bio-polyploid-tools 0.9.8 → 0.9.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 33b494dbc4bf2eca85c52524144ee8577b8a157952dc1de6d588c2a9afa1fbff
-  data.tar.gz: 9884092fea3663022caf6d56cd66bb1e024aba12e0d896fe8ee8691ce0354d03
+  metadata.gz: 48bdfc00532bec29d3ca2cd3214e22f8907ef45abb3bdf21802be60654fd188a
+  data.tar.gz: 8ade77f7455c3a38d16f011642ecc69325c4d9bcd650c7f440d524e870c702ba
 SHA512:
-  metadata.gz: e852c5da462b2978612b87ce6b71ba70ff030d42b547bb5283818ea525058c389935471d8003dae7cd817c426acfdea5ec3ce8ec58f58682e5c3e9636168d6ef
-  data.tar.gz: c8e7b741c92989c070b0aa0c8d452de5bc8611c53266305942ab5e383ffd70233445b1cb6e3853e842e17490d455ccab12e785b818e442a1e6021a28dd7bbc57
+  metadata.gz: e1fa868fc0d1f2d249a40c1a4f351d7bc2918d17303868e84342e0cc6a31656160af459efed2697b9b09bf0e47cf987d4ed3404d9ebf101e91f0b3d420f9c717
+  data.tar.gz: 66839a8ae1794b510a98c8c69b3819f8eebee58518907a4169955f12a7d5502c2438e8a0449dea9b58671ee177ba519384d35327a1d2e7adec957a0bd8f005c9

data/VERSION

@@ -1 +1 @@
-0.9.8
+0.9.9

data/bin/polymarker.rb

@@ -375,7 +375,7 @@ 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"
+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,repetitive,total_hits"
 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 0.9.8 ruby lib
+# stub: bio-polyploid-tools 0.9.9 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.9.8"
+  s.version = "0.9.9"
 
   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 = "2018-11-20"
+  s.date = "2018-11-21"
   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]

data/lib/bio/PolyploidTools/SNP.rb

@@ -117,9 +117,9 @@ module Bio::PolyploidTools
       return nil
     end
     
-     def to_fasta
+    def to_fasta
         return ">#{self.gene}\n#{self.template_sequence}\n"
-      end
+    end
 
     def add_exon(exon, arm, filter_best: true)
       if filter_best and exon_list[arm].size > 0

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.9.8
+  version: 0.9.9
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-11-20 00:00:00.000000000 Z
+date: 2018-11-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio