bio-polyploid-tools 0.3.1 → 0.3.3
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- checksums.yaml +4 -4
- data/VERSION +1 -1
- data/bin/polymarker.rb +30 -12
- data/bin/snps_between_bams.rb +1 -1
- data/bio-polyploid-tools.gemspec +3 -3
- data/lib/bio/PolyploidTools/SNP.rb +5 -4
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 381e678b7d15cffb675e941b461ccd7a8cbc1132
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data.tar.gz: bb2632d78ed15718ea6e295de21539e158896625
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 7c3c364a4fc0bdd6e20aa69eacb9e76c90e1a8b34de50775ce5a77177d4438c3f0b768e73e751f282bfa14dc88645e8e19c1c69c0ce4d60d9c01d5371bb0ea08
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data.tar.gz: f16d826561a31ac8d045ca9934068f6f7f2101d306405c5c5d0d0aaa8bc8976039fcc3d0f5f3d0170f08f150257e914a135a706f1f07ae8b6e85b0572d46cb0c
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.3.
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1
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0.3.3
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data/bin/polymarker.rb
CHANGED
@@ -10,8 +10,23 @@ $: << File.expand_path('.')
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path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
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require path
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arm_selection_functions = Hash.new;
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arm_selection_functions[:arm_selection_first_two] = lambda do | contig_name |
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ret = contig_name[0,2]
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return ret
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end
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#Function to parse stuff like: IWGSC_CSS_1AL_scaff_110
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arm_selection_functions[:arm_selection_embl] = lambda do | contig_name|
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ret = contig_name.split('_')[2][0,2]
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return ret
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end
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arm_selection_functions[:arm_selection_morex] = lambda do | contig_name |
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ret = contig_name.split(':')[0].split("_")[1];
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return ret
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end
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options = {}
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options[:path_to_contigs] = "/tgac/references/external/projects/iwgsc/css/IWGSC_CSS_all_scaff_v1.fa"
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@@ -19,6 +34,7 @@ options[:chunks] = 1
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options[:bucket_size] = 0
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options[:bucket] = 1
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options[:model] = "est2genome"
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options[:arm_selection] = arm_selection_functions[:arm_selection_embl] ;
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OptionParser.new do |opts|
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opts.banner = "Usage: polymarker.rb [options]"
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@@ -45,6 +61,10 @@ OptionParser.new do |opts|
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opts.on("-e", "--exonerate_model MODEL", "Model to be used in exonerate to search for the contigs") do |o|
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options[:model] = o
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end
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+
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opts.on("-a", "--arm_selection arm_selection_embl|arm_selection_morex|arm_selection_first_two", "Function to decide the chromome arm") do |o|
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options[:arm_selection] = arm_selection_functions[o.to_sym];
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end
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end.parse!
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@@ -115,8 +135,14 @@ File.open(test_file) do | f |
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snp = Bio::PolyploidTools::SNPSequence.parse(line)
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elsif options[:snp_list] and options[:reference] #List and fasta file
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snp = Bio::PolyploidTools::SNP.parse(line)
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-
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-
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entry = fasta_reference_db.index.region_for_entry(snp.gene)
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if entry
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region = fasta_reference_db.index.region_for_entry(snp.gene).get_full_region
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snp.template_sequence = fasta_reference_db.fetch_sequence(region)
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else
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$stderr.puts "Unable to find entry for #{snp.gene}"
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end
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else
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rise Bio::DB::Exonerate::ExonerateException.new "Wrong number of arguments. "
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end
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@@ -178,15 +204,7 @@ contigs_f.close()
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#Custom arm selection function that only uses the first two characters. Maybe
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#we want to make it a bit more cleaver
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write_status "Reading best alignment on each chromosome"
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-
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ret = contig_name[0,2]
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-
return ret
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-
end
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#Function to parse stuff like: IWGSC_CSS_1AL_scaff_110
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arm_selection_embl = lambda do | contig_name|
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ret = contig_name.split('_')[2][0,2]
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-
return ret
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-
end
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+
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container= Bio::PolyploidTools::ExonContainer.new
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container.flanking_size=100
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@@ -199,7 +217,7 @@ snps.each do |snp|
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snp.flanking_size = container.flanking_size
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container.add_snp(snp)
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end
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-
container.add_alignments({:exonerate_file=>exonerate_file, :arm_selection=>
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container.add_alignments({:exonerate_file=>exonerate_file, :arm_selection=>options[:arm_selection] , :min_identity=>min_identity})
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#4.1 generating primer3 file
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data/bin/snps_between_bams.rb
CHANGED
@@ -15,7 +15,7 @@ require path
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fasta_db = Bio::DB::Fasta::FastaFile.new(
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fasta_db = Bio::DB::Fasta::FastaFile.new( ARGV[0])
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fasta_db.load_fai_entries
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bam1 = Bio::DB::Sam.new({:fasta=>ARGV[0], :bam=>ARGV[1]})
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bam2 = Bio::DB::Sam.new({:fasta=>ARGV[0], :bam=>ARGV[2]})
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data/bio-polyploid-tools.gemspec
CHANGED
@@ -2,16 +2,16 @@
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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-polyploid-tools 0.3.
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# stub: bio-polyploid-tools 0.3.3 ruby lib
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Gem::Specification.new do |s|
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s.name = "bio-polyploid-tools"
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s.version = "0.3.
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s.version = "0.3.3"
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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 H. Ramirez-Gonzalez"]
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s.date = "2014-05-
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s.date = "2014-05-30"
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s.description = "Repository of tools developed in TGAC and Crop Genetics in JIC to work with polyploid wheat"
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s.email = "ricardo.ramirez-gonzalez@tgac.ac.uk"
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s.executables = ["bfr.rb", "count_variations.rb", "filter_blat_by_target_coverage.rb", "find_best_blat_hit.rb", "find_best_exonerate.rb", "hexaploid_primers.rb", "homokaryot_primers.rb", "map_markers_to_contigs.rb", "markers_in_region.rb", "polymarker.rb", "snps_between_bams.rb"]
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@@ -13,7 +13,7 @@ module Bio::PolyploidTools
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attr_accessor :use_reference
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attr_accessor :genomes_count
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attr_accessor :chromosome
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#Format:
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#Gene_name,Original,SNP_Pos,pos,chromosome
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@@ -40,9 +40,10 @@ module Bio::PolyploidTools
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#We Only want the chromosome, we drop the arm.
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-
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#We don't use this any more.
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#def chromosome= (chr)
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# @chromosome = chr
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#end
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def chromosome_group
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chromosome[0]
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metadata
CHANGED
@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: bio-polyploid-tools
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version: !ruby/object:Gem::Version
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version: 0.3.
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version: 0.3.3
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platform: ruby
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authors:
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- Ricardo H. Ramirez-Gonzalez
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2014-05-
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date: 2014-05-30 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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