bio-polyploid-tools 0.9.2 → 0.9.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA256:
-  metadata.gz: 80492a2607af467274ac7ca76979826e09dade8e59cba047a557c98448d71406
-  data.tar.gz: 94c59ed53e14840eb52ac2a628ba96a8bff6cc45f1490b66cb5bed8522eddafe
+SHA1:
+  metadata.gz: bfb72b7ca83304ff8327c9be9983bb1b61b1fee7
+  data.tar.gz: ee55c1474c0861a054aecd3b42248b750039fb95
 SHA512:
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-  data.tar.gz: 54ca702eb2348297f0a26d56f6fbb963da7dddf09a78a5783b9d4f6faac3b42e8213b814080852b2ce4f3c8dc61bad3233c2995660553d75ee77eb2f2e073290
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+  data.tar.gz: c2c622498e3537cc5ad16e5eba447d8b957bfd4d1ce0e4ca05f6f539a53e6b82f30b428736b17e1c4a799e12fafb22e96b229a49f53e33a0acd750c4dc0c63d8

data/VERSION

@@ -1 +1 @@
-0.9.2
+0.9.3

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 0.9.2 ruby lib
+# stub: bio-polyploid-tools 0.9.3 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.9.2"
+  s.version = "0.9.3"
 
   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 = "2018-08-17"
+  s.date = "2018-08-18"
   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]
@@ -154,6 +154,7 @@ Gem::Specification.new do |s|
     "test/data/chr1A_G540414846C/chr1A_G540414846C.csv",
     "test/data/chr1A_G540414846C/chr1A_G540414846C.fa",
     "test/data/chr1A_T517634750C/chr1A_T517634750C.csv",
+    "test/data/chr2D_C112180134A/chr2D_C112180134A.csv",
     "test/data/chr4D_C14473543T/chr4D_C14473543T.csv",
     "test/data/chr4D_C14473543T/chr4D_C14473543T.fa",
     "test/data/headerMergeed.txt",
@@ -180,7 +181,7 @@ 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/PolyploidTools/ExonContainer.rb

@@ -13,7 +13,6 @@ module Bio::PolyploidTools
     def initialize
       @parents=Hash.new
       @snp_map = Hash.new 
-      @snp_contigs
       @primer_3_min_seq_length = 50
       @max_hits = 10
     end
@@ -219,7 +218,7 @@ module Bio::PolyploidTools
     def remove_alignments_over_max_hits
       @snp_map.each_pair do | gene, snp_array| 
         snp_array.each do |snp|
-          total_hits = snp.exon_list.size
+          total_hits = snp.exon_list.map { |e| e.size }.inject(:+)
           snp.hit_count = total_hits
           if total_hits > max_hits
             snp.exon_list = {} 

data/test/data/chr2D_C112180134A/chr2D_C112180134A.csv

@@ -0,0 +1 @@
+chr2D_C112180134A,2D,aaacataaaggaatgagcaaaagggtcccggcctttctgtgggcggaagtactactgcgagaaaacgcccataaaaacgctcgctatgcgaactctttgc[C/A]tgtactgttgtgtgtatagcgtctaggttcacgcccgcaaccaaatgcggcatgcatgccatgtcacgtgggcggtgaaaatcacgcccaaatattacaa

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.9.2
+  version: 0.9.3
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-17 00:00:00.000000000 Z
+date: 2018-08-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -274,6 +274,7 @@ files:
 - test/data/chr1A_G540414846C/chr1A_G540414846C.csv
 - test/data/chr1A_G540414846C/chr1A_G540414846C.fa
 - test/data/chr1A_T517634750C/chr1A_T517634750C.csv
+- test/data/chr2D_C112180134A/chr2D_C112180134A.csv
 - test/data/chr4D_C14473543T/chr4D_C14473543T.csv
 - test/data/chr4D_C14473543T/chr4D_C14473543T.fa
 - test/data/headerMergeed.txt
@@ -317,7 +318,7 @@ 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