogram/test_scf.rb",
"test/unit/bio/db/test_aaindex.rb",
"test/unit/bio/db/test_fasta.rb",
+ "test/unit/bio/db/test_fastq.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_phyloxml.rb",
+ "test/unit/bio/db/test_phyloxml_writer.rb",
"test/unit/bio/db/test_prosite.rb",
+ "test/unit/bio/db/test_qual.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",
@@ -402,10 +545,11 @@
"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/sequence/test_quality_score.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",
@@ -441,9 +585,10 @@
s.extra_rdoc_files = [
"ChangeLog",
"KNOWN_ISSUES.rdoc",
"README.rdoc",
"README_DEV.rdoc",
+ "RELEASE_NOTES.rdoc",
"doc/Changes-1.3.rdoc"
]
s.rdoc_options << '--main' << 'README.rdoc'
s.rdoc_options << '--title' << 'BioRuby API documentation'
s.rdoc_options << '--exclude' << '\.yaml\z'