bio-polyploid-tools 0.3.1 → 0.3.3

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 16fa6b61e54d6a6da47867826435194605ce0d22
+  metadata.gz: 381e678b7d15cffb675e941b461ccd7a8cbc1132
+  data.tar.gz: bb2632d78ed15718ea6e295de21539e158896625
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data/VERSION

@@ -1 +1 @@
-0.3.1
+0.3.3

data/bin/polymarker.rb

@@ -10,8 +10,23 @@ $: << File.expand_path('.')
 path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
 require path
 
+arm_selection_functions = Hash.new;
 
 
+arm_selection_functions[:arm_selection_first_two] = lambda do | contig_name |
+  ret = contig_name[0,2]       
+  return ret
+end
+#Function to parse stuff like: IWGSC_CSS_1AL_scaff_110
+arm_selection_functions[:arm_selection_embl] = lambda do | contig_name|
+  ret = contig_name.split('_')[2][0,2]
+  return ret
+end
+
+arm_selection_functions[:arm_selection_morex] = lambda do | contig_name |
+  ret = contig_name.split(':')[0].split("_")[1];       
+  return ret
+end
 
 options = {}
 options[:path_to_contigs] = "/tgac/references/external/projects/iwgsc/css/IWGSC_CSS_all_scaff_v1.fa"
@@ -19,6 +34,7 @@ options[:chunks] = 1
 options[:bucket_size] = 0
 options[:bucket] = 1
 options[:model] = "est2genome"
+options[:arm_selection] = arm_selection_functions[:arm_selection_embl] ;
 OptionParser.new do |opts|
   opts.banner = "Usage: polymarker.rb [options]"
 
@@ -45,6 +61,10 @@ OptionParser.new do |opts|
   opts.on("-e", "--exonerate_model MODEL", "Model to be used in exonerate to search for the contigs") do |o|
      options[:model] = o
    end
+
+   opts.on("-a", "--arm_selection arm_selection_embl|arm_selection_morex|arm_selection_first_two", "Function to decide the chromome arm") do |o|
+    options[:arm_selection] = arm_selection_functions[o.to_sym];
+   end
   
     
 end.parse!
@@ -115,8 +135,14 @@ File.open(test_file) do | f |
       snp = Bio::PolyploidTools::SNPSequence.parse(line)  
     elsif options[:snp_list] and options[:reference] #List and fasta file
       snp = Bio::PolyploidTools::SNP.parse(line)
-      region = fasta_reference_db.index.region_for_entry(snp.gene).get_full_region
-      snp.template_sequence = fasta_reference_db.fetch_sequence(region)
+      entry = fasta_reference_db.index.region_for_entry(snp.gene)
+      if entry
+       region = fasta_reference_db.index.region_for_entry(snp.gene).get_full_region
+       snp.template_sequence = fasta_reference_db.fetch_sequence(region)
+     else
+        $stderr.puts "Unable to find entry for #{snp.gene}"
+      end
+
     else
       rise Bio::DB::Exonerate::ExonerateException.new "Wrong number of arguments. " 
     end
@@ -178,15 +204,7 @@ contigs_f.close()
 #Custom arm selection function that only uses the first two characters. Maybe
 #we want to make it a bit more cleaver
 write_status "Reading best alignment on each chromosome"
-arm_selection_first_two = lambda do | contig_name |
-  ret = contig_name[0,2]       
-  return ret
-end
-#Function to parse stuff like: IWGSC_CSS_1AL_scaff_110
-arm_selection_embl = lambda do | contig_name|
-  ret = contig_name.split('_')[2][0,2]
-  return ret
-end
+
 
 container= Bio::PolyploidTools::ExonContainer.new
 container.flanking_size=100
@@ -199,7 +217,7 @@ snps.each do |snp|
   snp.flanking_size = container.flanking_size
   container.add_snp(snp)
 end
-container.add_alignments({:exonerate_file=>exonerate_file, :arm_selection=>arm_selection_embl, :min_identity=>min_identity})
+container.add_alignments({:exonerate_file=>exonerate_file, :arm_selection=>options[:arm_selection] , :min_identity=>min_identity})
 
 
 #4.1 generating primer3 file

data/bin/snps_between_bams.rb

@@ -15,7 +15,7 @@ require path
 
 
 
-fasta_db = Bio::DB::Fasta::FastaFile.new(:fasta=>ARGV[0])
+fasta_db = Bio::DB::Fasta::FastaFile.new( ARGV[0])
 fasta_db.load_fai_entries
 bam1 =  Bio::DB::Sam.new({:fasta=>ARGV[0], :bam=>ARGV[1]})
 bam2 =  Bio::DB::Sam.new({:fasta=>ARGV[0], :bam=>ARGV[2]})

data/bio-polyploid-tools.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.3.1 ruby lib
+# stub: bio-polyploid-tools 0.3.3 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools"
-  s.version = "0.3.1"
+  s.version = "0.3.3"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Ricardo H.  Ramirez-Gonzalez"]
-  s.date = "2014-05-08"
+  s.date = "2014-05-30"
   s.description = "Repository of tools developed in TGAC and Crop Genetics in JIC to work with polyploid wheat"
   s.email = "ricardo.ramirez-gonzalez@tgac.ac.uk"
   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"]

data/lib/bio/PolyploidTools/SNP.rb

@@ -13,7 +13,7 @@ module Bio::PolyploidTools
     attr_accessor :use_reference
     attr_accessor :genomes_count
     
-    attr_reader :chromosome
+    attr_accessor :chromosome
 
     #Format: 
     #Gene_name,Original,SNP_Pos,pos,chromosome
@@ -40,9 +40,10 @@ module Bio::PolyploidTools
     
     
     #We Only want the chromosome, we drop the arm. 
-    def chromosome= (chr)
-      @chromosome = chr[0,2]
-    end
+    #We don't use this any more. 
+    #def chromosome= (chr)
+    #  @chromosome = chr
+    #end
     
     def chromosome_group
       chromosome[0]

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.3.3
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-05-08 00:00:00.000000000 Z
+date: 2014-05-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio