bio-polyploid-tools 0.8.5 → 0.8.6

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: d5427afc0216c123131894858aeb8d8ddd0eed53c47b4e47d4b34e63d67af1f2
+SHA1:
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+  data.tar.gz: b9f74e1d597b0d5dbbd53758f5c7b2f4a22e7308
 SHA512:
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data/README.md

@@ -128,7 +128,9 @@ To use blast instead of exonerate, use the following command:
 
 ## Release Notes
 
-### Next release
+### 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. 
 
 ### 0.8.5
 

data/VERSION

@@ -1 +1 @@
-0.8.5
+0.8.6

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,is_repetitive,SNP_type,#{original_name},#{snp_in},common,primer_type,orientation,#{original_name}_TM,#{snp_in}_TM,common_TM,selected_from,product_size,errors"
+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"
 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 0.8.5 ruby lib
+# stub: bio-polyploid-tools 0.8.6 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.8.5"
+  s.version = "0.8.6"
 
   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 = "2018-07-31"
+  s.date = "2018-08-03"
   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]
@@ -151,6 +151,8 @@ Gem::Specification.new do |s|
     "test/data/Test3Aspecific.csv",
     "test/data/Test3Aspecific_contigs.fa",
     "test/data/bfr_out_test.csv",
+    "test/data/chr1A_G540414846C/chr1A_G540414846C.csv",
+    "test/data/chr1A_G540414846C/chr1A_G540414846C.fa",
     "test/data/chr4D_C14473543T/chr4D_C14473543T.csv",
     "test/data/chr4D_C14473543T/chr4D_C14473543T.fa",
     "test/data/headerMergeed.txt",
@@ -177,7 +179,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "2.7.4".freeze
+  s.rubygems_version = "2.6.14".freeze
   s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze
 
   if s.respond_to? :specification_version then

data/lib/bio/db/primer3.rb

@@ -113,7 +113,7 @@ module Bio::DB::Primer3
       left_end = 0
       right_start = 0
       right_end = 0
-      total_columns_before_messages=18
+      total_columns_before_messages=17
       #puts "Values in primer3"
       #puts snp_from.inspect
       @values = Array.new
@@ -124,7 +124,6 @@ module Bio::DB::Primer3
       @values << snp_from.chromosome
       @values << regions.size
       @values << regions.join("|")
-      @values << repetitive
       if primer3_line_1 and primer3_line_2
         @values <<  primer3_line_1.polymorphism
 
@@ -248,7 +247,9 @@ module Bio::DB::Primer3
     end
 
     def print_primers
-      self.values.join(",")
+      to_print = values.dup
+      to_print << @repetitive
+      to_print.join(",")
     end
 
     def found_primers?

data/test/data/chr1A_G540414846C/chr1A_G540414846C.csv

@@ -0,0 +1 @@
+chr1A_G540414846C,1A,TTCGCCTTTGCTGCCTACCTATATGTACACATGCACGCCGATGCCAGTTGTGGATGCATCCATACGTAAACTATTGGATAGGTCAATCTTCTATACTTAG[G/C]GCATCTCCAACAGGCGCCGAACGCGCCGCGCGCAAAAAACAGCTTATAGCGCGCGCCCATCGTCTGGTTTGGCGCGGCGCGCAGCGCTGGCTCCAGCAGC

data/test/data/chr1A_G540414846C/chr1A_G540414846C.fa

@@ -0,0 +1,2 @@
+>chr1A_G540414846C
+ttcgcctttgctgcctacctatatgtacacatgcacgccgatgccagttgtggatgcatccatacgtaaactattggataggtcaatcttctatacttagSgcatctccaacaggcgccgaacgcgccgcgcgcaaaaaacagcttatagcgcgcgcccatcgtctggtttggcgcggcgcgcagcgctggctccagcagc

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.8.5
+  version: 0.8.6
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-07-31 00:00:00.000000000 Z
+date: 2018-08-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -271,6 +271,8 @@ files:
 - test/data/Test3Aspecific.csv
 - test/data/Test3Aspecific_contigs.fa
 - test/data/bfr_out_test.csv
+- test/data/chr1A_G540414846C/chr1A_G540414846C.csv
+- test/data/chr1A_G540414846C/chr1A_G540414846C.fa
 - test/data/chr4D_C14473543T/chr4D_C14473543T.csv
 - test/data/chr4D_C14473543T/chr4D_C14473543T.fa
 - test/data/headerMergeed.txt
@@ -314,7 +316,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.7.4
+rubygems_version: 2.6.14
 signing_key: 
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology