bio-polyploid-tools 0.9.10 → 0.10.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 73e03b0d4cf0869a9e1a6b7d146bbb0e3ed4c91e
-  data.tar.gz: 64e0efc76fc1cd424b3febf1f4f298e202619a94
+SHA256:
+  metadata.gz: e5c0d7a867bd4272b6457d4a742d9cea42bbd5086def51870cd10e3c351843f7
+  data.tar.gz: 49332a5bea0a00006eaa8ddaaa29c5ed73f6fbb6972eca5c7e83b6ae1eceaa3d
 SHA512:
-  metadata.gz: cd81ec303480157a64ac9af123bc331381cc825cfac4e557894c35ba3ab815f15d95d03b8d5e6f7921a8ff950cebefdb9a6182b81a274568d8dca9f1d0aa13db
-  data.tar.gz: 4104dc656d8b29604fc2293731f75a906c9d23941138ebb70e7b7a2a84a456a459e30be23530ca4c16d6ebdad03ca9dcbca4bd1e1ea7e068a734dee1c350e1b1
+  metadata.gz: 3b9fb60b9396e2c89dae20bdccc9c24371ffa6fea9e3274a75a15e5f2a8931b58cdf792ddb4a2332815ef52bb137dcbc9fe1b18f3fba05aeca08af96329cae37
+  data.tar.gz: 172abc52a0e56a4c37ea71ab35d20009171f250ef175cb8f31eb296164b7cd437cc890d932085131ae1bc187220928e21090df55f34dc1f20b589bae47d65fc3

data/.travis.yml

@@ -11,10 +11,9 @@ before_install:
   - gem update --system
   - export RUBYOPT="-W1"
 rvm:
-  - 2.1.10
-  - 2.2.5
   - 2.3.5
   - 2.4.2
   - 2.5.0
+  - 2.6.0
 
 

data/VERSION

@@ -1 +1 @@
-0.9.10
+0.10.0

data/bin/polymarker.rb

@@ -149,8 +149,8 @@ if options[:primer_3_preferences][:primer_product_size_range]
   options[:flanking_size] = max
 end
 
-p options
-p ARGV
+#p options
+#p ARGV
 
 
 #TODO: Use temporary files somewhere in the file system and add traps to delete them/forward them as a result. 
@@ -192,6 +192,17 @@ def write_status(status)
   f.close
 end
 
+Signal.trap("ABRT")  do
+  write_status "ERROR: Job aborted. Please try a small number of primers." 
+  Signal.trap("SIGABRT", "DEFAULT") # restore handler
+  Process.kill("ABRT", 0)   
+end
+
+Signal.trap("TERM")  do 
+  write_status "ERROR: Job terminated. Please try a small number of primers." 
+  Signal.trap("SIGTERM", "DEFAULT") # restore handler
+  Process.kill("TERM", 0)           # kill this process with correct signal
+end
 
 snps = Array.new
 
@@ -377,8 +388,7 @@ end
 kasp_container.add_primers_file(primer_3_output) if added_exons > 0
 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"
 File.open(output_primers, 'w') { |f| f.write("#{header}\n#{kasp_container.print_primers}") }
-
-File.open(output_to_order, "w") { |io|  io.write(kasp_container.print_primers_with_tails()) }
+File.open(output_to_order, "w") { |io|  io.write(kasp_container.print_primers_with_tails())}
 
 write_status "DONE"
 rescue StandardError => e

data/bin/vcfToPolyMarker.rb

@@ -16,7 +16,7 @@ options[:arm_selection] = Bio::PolyploidTools::ChromosomeArm.getArmSelection("nr
 
 
 OptionParser.new do |opts|
-	opts.banner = "Usage: polymarker.rb [options]"
+	opts.banner = "Usage: vcfToPolyMarker.rb [options]"
 
 	opts.on("-c", "--reference FILE", "File with genome reference to use as database") do |o|
 		options[:path_to_contigs] = o
@@ -75,7 +75,7 @@ $stdin.each do |line|
 	end
 	line.chomp!
 	#puts line
-	snp = Bio::PolyploidTools::SNP.parseVCF( line , options[:arm_selection])
+	snp = Bio::PolyploidTools::SNP.parseVCF( line , chr_arm_parser: options[:arm_selection])
 	#puts snp.inspect
 	snp.setTemplateFromFastaFile(fasta_reference_db, flanking_size: 100)
 	puts [snp.gene, snp.chromosome ,snp.to_polymarker_sequence(100)].join(",")

data/bio-polyploid-tools.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.9.10 ruby lib
+# stub: bio-polyploid-tools 0.10.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.9.10"
+  s.version = "0.10.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Ricardo H.  Ramirez-Gonzalez".freeze]
-  s.date = "2019-03-11"
+  s.date = "2019-03-28"
   s.description = "Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat".freeze
   s.email = "ricardo.ramirez-gonzalez@jic.ac.uk".freeze
   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]
@@ -185,7 +185,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "2.6.14".freeze
+  s.rubygems_version = "2.7.7".freeze
   s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze
 
   if s.respond_to? :specification_version then

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.9.10
+  version: 0.10.0
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-03-11 00:00:00.000000000 Z
+date: 2019-03-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -324,7 +324,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.14
+rubygems_version: 2.7.7
 signing_key: 
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology