bio-polyploid-tools 0.8.6 → 0.8.7
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- checksums.yaml +5 -5
- data/README.md +3 -0
- data/VERSION +1 -1
- data/bin/polymarker.rb +1 -1
- data/bio-polyploid-tools.gemspec +4 -4
- data/lib/bio/PolyploidTools/ExonContainer.rb +1 -0
- data/lib/bio/PolyploidTools/SNP.rb +5 -2
- data/lib/bio/db/blast.rb +1 -1
- data/lib/bio/db/primer3.rb +4 -1
- metadata +3 -3
checksums.yaml
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@@ -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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SHA256:
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metadata.gz: 4d9b4a477900c5cc8e587dbc3257daa7d8db50cf0e3e22ed10d6ca9ad76fec25
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data.tar.gz: 4a3bd8793e963890086f9a6394bb83adf19669ad9f89f8be24c89a6b0bdbd27b
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: c92453e975359a130337a46fb752be6e41862e0a78fc3bbc9786ab78f7419b544edd185be828f016c33f5eb9bdcf53ce251c312706f43382679ccd8206ba8f0d
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data.tar.gz: 2a8bf17cb57e117f35642f3447191744768cf2210e5f75ce0f6d82b855b18e6d7434e89179d654d6a6eaccee025e8741b3c8d088a605e52b6e36c78c6fbd9646
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data/README.md
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@@ -128,6 +128,9 @@ To use blast instead of exonerate, use the following command:
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## Release Notes
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### 0.8.7
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* FEATURE: ```polymarker.rb``` now also prints the total number of hits found.
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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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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.8.
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1
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0.8.7
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data/bin/polymarker.rb
CHANGED
@@ -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,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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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,hit_count"
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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
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 0.8.
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# stub: bio-polyploid-tools 0.8.7 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 = "0.8.7"
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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 = "2018-08-07"
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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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@@ -179,7 +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 = "2.7.4".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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@@ -221,6 +221,7 @@ module Bio::PolyploidTools
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snp_array.each do |snp|
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if snp.exon_list.size > max_hits
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total_hits = snp.exon_list.size
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snp.hit_count = total_hits
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snp.exon_list = {}
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snp.repetitive = true
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snp.errors << "The marker is in a repetitive region (#{total_hits} hits to reference)"
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attr_accessor :max_hits
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attr_accessor :errors
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attr_accessor :repetitive
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attr_accessor :hit_count
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@@ -69,6 +70,7 @@ module Bio::PolyploidTools
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@exon_list = Hash.new {|hsh, key| hsh[key] = [] }
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@errors = Array.new
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@repetitive = false
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@hit_count = 0
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end
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def to_polymarker_coordinates(flanking_size, total:nil)
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@@ -340,8 +342,9 @@ module Bio::PolyploidTools
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errors << "The sequence (#{seq_original.size}) is shorter than #{primer_3_min_seq_length}"
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return primer_3_propertes
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end
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-
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-
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hit_count = exon_list.size
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puts exon_list.inspect
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if hit_count > max_hits
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errors << "The marker maps to #{exon_list.size} positions (max_hits: #{max_hits}). "
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repetitive = true
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return primer_3_propertes
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data/lib/bio/db/blast.rb
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@@ -80,7 +80,7 @@ module Bio::DB::Blast
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target=opts[:target]
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query=opts[:query]
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max_target_seqs = 15
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max_target_seqs = opts[:max_hits]
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max_target_seqs = opts[:max_hits] * 2 if opts[:max_hits]
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cmdline = "blastn -max_target_seqs #{max_target_seqs} -query #{query} -db #{target} -outfmt '6 qseqid qstart qend qframe sseqid sstart send sframe score pident qlen slen qseq sseq'"
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status, stdout, stderr = systemu cmdline
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data/lib/bio/db/primer3.rb
CHANGED
@@ -60,6 +60,7 @@ module Bio::DB::Primer3
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attr_accessor :regions
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attr_accessor :primer3_errors
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attr_accessor :repetitive
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attr_accessor :hit_count
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def line_1_name
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"#{gene}:#{position}#{original}>#{snp} #{line_1}}"
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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 << hit_count
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to_print.join(",")
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end
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@@ -765,7 +767,8 @@ module Bio::DB::Primer3
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snp.position = snp_in.position
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snp.snp = snp_in.snp
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snp.repetitive = snp_in.repetitive
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-
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#puts snp_in.inspect
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snp.hit_count = snp_in.hit_count
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snp.line_1 = @line_1
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snp.line_2 = @line_2
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snp.snp_from = snp_in
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metadata
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@@ -1,14 +1,14 @@
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1
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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: 0.8.7
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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: 2018-08-07 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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@@ -316,7 +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: 2.7.4
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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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