bio-samtools 2.0.3 → 2.0.4

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data/VERSION CHANGED
@@ -1 +1 @@
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- 2.0.3
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+ 2.0.4
data/bio-samtools.gemspec CHANGED
@@ -2,17 +2,17 @@
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  # DO NOT EDIT THIS FILE DIRECTLY
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  # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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  # -*- encoding: utf-8 -*-
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- # stub: bio-samtools 2.0.3 ruby lib
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+ # stub: bio-samtools 2.0.4 ruby lib
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  # stub: ext/mkrf_conf.rb
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  Gem::Specification.new do |s|
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  s.name = "bio-samtools"
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- s.version = "2.0.3"
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+ s.version = "2.0.4"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.require_paths = ["lib"]
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  s.authors = ["Ricardo Ramirez-Gonzalez", "Dan MacLean", "Raoul J.P. Bonnal"]
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- s.date = "2014-04-18"
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+ s.date = "2014-04-28"
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  s.description = "Binder of samtools for ruby, on the top of FFI. \n\n This project was born from the need to add support of BAM files to \n the gee_fu genome browser (http://github.com/danmaclean/gee_fu)."
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  s.email = "ilpuccio.febo@gmail.com"
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  s.extensions = ["ext/mkrf_conf.rb"]
data/lib/bio-samtools.rb CHANGED
@@ -1,3 +1,4 @@
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+ require 'open3'
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  require 'bio-svgenes'
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  require 'bio'
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  require 'bio/db/sam'
@@ -5,5 +6,4 @@ require 'bio/db/pileup'
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  require 'bio/db/vcf'
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  require 'bio/db/alignment'
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  require 'bio/db/fastadb'
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- require 'open3'
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  require 'bio/BIOExtensions'
@@ -18,11 +18,12 @@ module Bio
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  class Alignment
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  attr_accessor :qname, :flag, :rname,:pos,:mapq,:cigar, :mrnm, :mpos, :isize, :seq, :qual, :tags, :al, :samstr, :calend, :qlen
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- attr_accessor :is_paired, :is_mapped, :query_unmapped, :mate_unmapped, :query_strand, :mate_strand, :first_in_pair,:second_in_pair, :primary, :failed_quality, :is_duplicate
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+ attr_accessor :sam_string, :is_paired, :is_mapped, :query_unmapped, :mate_unmapped, :query_strand, :mate_strand, :first_in_pair,:second_in_pair, :primary, :failed_quality, :is_duplicate
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  #parses the SAM string into its constituents and set its attributes
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  def initialize(sam_string)
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  s = sam_string.chomp.split("\t")
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+ @sam_string = sam_string
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  @qname = s[0]
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  @flag = s[1].to_i
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  @rname = s[2]
@@ -214,7 +214,7 @@ module Bio::DB::Fasta
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  query = region.to_s
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  query = region.to_region.to_s if region.respond_to?(:to_region)
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  command = "#{@samtools} faidx #{@fasta_path} '#{query}'"
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- puts command
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+ puts command if $VERBOSE
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  @last_command = command
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  seq = ""
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  yield_from_pipe(command, String, :text ) {|line| seq = seq + line unless line =~ /^>/}
data/lib/bio/db/sam.rb CHANGED
@@ -356,6 +356,26 @@ module Bio
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  end
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  alias_method :idxstats, :index_stats
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+
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+ #Retrive a hash with all the regions, with the region id as index or runs the function on each region
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+ def each_region
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+ stats=index_stats unless @stats
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+ if @regions
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+ return @regionss unless block_given?
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+ else
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+ @regions = Hash.new
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+ end
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+ stats.each do |k,v|
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+ reg = Bio::DB::Fasta::Region
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+ reg.entry = k
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+ reg.start = 1
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+ reg.end = v[:length]
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+ reg.orientation = :forward
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+
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+ yield reg if block_given?
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+ end
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+ @regions
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+ end
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  #Merge multiple sorted alignments
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  #* n - sort by read names
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: bio-samtools
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  version: !ruby/object:Gem::Version
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- version: 2.0.3
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+ version: 2.0.4
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  platform: ruby
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  authors:
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  - Ricardo Ramirez-Gonzalez
@@ -10,7 +10,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-04-18 00:00:00.000000000 Z
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+ date: 2014-04-28 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio-svgenes