bio 1.4.2 → 1.4.3
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- data/.travis.yml +66 -0
- data/ChangeLog +989 -4524
- data/KNOWN_ISSUES.rdoc +67 -2
- data/README.rdoc +89 -23
- data/README_DEV.rdoc +93 -2
- data/RELEASE_NOTES.rdoc +167 -95
- data/Rakefile +199 -7
- data/bioruby.gemspec +27 -12
- data/bioruby.gemspec.erb +6 -3
- data/doc/ChangeLog-before-1.4.2 +5013 -0
- data/doc/RELEASE_NOTES-1.4.2.rdoc +132 -0
- data/doc/Tutorial.rd +21 -3
- data/doc/Tutorial.rd.html +20 -12
- data/etc/bioinformatics/seqdatabase.ini +13 -196
- data/gemfiles/Gemfile.travis-jruby1.8 +7 -0
- data/gemfiles/Gemfile.travis-jruby1.9 +10 -0
- data/gemfiles/Gemfile.travis-ruby1.8 +7 -0
- data/gemfiles/Gemfile.travis-ruby1.9 +10 -0
- data/gemfiles/modify-Gemfile.rb +28 -0
- data/gemfiles/prepare-gemspec.rb +25 -0
- data/lib/bio/alignment.rb +1 -1
- data/lib/bio/appl/bl2seq/report.rb +3 -3
- data/lib/bio/appl/blast/ddbj.rb +0 -3
- data/lib/bio/appl/blast/format0.rb +4 -22
- data/lib/bio/appl/blast/genomenet.rb +33 -16
- data/lib/bio/appl/blast/ncbioptions.rb +8 -3
- data/lib/bio/appl/blast/remote.rb +6 -5
- data/lib/bio/appl/blast/report.rb +10 -6
- data/lib/bio/appl/blast/rpsblast.rb +3 -2
- data/lib/bio/appl/blast/wublast.rb +3 -3
- data/lib/bio/command.rb +118 -36
- data/lib/bio/data/na.rb +1 -1
- data/lib/bio/db/embl/embl.rb +74 -0
- data/lib/bio/db/embl/format_embl.rb +0 -4
- data/lib/bio/db/fasta.rb +57 -45
- data/lib/bio/db/fasta/defline.rb +1 -1
- data/lib/bio/db/fasta/format_fasta.rb +0 -4
- data/lib/bio/db/fasta/format_qual.rb +0 -5
- data/lib/bio/db/fastq/format_fastq.rb +0 -1
- data/lib/bio/db/genbank/format_genbank.rb +0 -4
- data/lib/bio/db/gff.rb +41 -12
- data/lib/bio/db/kegg/genes.rb +3 -3
- data/lib/bio/db/kegg/kgml.rb +465 -64
- data/lib/bio/db/newick.rb +0 -244
- data/lib/bio/db/pdb.rb +1 -4
- data/lib/bio/db/pdb/atom.rb +3 -2
- data/lib/bio/db/pdb/chain.rb +2 -3
- data/lib/bio/db/pdb/chemicalcomponent.rb +3 -2
- data/lib/bio/db/pdb/model.rb +2 -2
- data/lib/bio/db/pdb/pdb.rb +2 -1
- data/lib/bio/db/pdb/residue.rb +2 -2
- data/lib/bio/db/pdb/utils.rb +7 -4
- data/lib/bio/db/phyloxml/phyloxml_parser.rb +52 -5
- data/lib/bio/feature.rb +2 -3
- data/lib/bio/io/flatfile/autodetection.rb +1 -1
- data/lib/bio/io/flatfile/buffer.rb +84 -0
- data/lib/bio/sequence.rb +6 -4
- data/lib/bio/sequence/aa.rb +3 -5
- data/lib/bio/sequence/adapter.rb +6 -6
- data/lib/bio/sequence/common.rb +3 -3
- data/lib/bio/sequence/compat.rb +2 -7
- data/lib/bio/sequence/dblink.rb +6 -5
- data/lib/bio/sequence/format.rb +0 -6
- data/lib/bio/sequence/format_raw.rb +0 -4
- data/lib/bio/sequence/generic.rb +3 -4
- data/lib/bio/sequence/na.rb +4 -6
- data/lib/bio/sequence/quality_score.rb +2 -0
- data/lib/bio/sequence/sequence_masker.rb +3 -0
- data/lib/bio/shell/core.rb +1 -0
- data/lib/bio/tree.rb +1 -2
- data/lib/bio/tree/output.rb +264 -0
- data/lib/bio/util/restriction_enzyme.rb +1 -3
- data/lib/bio/util/restriction_enzyme/analysis.rb +8 -5
- data/lib/bio/util/restriction_enzyme/analysis_basic.rb +4 -3
- data/lib/bio/util/restriction_enzyme/cut_symbol.rb +3 -2
- data/lib/bio/util/restriction_enzyme/dense_int_array.rb +3 -0
- data/lib/bio/util/restriction_enzyme/double_stranded.rb +3 -4
- data/lib/bio/util/restriction_enzyme/double_stranded/aligned_strands.rb +3 -4
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb +3 -4
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb +3 -4
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations.rb +3 -4
- data/lib/bio/util/restriction_enzyme/double_stranded/cut_locations_in_enzyme_notation.rb +3 -4
- data/lib/bio/util/restriction_enzyme/range/cut_range.rb +3 -4
- data/lib/bio/util/restriction_enzyme/range/cut_ranges.rb +3 -4
- data/lib/bio/util/restriction_enzyme/range/horizontal_cut_range.rb +3 -4
- data/lib/bio/util/restriction_enzyme/range/sequence_range.rb +3 -4
- data/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb +3 -4
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragment.rb +3 -4
- data/lib/bio/util/restriction_enzyme/range/sequence_range/fragments.rb +3 -4
- data/lib/bio/util/restriction_enzyme/range/vertical_cut_range.rb +3 -4
- data/lib/bio/util/restriction_enzyme/single_strand.rb +3 -3
- data/lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb +3 -4
- data/lib/bio/util/restriction_enzyme/single_strand_complement.rb +3 -4
- data/lib/bio/util/restriction_enzyme/sorted_num_array.rb +3 -0
- data/lib/bio/util/restriction_enzyme/string_formatting.rb +3 -4
- data/lib/bio/version.rb +11 -2
- data/sample/seqdatabase.ini +210 -0
- data/test/bioruby_test_helper.rb +37 -12
- data/test/data/KEGG/test.kgml +37 -0
- data/test/data/command/echoarg2.bat +0 -0
- data/test/data/command/echoarg2.sh +4 -0
- data/test/functional/bio/test_command.rb +58 -28
- data/test/{functional → network}/bio/appl/blast/test_remote.rb +0 -0
- data/test/{functional → network}/bio/appl/test_blast.rb +0 -0
- data/test/{functional → network}/bio/appl/test_pts1.rb +0 -0
- data/test/{functional → network}/bio/io/test_ddbjrest.rb +0 -0
- data/test/{functional → network}/bio/io/test_ensembl.rb +0 -0
- data/test/{functional → network}/bio/io/test_pubmed.rb +0 -0
- data/test/{functional → network}/bio/io/test_soapwsdl.rb +0 -0
- data/test/{functional → network}/bio/io/test_togows.rb +0 -0
- data/test/network/bio/test_command.rb +35 -0
- data/test/runner.rb +16 -6
- data/test/unit/bio/appl/blast/test_report.rb +119 -0
- data/test/unit/bio/appl/blast/test_rpsblast.rb +1 -0
- data/test/unit/bio/data/test_na.rb +1 -1
- data/test/unit/bio/db/embl/test_embl.rb +2 -7
- data/test/unit/bio/db/embl/test_embl_rel89.rb +2 -7
- data/test/unit/bio/db/fasta/test_defline.rb +1 -1
- data/test/unit/bio/db/genbank/test_genpept.rb +1 -1
- data/test/unit/bio/db/kegg/test_drug.rb +1 -1
- data/test/unit/bio/db/kegg/test_genome.rb +1 -1
- data/test/unit/bio/db/kegg/test_glycan.rb +1 -1
- data/test/unit/bio/db/kegg/test_kgml.rb +1022 -0
- data/test/unit/bio/db/sanger_chromatogram/test_abif.rb +2 -1
- data/test/unit/bio/db/sanger_chromatogram/test_scf.rb +4 -2
- data/test/unit/bio/db/test_newick.rb +2 -0
- data/test/unit/bio/db/test_phyloxml.rb +54 -2
- data/test/unit/bio/db/test_phyloxml_writer.rb +15 -9
- data/test/unit/bio/db/test_soft.rb +1 -1
- data/test/unit/bio/io/flatfile/test_autodetection.rb +6 -0
- data/test/unit/bio/io/flatfile/test_buffer.rb +141 -0
- data/test/unit/bio/sequence/test_common.rb +36 -4
- data/test/unit/bio/sequence/test_na.rb +1 -1
- data/test/unit/bio/test_command.rb +9 -4
- data/test/unit/bio/test_sequence.rb +2 -2
- data/test/unit/bio/test_tree.rb +11 -11
- data/test/unit/bio/util/test_restriction_enzyme.rb +1 -1
- metadata +1428 -655
- data/rdoc.zsh +0 -8
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# $Id:$
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module Bio
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autoload :REBASE, 'bio/db/rebase'
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autoload :REBASE, 'bio/db/rebase' unless const_defined?(:REBASE)
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# = Description
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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require 'bio/util/restriction_enzyme'
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require 'bio/util/restriction_enzyme/analysis_basic'
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module Bio
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require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
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class RestrictionEnzyme
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class Analysis
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#--
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# require "analysis_basic.rb" here to avoid cyclic require
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#++
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require 'bio/util/restriction_enzyme/analysis_basic'
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# See cut instance method
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def self.cut( sequence, *args )
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self.new.cut( sequence, *args )
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require 'set' # for method create_enzyme_actions
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require 'bio/
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require 'bio/sequence'
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class Analysis
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# = Usage
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# A pair of SingleStrand and SingleStrandComplement objects with methods to
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module Bio
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require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
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class RestrictionEnzyme
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class DoubleStranded
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module Bio
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require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
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class RestrictionEnzyme
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class DoubleStranded
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data/lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair_in_enzyme_notation.rb
CHANGED
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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#
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# $Id: cut_location_pair_in_enzyme_notation.rb,v 1.7 2007/07/16 19:28:48 k Exp $
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require 'bio/util/restriction_enzyme'
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module Bio
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require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
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class RestrictionEnzyme
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class DoubleStranded
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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#
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# $Id: cut_locations.rb,v 1.6 2007/07/16 19:28:48 k Exp $
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require 'bio/util/restriction_enzyme'
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module Bio
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require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
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class RestrictionEnzyme
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class DoubleStranded
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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#
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# $Id: cut_locations_in_enzyme_notation.rb,v 1.7 2007/07/16 19:28:48 k Exp $
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module Bio
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require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
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class RestrictionEnzyme
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class DoubleStranded
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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module Bio
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require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
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class RestrictionEnzyme
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class Range
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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# $Id: cut_ranges.rb,v 1.5 2007/07/16 19:28:48 k Exp $
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module Bio
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require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
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class RestrictionEnzyme
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class Range
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# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
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# License:: The Ruby License
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# $Id: horizontal_cut_range.rb,v 1.5 2007/07/16 19:28:48 k Exp $
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require 'bio/util/restriction_enzyme'
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module Bio
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require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
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class RestrictionEnzyme
|
|
15
14
|
class Range
|
|
16
15
|
|
|
@@ -5,12 +5,11 @@
|
|
|
5
5
|
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
|
6
6
|
# License:: The Ruby License
|
|
7
7
|
#
|
|
8
|
-
# $Id:$
|
|
9
|
-
#
|
|
10
|
-
|
|
11
|
-
require 'bio/util/restriction_enzyme'
|
|
12
8
|
|
|
13
9
|
module Bio
|
|
10
|
+
|
|
11
|
+
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
|
|
12
|
+
|
|
14
13
|
class RestrictionEnzyme
|
|
15
14
|
class Range
|
|
16
15
|
|
|
@@ -5,12 +5,11 @@
|
|
|
5
5
|
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
|
6
6
|
# License:: The Ruby License
|
|
7
7
|
#
|
|
8
|
-
# $Id:$
|
|
9
|
-
#
|
|
10
|
-
|
|
11
|
-
require 'bio/util/restriction_enzyme'
|
|
12
8
|
|
|
13
9
|
module Bio
|
|
10
|
+
|
|
11
|
+
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
|
|
12
|
+
|
|
14
13
|
class RestrictionEnzyme
|
|
15
14
|
class Range
|
|
16
15
|
class SequenceRange
|
|
@@ -5,12 +5,11 @@
|
|
|
5
5
|
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
|
6
6
|
# License:: The Ruby License
|
|
7
7
|
#
|
|
8
|
-
# $Id:$
|
|
9
|
-
#
|
|
10
|
-
|
|
11
|
-
require 'bio/util/restriction_enzyme'
|
|
12
8
|
|
|
13
9
|
module Bio
|
|
10
|
+
|
|
11
|
+
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
|
|
12
|
+
|
|
14
13
|
class RestrictionEnzyme
|
|
15
14
|
class Range
|
|
16
15
|
class SequenceRange
|
|
@@ -5,12 +5,11 @@
|
|
|
5
5
|
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
|
6
6
|
# License:: The Ruby License
|
|
7
7
|
#
|
|
8
|
-
# $Id: fragments.rb,v 1.5 2007/07/16 19:28:48 k Exp $
|
|
9
|
-
#
|
|
10
|
-
|
|
11
|
-
require 'bio/util/restriction_enzyme'
|
|
12
8
|
|
|
13
9
|
module Bio
|
|
10
|
+
|
|
11
|
+
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
|
|
12
|
+
|
|
14
13
|
class RestrictionEnzyme
|
|
15
14
|
class Range
|
|
16
15
|
class SequenceRange
|
|
@@ -5,12 +5,11 @@
|
|
|
5
5
|
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
|
6
6
|
# License:: The Ruby License
|
|
7
7
|
#
|
|
8
|
-
# $Id: vertical_cut_range.rb,v 1.5 2007/07/16 19:28:48 k Exp $
|
|
9
|
-
#
|
|
10
|
-
|
|
11
|
-
require 'bio/util/restriction_enzyme'
|
|
12
8
|
|
|
13
9
|
module Bio
|
|
10
|
+
|
|
11
|
+
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
|
|
12
|
+
|
|
14
13
|
class RestrictionEnzyme
|
|
15
14
|
class Range
|
|
16
15
|
|
|
@@ -5,13 +5,13 @@
|
|
|
5
5
|
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
|
6
6
|
# License:: The Ruby License
|
|
7
7
|
#
|
|
8
|
-
# $Id:$
|
|
9
|
-
#
|
|
10
8
|
|
|
11
|
-
require 'bio/util/restriction_enzyme'
|
|
12
9
|
require 'bio/sequence'
|
|
13
10
|
|
|
14
11
|
module Bio
|
|
12
|
+
|
|
13
|
+
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
|
|
14
|
+
|
|
15
15
|
class RestrictionEnzyme
|
|
16
16
|
|
|
17
17
|
# A single strand of restriction enzyme sequence pattern with a 5' to 3'
|
|
@@ -5,12 +5,11 @@
|
|
|
5
5
|
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
|
6
6
|
# License:: The Ruby License
|
|
7
7
|
#
|
|
8
|
-
# $Id: cut_locations_in_enzyme_notation.rb,v 1.7 2007/07/16 19:28:48 k Exp $
|
|
9
|
-
#
|
|
10
|
-
|
|
11
|
-
require 'bio/util/restriction_enzyme'
|
|
12
8
|
|
|
13
9
|
module Bio
|
|
10
|
+
|
|
11
|
+
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
|
|
12
|
+
|
|
14
13
|
class RestrictionEnzyme
|
|
15
14
|
class SingleStrand
|
|
16
15
|
|
|
@@ -5,12 +5,11 @@
|
|
|
5
5
|
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
|
6
6
|
# License:: The Ruby License
|
|
7
7
|
#
|
|
8
|
-
# $Id: single_strand_complement.rb,v 1.5 2007/07/16 19:28:48 k Exp $
|
|
9
|
-
#
|
|
10
|
-
|
|
11
|
-
require 'bio/util/restriction_enzyme'
|
|
12
8
|
|
|
13
9
|
module Bio
|
|
10
|
+
|
|
11
|
+
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
|
|
12
|
+
|
|
14
13
|
class RestrictionEnzyme
|
|
15
14
|
|
|
16
15
|
# A single strand of restriction enzyme sequence pattern with a 3' to 5' orientation.
|
|
@@ -5,12 +5,11 @@
|
|
|
5
5
|
# Copyright:: Copyright (c) 2005-2007 Midwinter Laboratories, LLC (http://midwinterlabs.com)
|
|
6
6
|
# License:: The Ruby License
|
|
7
7
|
#
|
|
8
|
-
# $Id: string_formatting.rb,v 1.6 2007/07/16 19:28:48 k Exp $
|
|
9
|
-
#
|
|
10
|
-
|
|
11
|
-
require 'bio/util/restriction_enzyme'
|
|
12
8
|
|
|
13
9
|
module Bio
|
|
10
|
+
|
|
11
|
+
require 'bio/util/restriction_enzyme' unless const_defined?(:RestrictionEnzyme)
|
|
12
|
+
|
|
14
13
|
class RestrictionEnzyme
|
|
15
14
|
|
|
16
15
|
module StringFormatting
|
data/lib/bio/version.rb
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
#
|
|
2
2
|
# = bio/version.rb - BioRuby version information
|
|
3
3
|
#
|
|
4
|
-
# Copyright:: Copyright (C) 2001-
|
|
4
|
+
# Copyright:: Copyright (C) 2001-2012
|
|
5
5
|
# Toshiaki Katayama <k@bioruby.org>,
|
|
6
6
|
# Naohisa Goto <ng@bioruby.org>
|
|
7
7
|
# License:: The Ruby License
|
|
@@ -10,10 +10,19 @@
|
|
|
10
10
|
module Bio
|
|
11
11
|
|
|
12
12
|
# BioRuby version (Array containing Integer)
|
|
13
|
-
BIORUBY_VERSION = [1, 4,
|
|
13
|
+
BIORUBY_VERSION = [1, 4, 3].extend(Comparable).freeze
|
|
14
14
|
|
|
15
15
|
# Extra version specifier (String or nil).
|
|
16
16
|
# Existance of the value indicates pre-release version or modified version.
|
|
17
|
+
#
|
|
18
|
+
# nil :: Release version.
|
|
19
|
+
# ".0000"..".4999" :: Release version with patches.
|
|
20
|
+
# ".5000" :: Development unstable version.
|
|
21
|
+
# ".5001"..".8999" :: Pre-alpha version.
|
|
22
|
+
# "-alphaN" (N=0..99) :: Alpha version.
|
|
23
|
+
# "-preN" (N=0..99) :: Pre-release test version.
|
|
24
|
+
# "-rcN" (N=0..99) :: Release candidate version.
|
|
25
|
+
#
|
|
17
26
|
BIORUBY_EXTRA_VERSION = nil
|
|
18
27
|
|
|
19
28
|
# Version identifier, including extra version string (String)
|
|
@@ -0,0 +1,210 @@
|
|
|
1
|
+
VERSION=1.00
|
|
2
|
+
|
|
3
|
+
[embl]
|
|
4
|
+
protocol=biofetch
|
|
5
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
6
|
+
dbname=embl
|
|
7
|
+
|
|
8
|
+
[embl-upd]
|
|
9
|
+
protocol=biofetch
|
|
10
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
11
|
+
dbname=embl-upd
|
|
12
|
+
|
|
13
|
+
[embl_biofetch]
|
|
14
|
+
protocol=biofetch
|
|
15
|
+
location=http://www.ebi.ac.uk/cgi-bin/dbfetch
|
|
16
|
+
dbname=embl
|
|
17
|
+
|
|
18
|
+
[embl_biosql]
|
|
19
|
+
protocol=biosql
|
|
20
|
+
location=localhost
|
|
21
|
+
dbname=biosql
|
|
22
|
+
driver=postgres
|
|
23
|
+
user=hack
|
|
24
|
+
pass=
|
|
25
|
+
biodbname=embl
|
|
26
|
+
|
|
27
|
+
[embl_biocorba]
|
|
28
|
+
protocol=bsane-corba
|
|
29
|
+
location=sqldbsrv.ior
|
|
30
|
+
|
|
31
|
+
[embl_xembl]
|
|
32
|
+
protocol=xembl
|
|
33
|
+
location=http://www.ebi.ac.uk/xembl/XEMBL.wsdl
|
|
34
|
+
format=Bsml
|
|
35
|
+
|
|
36
|
+
[embl_flat]
|
|
37
|
+
protcol=flat
|
|
38
|
+
location=/export/database/
|
|
39
|
+
dbname=embl
|
|
40
|
+
|
|
41
|
+
[genbank_bdb]
|
|
42
|
+
protcol=flat
|
|
43
|
+
location=/export/database/
|
|
44
|
+
dbname=genbank
|
|
45
|
+
|
|
46
|
+
[swissprot]
|
|
47
|
+
protocol=biofetch
|
|
48
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
49
|
+
dbname=swissprot
|
|
50
|
+
|
|
51
|
+
[swissprot-upd]
|
|
52
|
+
protocol=biofetch
|
|
53
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
54
|
+
dbname=swissprot-upd
|
|
55
|
+
|
|
56
|
+
[swissprot_biofetch]
|
|
57
|
+
protocol=biofetch
|
|
58
|
+
location=http://www.ebi.ac.uk/cgi-bin/dbfetch
|
|
59
|
+
dbname=swall
|
|
60
|
+
|
|
61
|
+
[swissprot_biosql]
|
|
62
|
+
protocol=biosql
|
|
63
|
+
location=db.bioruby.org
|
|
64
|
+
dbname=biosql
|
|
65
|
+
driver=mysql
|
|
66
|
+
user=root
|
|
67
|
+
pass=
|
|
68
|
+
biodbname=sp
|
|
69
|
+
|
|
70
|
+
|
|
71
|
+
[genbank]
|
|
72
|
+
protocol=biofetch
|
|
73
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
74
|
+
dbname=genbank
|
|
75
|
+
|
|
76
|
+
[genbank-upd]
|
|
77
|
+
protocol=biofetch
|
|
78
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
79
|
+
dbname=genbank-upd
|
|
80
|
+
|
|
81
|
+
[genbank_biosql]
|
|
82
|
+
protocol=biosql
|
|
83
|
+
location=db.bioruby.org
|
|
84
|
+
dbname=biosql
|
|
85
|
+
driver=mysql
|
|
86
|
+
user=root
|
|
87
|
+
pass=
|
|
88
|
+
biodbname=gb
|
|
89
|
+
|
|
90
|
+
|
|
91
|
+
[refseq]
|
|
92
|
+
protocol=biofetch
|
|
93
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
94
|
+
dbname=refseq
|
|
95
|
+
|
|
96
|
+
[refseq_biosql]
|
|
97
|
+
protocol=biosql
|
|
98
|
+
location=db.bioruby.org
|
|
99
|
+
dbname=biosql
|
|
100
|
+
driver=mysql
|
|
101
|
+
user=
|
|
102
|
+
pass=
|
|
103
|
+
biodbname=rs
|
|
104
|
+
|
|
105
|
+
|
|
106
|
+
[kegg-pathway]
|
|
107
|
+
protocol=biofetch
|
|
108
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
109
|
+
dbname=pathway
|
|
110
|
+
|
|
111
|
+
[kegg-genome]
|
|
112
|
+
protocol=biofetch
|
|
113
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
114
|
+
dbname=genome
|
|
115
|
+
|
|
116
|
+
[kegg-genes]
|
|
117
|
+
protocol=biofetch
|
|
118
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
119
|
+
dbname=genes
|
|
120
|
+
|
|
121
|
+
[kegg-vgenes]
|
|
122
|
+
protocol=biofetch
|
|
123
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
124
|
+
dbname=vgenes
|
|
125
|
+
|
|
126
|
+
[aaindex]
|
|
127
|
+
protocol=biofetch
|
|
128
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
129
|
+
dbname=aaindex
|
|
130
|
+
|
|
131
|
+
[blocks]
|
|
132
|
+
protocol=biofetch
|
|
133
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
134
|
+
dbname=blocks
|
|
135
|
+
|
|
136
|
+
[enzyme]
|
|
137
|
+
protocol=biofetch
|
|
138
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
139
|
+
dbname=enzyme
|
|
140
|
+
|
|
141
|
+
[epd]
|
|
142
|
+
protocol=biofetch
|
|
143
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
144
|
+
dbname=epd
|
|
145
|
+
|
|
146
|
+
[litdb]
|
|
147
|
+
protocol=biofetch
|
|
148
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
149
|
+
dbname=litdb
|
|
150
|
+
|
|
151
|
+
[omim]
|
|
152
|
+
protocol=biofetch
|
|
153
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
154
|
+
dbname=omim
|
|
155
|
+
|
|
156
|
+
[pdb]
|
|
157
|
+
protocol=biofetch
|
|
158
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
159
|
+
dbname=pdb
|
|
160
|
+
|
|
161
|
+
[pdbstr]
|
|
162
|
+
protocol=biofetch
|
|
163
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
164
|
+
dbname=pdbstr
|
|
165
|
+
|
|
166
|
+
[pfam]
|
|
167
|
+
protocol=biofetch
|
|
168
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
169
|
+
dbname=pfam
|
|
170
|
+
|
|
171
|
+
[pir]
|
|
172
|
+
protocol=biofetch
|
|
173
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
174
|
+
dbname=pir
|
|
175
|
+
|
|
176
|
+
[pmd]
|
|
177
|
+
protocol=biofetch
|
|
178
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
179
|
+
dbname=pmd
|
|
180
|
+
|
|
181
|
+
[prf]
|
|
182
|
+
protocol=biofetch
|
|
183
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
184
|
+
dbname=prf
|
|
185
|
+
|
|
186
|
+
[prints]
|
|
187
|
+
protocol=biofetch
|
|
188
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
189
|
+
dbname=prints
|
|
190
|
+
|
|
191
|
+
[prodom]
|
|
192
|
+
protocol=biofetch
|
|
193
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
194
|
+
dbname=prodom
|
|
195
|
+
|
|
196
|
+
[prosdoc]
|
|
197
|
+
protocol=biofetch
|
|
198
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
199
|
+
dbname=prosdoc
|
|
200
|
+
|
|
201
|
+
[prosite]
|
|
202
|
+
protocol=biofetch
|
|
203
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
204
|
+
dbname=prosite
|
|
205
|
+
|
|
206
|
+
[transfac]
|
|
207
|
+
protocol=biofetch
|
|
208
|
+
location=http://bioruby.org/cgi-bin/biofetch.rb
|
|
209
|
+
dbname=transfac
|
|
210
|
+
|