bio-polyploid-tools 0.9.10 → 0.10.0
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- checksums.yaml +5 -5
- data/.travis.yml +1 -2
- data/VERSION +1 -1
- data/bin/polymarker.rb +14 -4
- data/bin/vcfToPolyMarker.rb +2 -2
- data/bio-polyploid-tools.gemspec +4 -4
- metadata +3 -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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SHA256:
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metadata.gz: e5c0d7a867bd4272b6457d4a742d9cea42bbd5086def51870cd10e3c351843f7
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data.tar.gz: 49332a5bea0a00006eaa8ddaaa29c5ed73f6fbb6972eca5c7e83b6ae1eceaa3d
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 3b9fb60b9396e2c89dae20bdccc9c24371ffa6fea9e3274a75a15e5f2a8931b58cdf792ddb4a2332815ef52bb137dcbc9fe1b18f3fba05aeca08af96329cae37
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data.tar.gz: 172abc52a0e56a4c37ea71ab35d20009171f250ef175cb8f31eb296164b7cd437cc890d932085131ae1bc187220928e21090df55f34dc1f20b589bae47d65fc3
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data/.travis.yml
CHANGED
data/VERSION
CHANGED
@@ -1 +1 @@
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1
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0.
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1
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0.10.0
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data/bin/polymarker.rb
CHANGED
@@ -149,8 +149,8 @@ if options[:primer_3_preferences][:primer_product_size_range]
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options[:flanking_size] = max
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end
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-
p options
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p ARGV
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#p options
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#p ARGV
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#TODO: Use temporary files somewhere in the file system and add traps to delete them/forward them as a result.
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@@ -192,6 +192,17 @@ def write_status(status)
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f.close
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end
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Signal.trap("ABRT") do
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write_status "ERROR: Job aborted. Please try a small number of primers."
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Signal.trap("SIGABRT", "DEFAULT") # restore handler
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Process.kill("ABRT", 0)
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end
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Signal.trap("TERM") do
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write_status "ERROR: Job terminated. Please try a small number of primers."
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Signal.trap("SIGTERM", "DEFAULT") # restore handler
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Process.kill("TERM", 0) # kill this process with correct signal
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end
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snps = Array.new
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@@ -377,8 +388,7 @@ 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,repetitive,total_hits"
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File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }
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-
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File.open(output_to_order, "w") { |io| io.write(kasp_container.print_primers_with_tails()) }
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File.open(output_to_order, "w") { |io| io.write(kasp_container.print_primers_with_tails())}
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write_status "DONE"
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rescue StandardError => e
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data/bin/vcfToPolyMarker.rb
CHANGED
@@ -16,7 +16,7 @@ options[:arm_selection] = Bio::PolyploidTools::ChromosomeArm.getArmSelection("nr
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OptionParser.new do |opts|
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opts.banner = "Usage:
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opts.banner = "Usage: vcfToPolyMarker.rb [options]"
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opts.on("-c", "--reference FILE", "File with genome reference to use as database") do |o|
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options[:path_to_contigs] = o
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@@ -75,7 +75,7 @@ $stdin.each do |line|
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end
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line.chomp!
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#puts line
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snp = Bio::PolyploidTools::SNP.parseVCF( line , options[:arm_selection])
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snp = Bio::PolyploidTools::SNP.parseVCF( line , chr_arm_parser: options[:arm_selection])
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#puts snp.inspect
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snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size: 100)
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puts [snp.gene, snp.chromosome ,snp.to_polymarker_sequence(100)].join(",")
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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.
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# stub: bio-polyploid-tools 0.10.0 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.
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s.version = "0.10.0"
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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 = "2019-03-
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s.date = "2019-03-28"
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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, "marker_to_vcf.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, "vcfToPolyMarker.rb".freeze]
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@@ -185,7 +185,7 @@ 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 = "2.7.7".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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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.
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version: 0.10.0
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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: 2019-03-
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date: 2019-03-28 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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@@ -324,7 +324,7 @@ 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: 2.7.7
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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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