bio-polyploid-tools 0.8.5 → 0.8.6
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- checksums.yaml +5 -5
- data/README.md +3 -1
- data/VERSION +1 -1
- data/bin/polymarker.rb +1 -1
- data/bio-polyploid-tools.gemspec +6 -4
- data/lib/bio/db/primer3.rb +4 -3
- data/test/data/chr1A_G540414846C/chr1A_G540414846C.csv +1 -0
- data/test/data/chr1A_G540414846C/chr1A_G540414846C.fa +2 -0
- metadata +5 -3
checksums.yaml
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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: 7119d8a9ed1f4b73077a420a1d67ef3de381a256
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data.tar.gz: b9f74e1d597b0d5dbbd53758f5c7b2f4a22e7308
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: b8c8ec899b07c2b32b17fb2c3313dd57eab1fffa44cf4e4cad57fd985637e310b80a10a9d2f5a326c3493cf584bb2f7485280a3112672d064f4c9a89189bb244
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data.tar.gz: 79ffb338f75150e140219e3f16068af9b8401a02336b97398daa1ad7181dfb59d30fc4e61a39ec1435722f362b77e4c338b359ccd28bb384d73f94bc936fb398
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data/README.md
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@@ -128,7 +128,9 @@ To use blast instead of exonerate, use the following command:
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## Release Notes
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###
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### 0.8.6
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* 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.
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### 0.8.5
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data/VERSION
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@@ -1 +1 @@
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1
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0.8.
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1
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0.8.6
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data/bin/polymarker.rb
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@@ -392,7 +392,7 @@ snps.each do |snp|
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end
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kasp_container.add_primers_file(primer_3_output) if added_exons > 0
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header = "Marker,SNP,RegionSize,chromosome,total_contigs,contig_regions,
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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"
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File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }
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File.open(output_to_order, "w") { |io| io.write(kasp_container.print_primers_with_tails()) }
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data/bio-polyploid-tools.gemspec
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@@ -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 0.8.
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# stub: bio-polyploid-tools 0.8.6 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 = "0.8.
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s.version = "0.8.6"
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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-
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s.date = "2018-08-03"
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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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@@ -151,6 +151,8 @@ Gem::Specification.new do |s|
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"test/data/Test3Aspecific.csv",
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"test/data/Test3Aspecific_contigs.fa",
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"test/data/bfr_out_test.csv",
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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/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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@@ -177,7 +179,7 @@ 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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data/lib/bio/db/primer3.rb
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left_end = 0
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right_start = 0
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right_end = 0
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total_columns_before_messages=
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total_columns_before_messages=17
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#puts "Values in primer3"
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#puts snp_from.inspect
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@values = Array.new
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@values << snp_from.chromosome
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@values << regions.size
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@values << regions.join("|")
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@values << repetitive
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if primer3_line_1 and primer3_line_2
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@values << primer3_line_1.polymorphism
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@@ -248,7 +247,9 @@ module Bio::DB::Primer3
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end
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def print_primers
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to_print = values.dup
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to_print << @repetitive
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to_print.join(",")
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end
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def found_primers?
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chr1A_G540414846C,1A,TTCGCCTTTGCTGCCTACCTATATGTACACATGCACGCCGATGCCAGTTGTGGATGCATCCATACGTAAACTATTGGATAGGTCAATCTTCTATACTTAG[G/C]GCATCTCCAACAGGCGCCGAACGCGCCGCGCGCAAAAAACAGCTTATAGCGCGCGCCCATCGTCTGGTTTGGCGCGGCGCGCAGCGCTGGCTCCAGCAGC
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metadata
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@@ -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: 0.8.
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version: 0.8.6
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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-
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date: 2018-08-03 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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@@ -271,6 +271,8 @@ files:
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- test/data/Test3Aspecific.csv
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- test/data/Test3Aspecific_contigs.fa
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- test/data/bfr_out_test.csv
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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/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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@@ -314,7 +316,7 @@ 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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