bio-polyploid-tools 0.4.2 → 0.4.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 1cc46774ab2f15eaee35b984c144c44c122802ef
-  data.tar.gz: 36ab34ac34994a67bd56eb9748a6106bffd3045f
+  metadata.gz: e18c33d6f59147dfc491ff461b64d29a8633f1d2
+  data.tar.gz: 715a7c85a2543040aac59aa877df1af68fb9eac9
 SHA512:
-  metadata.gz: 9d08e9a320ce0994620c3687915f96cb7badf54a59f8ec3fda15bdc7497638d6d2dac815d8eadb2ac9d279b0fb781cc8d4e284dd6542cdc89a0b579b183f804a
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+  metadata.gz: b1fffb8d0e4a70d30632f9db81a51c5292f7867d3e64f66f468a9875b3336885b3952bb3fbb701ba4470d9e5bab66fd43638565c0f83540d7937f0e1100f5bb7
+  data.tar.gz: 4938c8487632b74f53778b695cc896d3bcf542e1a9e92eca24076b2d6b6fbe3744c18df1258bee751a0d5491d7d6cc99120b2429d0c597fe53c7cec387dbf288

data/VERSION

@@ -1 +1 @@
-0.4.2
+0.4.3

data/bin/filter_blat_by_target_coverage.rb

@@ -1,15 +1,69 @@
 #!/usr/bin/env ruby
 require 'bio'
+require 'optparse'
 $: << File.expand_path(File.dirname(__FILE__) + '/../lib')
 $: << File.expand_path('.')
 path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
 require path
+module Bio
+	class Blat
+  		class StreamedReport < Report 
 
-blat_file=ARGV[0]
+  			def self.each_hit(text = '')
+  				flag = false
+  				head = []
 
-blat_aln = Bio::Blat::Report.new(Bio::FlatFile.open(blat_file).to_io)
-blat_aln.each_hit() do |hit|
-  if hit.percentage_covered >= 50
+  				text.each_line do |line|
+  					if flag then
+  						yield Hit.new(line)
+  					else
+            		# for headerless data
+            			if /^\d/ =~ line then
+            				flag = true
+            				redo
+            			end
+            			line = line.chomp
+            			if /\A\-+\s*\z/ =~ line
+            				flag = true
+            			else
+            				head << line
+            			end
+            		end
+            	end
+            end
+        end
+    end
+end
+
+
+#blat_file=ARGV[0]
+
+options = {}
+options[:identity] = 95
+options[:covered] = 60
+OptionParser.new do |opts|
+  
+  opts.banner = "Usage: polymarker.rb [options]"
+
+  opts.on("-p", "--psl FILE", "PSL file") do |o|
+    options[:blat_file] = o.upcase
+  end
+  opts.on("-i", "--identity FLOAT", "Minimum percentage identity") do |o|
+    options[:identity] = o.to_f
+  end
+  opts.on("-c", "--covered FLOAT", "Minimum percentage coverage") do |o|
+    options[:covered] = o.to_f
+  end
+  
+end.parse!
+
+
+blat_file = options[:blat_file]
+
+Bio::Blat::StreamedReport.each_hit(Bio::FlatFile.open(blat_file).to_io) do |hit|
+  if hit.percentage_covered >= options[:covered] and hit.percent_identity >= options[:identity]
     puts hit.data.join("\t")
   end
-end
+end
+
+

data/bin/find_best_blat_hit.rb

@@ -28,5 +28,6 @@ best_aln = Hash.new
 load_blat_alignments( blat_file,best_aln)
 puts "QUERY\tTARGET"
 best_aln.each do |k, hit|
-  puts "#{k}\t#{hit.target_id}"
+  #puts "#{k}\t#{hit.target_id}"
+   puts hit.data.join("\t")
 end

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 0.4.2 ruby lib
+# stub: bio-polyploid-tools 0.4.3 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools"
-  s.version = "0.4.2"
+  s.version = "0.4.3"
 
   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 = "2014-09-26"
+  s.date = "2014-10-04"
   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", "snp_position_to_polymarker.rb", "snps_between_bams.rb"]

data/lib/bio/PolyploidTools/ExonContainer.rb

@@ -128,6 +128,7 @@ module Bio::PolyploidTools
 
     def print_primer_3_exons (file, target_chromosome , parental )
       added = 0
+     
       @snp_map.each do | gene, snp_array|
         snp_array.each do |snp|
           string = ""
@@ -140,7 +141,8 @@ module Bio::PolyploidTools
             end 
            rescue Exception=>e
              @missing_exons << snp.to_s
-              #$stderr.puts e.to_s
+
+              $stderr.puts e.to_s
             end
         end 
       end

data/lib/bio/PolyploidTools/SNP.rb

@@ -288,7 +288,7 @@ module Bio::PolyploidTools
       primer_3_propertes = Array.new
 
       seq_original = String.new(pr.sequence)
-      put seq_original.size << "-" << primer_3_min_seq_length
+      #puts seq_original.size.to_s << "-" << primer_3_min_seq_length.to_s
       return primer_3_propertes if seq_original.size < primer_3_min_seq_length
       seq_original[pr.snp_pos] = self.original
       seq_original_reverse = reverse_complement_string(seq_original)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.4.2
+  version: 0.4.3
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-09-26 00:00:00.000000000 Z
+date: 2014-10-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio