bio-polyploid-tools 0.9.2 → 0.9.3
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- checksums.yaml +5 -5
- data/VERSION +1 -1
- data/bio-polyploid-tools.gemspec +5 -4
- data/lib/bio/PolyploidTools/ExonContainer.rb +1 -2
- data/test/data/chr2D_C112180134A/chr2D_C112180134A.csv +1 -0
- metadata +4 -3
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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metadata.gz:
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data.tar.gz:
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SHA1:
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metadata.gz: bfb72b7ca83304ff8327c9be9983bb1b61b1fee7
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data.tar.gz: ee55c1474c0861a054aecd3b42248b750039fb95
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 1303cb00a3776edffe3a76f2fcb2bccd4dd7d66e29bd252a370312a60e8b8a83fe8ff94dac17a23f68d8ddfc658f289c24b0c4401cf1af1b458d75568a59c718
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data.tar.gz: c2c622498e3537cc5ad16e5eba447d8b957bfd4d1ce0e4ca05f6f539a53e6b82f30b428736b17e1c4a799e12fafb22e96b229a49f53e33a0acd750c4dc0c63d8
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.9.
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1
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0.9.3
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data/bio-polyploid-tools.gemspec
CHANGED
@@ -2,16 +2,16 @@
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# DO NOT EDIT THIS FILE DIRECTLY
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# Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
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# -*- encoding: utf-8 -*-
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# stub: bio-polyploid-tools 0.9.
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# stub: bio-polyploid-tools 0.9.3 ruby lib
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Gem::Specification.new do |s|
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s.name = "bio-polyploid-tools".freeze
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s.version = "0.9.
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9
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s.version = "0.9.3"
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s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
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s.require_paths = ["lib".freeze]
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s.authors = ["Ricardo H. Ramirez-Gonzalez".freeze]
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s.date = "2018-08-
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s.date = "2018-08-18"
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s.description = "Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat".freeze
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s.email = "ricardo.ramirez-gonzalez@jic.ac.uk".freeze
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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]
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@@ -154,6 +154,7 @@ Gem::Specification.new do |s|
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"test/data/chr1A_G540414846C/chr1A_G540414846C.csv",
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"test/data/chr1A_G540414846C/chr1A_G540414846C.fa",
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"test/data/chr1A_T517634750C/chr1A_T517634750C.csv",
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"test/data/chr2D_C112180134A/chr2D_C112180134A.csv",
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"test/data/chr4D_C14473543T/chr4D_C14473543T.csv",
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"test/data/chr4D_C14473543T/chr4D_C14473543T.fa",
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"test/data/headerMergeed.txt",
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@@ -180,7 +181,7 @@ Gem::Specification.new do |s|
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]
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s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
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s.licenses = ["MIT".freeze]
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s.rubygems_version = "2.
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s.rubygems_version = "2.6.14".freeze
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s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze
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if s.respond_to? :specification_version then
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@@ -13,7 +13,6 @@ module Bio::PolyploidTools
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def initialize
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@parents=Hash.new
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@snp_map = Hash.new
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@snp_contigs
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@primer_3_min_seq_length = 50
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@max_hits = 10
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end
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@@ -219,7 +218,7 @@ module Bio::PolyploidTools
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def remove_alignments_over_max_hits
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@snp_map.each_pair do | gene, snp_array|
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snp_array.each do |snp|
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total_hits = snp.exon_list.size
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total_hits = snp.exon_list.map { |e| e.size }.inject(:+)
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snp.hit_count = total_hits
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if total_hits > max_hits
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snp.exon_list = {}
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@@ -0,0 +1 @@
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1
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chr2D_C112180134A,2D,aaacataaaggaatgagcaaaagggtcccggcctttctgtgggcggaagtactactgcgagaaaacgcccataaaaacgctcgctatgcgaactctttgc[C/A]tgtactgttgtgtgtatagcgtctaggttcacgcccgcaaccaaatgcggcatgcatgccatgtcacgtgggcggtgaaaatcacgcccaaatattacaa
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metadata
CHANGED
@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: bio-polyploid-tools
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version: !ruby/object:Gem::Version
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version: 0.9.
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version: 0.9.3
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platform: ruby
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authors:
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- Ricardo H. Ramirez-Gonzalez
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2018-08-
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date: 2018-08-18 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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@@ -274,6 +274,7 @@ files:
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- test/data/chr1A_G540414846C/chr1A_G540414846C.csv
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- test/data/chr1A_G540414846C/chr1A_G540414846C.fa
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- test/data/chr1A_T517634750C/chr1A_T517634750C.csv
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- test/data/chr2D_C112180134A/chr2D_C112180134A.csv
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- test/data/chr4D_C14473543T/chr4D_C14473543T.csv
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- test/data/chr4D_C14473543T/chr4D_C14473543T.fa
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- test/data/headerMergeed.txt
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@@ -317,7 +318,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 2.
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rubygems_version: 2.6.14
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signing_key:
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specification_version: 4
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summary: Tool to work with polyploids, NGS and molecular biology
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