bio-ucsc-api 0.5.1 → 0.5.2
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- data/ChangeLog.md +1 -0
- data/README.md +3 -4
- data/VERSION +1 -1
- data/bio-ucsc-api.gemspec +2 -2
- data/lib/bio-ucsc.rb +1 -1
- data/lib/bio-ucsc/file/twobit.rb +10 -6
- metadata +25 -25
data/ChangeLog.md
CHANGED
@@ -1,4 +1,5 @@
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1
1
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#Change Log
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+
* **BUG-FIX** (v 0.5.2): Fix a Bio::Ucsc::File::Twobit#subseq error when a query region is all included by a masked (Ns) region
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* **UPDATE** (v.0.5.1): Mouse mm10 database is supported.
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* **BUG-FIX** (v.0.5.0): Connecting multiple databeses simultaneously now works well.
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* **NEW** (v0.5.0): Support automatic definitions of table association using the "all.joiner" schema file.
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data/README.md
CHANGED
@@ -1,4 +1,4 @@
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-
# bio-ucsc-api version 0.5.
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# bio-ucsc-api version 0.5.2
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**The Ruby UCSC API**: accessing the UCSC Genome Database using Ruby.
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@@ -124,9 +124,8 @@ Sometimes, queries using raw SQLs provide elegant solutions.
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For gene prediction (genePred) tables, such as RefSeq, EndGene, and WgEncodeGencodeBasicV12, Ruby UCSC API automatically implements `#exon`, `#introns`, `#cdss` (or an alias `#cdses`) methods. Exons, introns, and CDSes are accessible as Array objects of `Bio::GenomicInterval`.
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```ruby
|
127
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-
Bio::Ucsc::Hg19.
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128
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-
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129
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-
r = Bio::Ucsc::Hg19::RefGene.find_by_interval(i)
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127
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+
Bio::Ucsc::Hg19.connect
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128
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+
r = Bio::Ucsc::Hg19::RefGene.with_interval("chr1:1,000,000-1,100,000").first
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puts "gene strand = #{r.strand}"
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r.exons.each{|x|puts "[#{x.chr_start}, #{x.chr_end}]"}
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r.cdss.each{|x|puts "[#{x.chr_start}, #{x.chr_end}]"}
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.5.
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1
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+
0.5.2
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data/bio-ucsc-api.gemspec
CHANGED
@@ -5,11 +5,11 @@
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5
5
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Gem::Specification.new do |s|
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s.name = "bio-ucsc-api"
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-
s.version = "0.5.
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8
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+
s.version = "0.5.2"
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s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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s.authors = ["Hiroyuki Mishima", "Jan Aerts"]
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12
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-
s.date = "2012-
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12
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+
s.date = "2012-12-20"
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s.description = "Ruby UCSC API: accessing the UCSC Genome Database using Ruby"
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s.email = "missy@be.to"
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s.extra_rdoc_files = [
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data/lib/bio-ucsc.rb
CHANGED
data/lib/bio-ucsc/file/twobit.rb
CHANGED
@@ -112,18 +112,22 @@ module Bio
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end
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def find_by_interval(interval)
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# does not support an interval involving multiple N-blocks
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+
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interval = Bio::Ucsc::Gi.wrap(interval)
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seq = self.find_by_interval_raw(interval)
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@records[interval.chrom].n_block_intervals.map do |nb|
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if interval.overlapped?(nb)
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case interval.compare(nb)
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when :equal,:
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when :equal,:contains
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seq = 'N' * interval.overlap(nb)
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-
when :
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123
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-
left_len = nb.chr_start - interval.chr_start + 1
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-
right_len = interval.chr_end - nb.chr_end + 1
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-
seq
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-
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when :contained_by
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left_len = nb.chr_start - interval.chr_start + 1
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right_len = interval.chr_end - nb.chr_end + 1
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seq =
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seq[0 .. left_len] +
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'N' * (seq.length - left_len - right_len) +
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seq[-right_len .. -1]
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when :left_overlapped
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left_len = nb.chr_end - interval.chr_start + 1
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seq[0, left_len] = 'N' * left_len
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metadata
CHANGED
@@ -1,7 +1,7 @@
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1
1
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--- !ruby/object:Gem::Specification
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name: bio-ucsc-api
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version: !ruby/object:Gem::Version
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-
version: 0.5.
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+
version: 0.5.2
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prerelease:
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platform: ruby
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authors:
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@@ -10,11 +10,11 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2012-
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+
date: 2012-12-20 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: activerecord
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-
requirement: &
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requirement: &254854620 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -22,10 +22,10 @@ dependencies:
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version: 3.0.7
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type: :runtime
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prerelease: false
|
25
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-
version_requirements: *
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+
version_requirements: *254854620
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- !ruby/object:Gem::Dependency
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name: activesupport
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-
requirement: &
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requirement: &254853820 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -33,10 +33,10 @@ dependencies:
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version: 3.0.7
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type: :runtime
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prerelease: false
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-
version_requirements: *
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+
version_requirements: *254853820
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- !ruby/object:Gem::Dependency
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name: mysql
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-
requirement: &
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requirement: &254853120 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -44,10 +44,10 @@ dependencies:
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version: 2.8.1
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type: :runtime
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prerelease: false
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-
version_requirements: *
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+
version_requirements: *254853120
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- !ruby/object:Gem::Dependency
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name: bio-genomic-interval
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-
requirement: &
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+
requirement: &254868560 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -55,10 +55,10 @@ dependencies:
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version: 0.1.2
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type: :runtime
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prerelease: false
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-
version_requirements: *
|
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+
version_requirements: *254868560
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- !ruby/object:Gem::Dependency
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name: safe_attributes
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-
requirement: &
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+
requirement: &254867560 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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@@ -66,10 +66,10 @@ dependencies:
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version: 1.0.8
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type: :runtime
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prerelease: false
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-
version_requirements: *
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+
version_requirements: *254867560
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- !ruby/object:Gem::Dependency
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name: rake
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-
requirement: &
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+
requirement: &254866900 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -77,10 +77,10 @@ dependencies:
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version: 0.9.2.2
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type: :development
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prerelease: false
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-
version_requirements: *
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+
version_requirements: *254866900
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- !ruby/object:Gem::Dependency
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name: rspec
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-
requirement: &
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requirement: &254866200 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -88,10 +88,10 @@ dependencies:
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version: 2.9.0
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type: :development
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prerelease: false
|
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-
version_requirements: *
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+
version_requirements: *254866200
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- !ruby/object:Gem::Dependency
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name: bundler
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-
requirement: &
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requirement: &254865620 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -99,10 +99,10 @@ dependencies:
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version: 1.1.0
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type: :development
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prerelease: false
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-
version_requirements: *
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+
version_requirements: *254865620
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- !ruby/object:Gem::Dependency
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name: jeweler
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-
requirement: &
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requirement: &254864760 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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@@ -110,10 +110,10 @@ dependencies:
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version: 1.8.3
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type: :development
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prerelease: false
|
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-
version_requirements: *
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+
version_requirements: *254864760
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- !ruby/object:Gem::Dependency
|
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name: bio
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-
requirement: &
|
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requirement: &254864120 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
|
@@ -121,10 +121,10 @@ dependencies:
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version: 1.4.1
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type: :development
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prerelease: false
|
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-
version_requirements: *
|
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+
version_requirements: *254864120
|
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- !ruby/object:Gem::Dependency
|
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name: rdoc
|
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-
requirement: &
|
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+
requirement: &254863240 !ruby/object:Gem::Requirement
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none: false
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requirements:
|
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|
- - ! '>='
|
@@ -132,7 +132,7 @@ dependencies:
|
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version: 3.9.1
|
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type: :development
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prerelease: false
|
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-
version_requirements: *
|
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+
version_requirements: *254863240
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description: ! 'Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
|
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email: missy@be.to
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executables: []
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@@ -575,7 +575,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
|
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version: '0'
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segments:
|
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- 0
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-
hash:
|
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+
hash: 3725389478649005497
|
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|
required_rubygems_version: !ruby/object:Gem::Requirement
|
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none: false
|
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requirements:
|