bio-polyploid-tools 0.8.6 → 0.8.7

checksums.yaml

@@ -1,7 +1,7 @@
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+SHA256:
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data/README.md

@@ -128,6 +128,9 @@ To use blast instead of exonerate, use the following command:
 
 ## Release Notes
 
+### 0.8.7
+* FEATURE: ```polymarker.rb``` now also prints the total number of hits found. 
+
 ### 0.8.6
 
 * BUGFIX: ```priemr3.rb``` had a regression when adding the repetitive flag to the ```@values``` array. This lead to the wrong order of the columns in the output and possibly other secondary effects. 

data/VERSION

@@ -1 +1 @@
-0.8.6
+0.8.7

data/bin/polymarker.rb

@@ -392,7 +392,7 @@ snps.each do |snp|
 end
 
 kasp_container.add_primers_file(primer_3_output) if added_exons > 0
-header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,SNP_type,#{original_name},#{snp_in},common,primer_type,orientation,#{original_name}_TM,#{snp_in}_TM,common_TM,selected_from,product_size,errors,is_repetitive"
+header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,SNP_type,#{original_name},#{snp_in},common,primer_type,orientation,#{original_name}_TM,#{snp_in}_TM,common_TM,selected_from,product_size,errors,is_repetitive,hit_count"
 File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }
 
 File.open(output_to_order, "w") { |io|  io.write(kasp_container.print_primers_with_tails()) }

data/bio-polyploid-tools.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.8.6 ruby lib
+# stub: bio-polyploid-tools 0.8.7 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.8.6"
+  s.version = "0.8.7"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Ricardo H.  Ramirez-Gonzalez".freeze]
-  s.date = "2018-08-03"
+  s.date = "2018-08-07"
   s.description = "Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat".freeze
   s.email = "ricardo.ramirez-gonzalez@jic.ac.uk".freeze
   s.executables = ["bfr.rb".freeze, "blast_triads.rb".freeze, "blast_triads_promoters.rb".freeze, "count_variations.rb".freeze, "filter_blat_by_target_coverage.rb".freeze, "filter_exonerate_by_identity.rb".freeze, "find_best_blat_hit.rb".freeze, "find_best_exonerate.rb".freeze, "find_homoeologue_variations.rb".freeze, "get_longest_hsp_blastx_triads.rb".freeze, "hexaploid_primers.rb".freeze, "homokaryot_primers.rb".freeze, "mafft_triads.rb".freeze, "mafft_triads_promoters.rb".freeze, "map_markers_to_contigs.rb".freeze, "markers_in_region.rb".freeze, "mask_triads.rb".freeze, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "tag_stats.rb".freeze, "vcfLineToTable.rb".freeze]
@@ -179,7 +179,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "2.6.14".freeze
+  s.rubygems_version = "2.7.4".freeze
   s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze
 
   if s.respond_to? :specification_version then

data/lib/bio/PolyploidTools/ExonContainer.rb

@@ -221,6 +221,7 @@ module Bio::PolyploidTools
         snp_array.each do |snp|
           if snp.exon_list.size > max_hits
             total_hits = snp.exon_list.size
+            snp.hit_count = total_hits
             snp.exon_list = {} 
             snp.repetitive = true
             snp.errors << "The marker is in a repetitive region (#{total_hits} hits to reference)"

data/lib/bio/PolyploidTools/SNP.rb

@@ -18,6 +18,7 @@ module Bio::PolyploidTools
     attr_accessor :max_hits
     attr_accessor :errors
     attr_accessor :repetitive
+    attr_accessor :hit_count
 
 
 
@@ -69,6 +70,7 @@ module Bio::PolyploidTools
       @exon_list = Hash.new {|hsh, key| hsh[key] = [] }
       @errors = Array.new
       @repetitive = false
+      @hit_count = 0
     end
 
     def to_polymarker_coordinates(flanking_size, total:nil)
@@ -340,8 +342,9 @@ module Bio::PolyploidTools
         errors << "The sequence (#{seq_original.size}) is shorter than #{primer_3_min_seq_length}"
         return primer_3_propertes 
       end
-
-      if exon_list.size > max_hits
+      hit_count = exon_list.size
+      puts exon_list.inspect
+      if hit_count > max_hits
         errors << "The marker maps to #{exon_list.size} positions (max_hits: #{max_hits}). "
         repetitive = true
         return primer_3_propertes 

data/lib/bio/db/blast.rb

@@ -80,7 +80,7 @@ module Bio::DB::Blast
 		target=opts[:target]
 		query=opts[:query]
 		max_target_seqs = 15
-		max_target_seqs = opts[:max_hits] + 1 if opts[:max_hits]
+		max_target_seqs = opts[:max_hits] * 2 if opts[:max_hits]
 		cmdline = "blastn -max_target_seqs #{max_target_seqs} -query #{query} -db #{target} -outfmt '6 qseqid qstart qend qframe sseqid sstart send sframe score pident qlen slen qseq sseq'"
 
 		status, stdout, stderr = systemu cmdline

data/lib/bio/db/primer3.rb

@@ -60,6 +60,7 @@ module Bio::DB::Primer3
     attr_accessor :regions
     attr_accessor :primer3_errors
     attr_accessor :repetitive
+    attr_accessor :hit_count
     
     def line_1_name
       "#{gene}:#{position}#{original}>#{snp} #{line_1}}"
@@ -249,6 +250,7 @@ module Bio::DB::Primer3
     def print_primers
       to_print = values.dup
       to_print << @repetitive
+      to_print << hit_count
       to_print.join(",")
     end
 
@@ -765,7 +767,8 @@ module Bio::DB::Primer3
       snp.position = snp_in.position
       snp.snp = snp_in.snp
       snp.repetitive = snp_in.repetitive
-
+      #puts snp_in.inspect
+      snp.hit_count = snp_in.hit_count
       snp.line_1 = @line_1
       snp.line_2 = @line_2 
       snp.snp_from = snp_in

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.8.6
+  version: 0.8.7
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-03 00:00:00.000000000 Z
+date: 2018-08-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -316,7 +316,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.14
+rubygems_version: 2.7.4
 signing_key: 
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology