bio-ucsc-api 0.5.1 → 0.5.2

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Files changed (7) hide show
  1. data/ChangeLog.md +1 -0
  2. data/README.md +3 -4
  3. data/VERSION +1 -1
  4. data/bio-ucsc-api.gemspec +2 -2
  5. data/lib/bio-ucsc.rb +1 -1
  6. data/lib/bio-ucsc/file/twobit.rb +10 -6
  7. metadata +25 -25
data/ChangeLog.md CHANGED
@@ -1,4 +1,5 @@
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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.
data/README.md CHANGED
@@ -1,4 +1,4 @@
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- # bio-ucsc-api version 0.5.1
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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
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- Bio::Ucsc::Hg19.connec
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- i = Bio::GenomicInterval.parse("chr1:1,000,000-1,100,000")
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- r = Bio::Ucsc::Hg19::RefGene.find_by_interval(i)
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+ Bio::Ucsc::Hg19.connect
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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}]"}
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.5.1
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+ 0.5.2
data/bio-ucsc-api.gemspec CHANGED
@@ -5,11 +5,11 @@
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  Gem::Specification.new do |s|
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  s.name = "bio-ucsc-api"
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- s.version = "0.5.1"
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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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- s.date = "2012-09-27"
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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 = [
data/lib/bio-ucsc.rb CHANGED
@@ -17,7 +17,7 @@ require "#{base}/gi.rb"
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  module Bio
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  module Ucsc
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- VERSION = "0.5.1"
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+ VERSION = "0.5.2"
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  base = "#{::File.dirname(__FILE__)}/bio-ucsc"
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  # mammmals #####################################
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,:contained_by
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+ when :equal,:contains
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  seq = 'N' * interval.overlap(nb)
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- when :contains
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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[0, left_len] = 'N' * left_len
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- seq[-right_len, right_len] = 'N' * right_len
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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
metadata CHANGED
@@ -1,7 +1,7 @@
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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: 0.5.1
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+ version: 0.5.2
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  prerelease:
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  platform: ruby
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  authors:
@@ -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: 2012-09-27 00:00:00.000000000 Z
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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: &158480880 !ruby/object:Gem::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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  - - ! '>='
@@ -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
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- version_requirements: *158480880
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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: &158480020 !ruby/object:Gem::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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  - - ! '>='
@@ -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: *158480020
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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: &158479400 !ruby/object:Gem::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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  - - ~>
@@ -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: *158479400
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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: &158478820 !ruby/object:Gem::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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  - - ! '>='
@@ -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: *158478820
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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: &158494120 !ruby/object:Gem::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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  - - ! '>='
@@ -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: *158494120
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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: &158493200 !ruby/object:Gem::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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  - - ~>
@@ -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: *158493200
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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: &158492580 !ruby/object:Gem::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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  - - ~>
@@ -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: *158492580
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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: &158491920 !ruby/object:Gem::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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  - - ~>
@@ -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: *158491920
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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: &158491160 !ruby/object:Gem::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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  - - ~>
@@ -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: *158491160
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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: &158490320 !ruby/object:Gem::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: *158490320
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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: &158488760 !ruby/object:Gem::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: *158488760
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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: []
@@ -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: 4141800298986362982
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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: