bio-polyploid-tools 0.8.8 → 0.8.9
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml
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metadata.gz: 5e84c23b6cdb94ec8e7537de6d6a85bb5c807e99417aee64f300f567f9ed06fa
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data.tar.gz: 5f597fa54fc9d9be8a10efb27ecbacf261d4285a950a24c2b49b8f6ad09f954a
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metadata.gz: 56ffd2291cb36799fcf1c96790a08fb82a58bd98480fc4315fcf26b34df87c5bbc048b2f88be5e7788ab382b95aee78b9d88c4389ca1ee12e88a84c8326e143d
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data.tar.gz: 13f38b6eb9a175f48bd04d8ae2b58070c21055c64dcd68d3cca4d691587b0392876a5f5c5fe5d801f1b61e73d8f6104b5515a8348c8e6ab914ab978bdae3c2cb
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data/VERSION
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0.8.
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0.8.9
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data/bio-polyploid-tools.gemspec
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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 0.8.9 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 = "0.8.9"
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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 = "2018-08-16"
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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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"test/data/BS00068396_51_contigs.nin",
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"test/data/BS00068396_51_contigs.nsq",
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"test/data/BS00068396_51_exonerate.tab",
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"test/data/BS00068396_51_for_polymarker.
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"test/data/BS00068396_51_for_polymarker.txt",
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"test/data/BS00068396_51_genes.txt",
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"test/data/IWGSC_CSS_1AL_scaff_1455974.fa",
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"test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa",
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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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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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hit_count = exon_list.size
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errors << "The marker maps to #{exon_list.size} positions (max_hits: #{max_hits}). "
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@hit_count = exon_list.size
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if @hit_count > max_hits
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errors << "The marker maps to #{@hit_count} positions (max_hits: #{max_hits}). "
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repetitive = true
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return primer_3_propertes
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end
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File without changes
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metadata
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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: 0.8.9
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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: 2018-08-16 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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- test/data/BS00068396_51_contigs.nin
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- test/data/BS00068396_51_contigs.nsq
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- test/data/BS00068396_51_exonerate.tab
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- test/data/BS00068396_51_for_polymarker.
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- test/data/BS00068396_51_for_polymarker.txt
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- test/data/BS00068396_51_genes.txt
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- test/data/IWGSC_CSS_1AL_scaff_1455974.fa
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- test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa
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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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