bio-polyploid-tools 1.2.0 → 1.2.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: '0449ab8d09b268538d3604f20b555d94be53cac35ff8d591a29c792f98df3def'
+  metadata.gz: f0d5a3af7b47246e8be286fd81aa93319375bcc3b09c3f7a8fe18435a187d301
+  data.tar.gz: 594953032a8c400e0f0868f44ee82f80d38d784b9f377f0c39b16ae42b930884
 SHA512:
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+  data.tar.gz: ed90f0431a82e2492a703b607ccc92c4ea339a12c9098084112b885221fe8e3745e192ff92f971b751bad0ad5ddf851f3128266db98b5966d8686e6379a6a0de

data/.travis.yml

@@ -7,13 +7,18 @@ addons:
     - libncurses5-dev
     - libtinfo-dev 
     - exonerate  
+    - blast2
+    - ncbi-blast+
+    - mafft
+    - primer3
 before_install:
   - gem update --system
   - export RUBYOPT="-W1"
 rvm:
-  - 2.3.5
-  - 2.4.2
-  - 2.5.0
-  - 2.6.0
+  - 2.3
+  - 2.4
+  - 2.5
+  - 2.6
+  - 2.7
 
 

data/VERSION

@@ -1 +1 @@
-1.2.0
+1.2.1

data/bin/polymarker.rb

@@ -41,7 +41,7 @@ options[:database]  = false
 options[:filter_best]  = false
 options[:aligner] = :blast
 options[:max_hits] = 8
-options[:max_specific_primers]  = 15
+options[:max_specific_primers]  = 20
 options[:primer_3_preferences] = {
       :primer_product_size_range => "50-150" ,
       :primer_max_size => 25 , 
@@ -288,18 +288,19 @@ file.close
 #chr_group = chromosome[0]
 write_status "Searching markers in genome"
 exo_f = File.open(exonerate_file, "w")
+contigs_f = nil
 contigs_f = File.open(temp_contigs, "w") if options[:extract_found_contigs]
 filename=path_to_contigs 
 #puts filename
 target=filename
 
-fasta_file = Bio::DB::Fasta::FastaFile.new({:fasta=>target})
+fasta_file = Bio::DB::Fasta::FastaFile.new(fasta: target)
 fasta_file.load_fai_entries
 
 found_contigs = Set.new
 
 
-def do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options)
+def do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options, contigs_f: nil)
   if aln.identity > min_identity
     exo_f.puts aln.line
     unless found_contigs.include?(aln.target_id) #We only add once each contig. Should reduce the size of the output file. 
@@ -317,11 +318,11 @@ def do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options)
 end
 
 Bio::DB::Blast.align({:query=>temp_fasta_query, :target=>options[:database], :model=>model, :max_hits=>options[:max_hits]}) do |aln|
-  do_align(aln, exo_f, found_contigs,min_identity, fasta_file,options)
+  do_align(aln, exo_f, found_contigs,min_identity, fasta_file,options, contigs_f: contigs_f)
 end if options[:aligner] == :blast
 
 Bio::DB::Exonerate.align({:query=>temp_fasta_query, :target=>target, :model=>model}) do |aln|
-  do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options)
+  do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options, contigs_f: contigs_f)
 end if options[:aligner] == :exonerate
  
 exo_f.close() 

data/bin/polymarker_capillary.rb

@@ -53,7 +53,7 @@ OptionParser.new do |opts|
     options[:markers] = o
   end
 
-  opts.on("-o", "--output_folder FOLDER", "Path to a folder where the outputs are going to be stored") do |o|
+  opts.on("-o", "--output FOLDER", "Path to a folder where the outputs are going to be stored") do |o|
     options[:output_folder] = o
   end
   opts.on("-g", "--genomes_count INT", "Number of genomes (default 3, for hexaploid)") do |o|

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 1.2.0 ruby lib
+# stub: bio-polyploid-tools 1.2.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "1.2.0"
+  s.version = "1.2.1"
 
   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 = "2020-10-28"
+  s.date = "2021-05-10"
   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, "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, "polymarker_deletions.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "tag_stats.rb".freeze, "vcfLineToTable.rb".freeze, "vcfToPolyMarker.rb".freeze]
@@ -105,13 +105,7 @@ Gem::Specification.new do |s|
     "test/data/7B_amplicon_test.fa.fai",
     "test/data/7B_amplicon_test_reference.fa",
     "test/data/7B_amplicon_test_reference.fa.fai",
-    "test/data/7B_amplicon_test_reference.fa.ndb",
-    "test/data/7B_amplicon_test_reference.fa.nhr",
-    "test/data/7B_amplicon_test_reference.fa.nin",
-    "test/data/7B_amplicon_test_reference.fa.not",
-    "test/data/7B_amplicon_test_reference.fa.nsq",
-    "test/data/7B_amplicon_test_reference.fa.ntf",
-    "test/data/7B_amplicon_test_reference.fa.nto",
+    "test/data/7B_marker_test.txt",
     "test/data/BS00068396_51.fa",
     "test/data/BS00068396_51_blast.tab",
     "test/data/BS00068396_51_contigs.aln",
@@ -141,6 +135,13 @@ Gem::Specification.new do |s|
     "test/data/PST130_7067.csv",
     "test/data/PST130_7067.fa",
     "test/data/PST130_7067.fa.fai",
+    "test/data/PST130_7067.fa.ndb",
+    "test/data/PST130_7067.fa.nhr",
+    "test/data/PST130_7067.fa.nin",
+    "test/data/PST130_7067.fa.not",
+    "test/data/PST130_7067.fa.nsq",
+    "test/data/PST130_7067.fa.ntf",
+    "test/data/PST130_7067.fa.nto",
     "test/data/PST130_reverse_primer.csv",
     "test/data/S22380157.fa",
     "test/data/S22380157.fa.fai",
@@ -190,12 +191,13 @@ Gem::Specification.new do |s|
     "test/test_blast.rb",
     "test/test_exon_container.rb",
     "test/test_exonearate.rb",
+    "test/test_integration.rb",
     "test/test_snp_parsing.rb",
     "test/test_wrong_selection.sh"
   ]
   s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "3.1.2".freeze
+  s.rubygems_version = "3.1.4".freeze
   s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze
 
   if s.respond_to? :specification_version then

data/lib/bio/BFRTools.rb

@@ -31,7 +31,7 @@ module Bio::BFRTools
     BASES = [:A, :C, :G, :T]
     #Sets the reference file
     def reference(path)
-      @reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
+      @reference_db = Bio::DB::Fasta::FastaFile.new(fasta: path)
       @reference_path = path
     end
 
@@ -49,7 +49,7 @@ module Bio::BFRTools
       raise BFRToolsException.new("Unable to open #{path}") unless path.readable? or path.directory?        
 
       @parental_1_name = opts[:name] ? opts[:name] : path.basename(".bam").to_s
-      @parental_1_sam =  Bio::DB::Sam.new({:fasta=>@reference_path, :bam=>path.realpath.to_s})
+      @parental_1_sam =  Bio::DB::Sam.new(fasta: @reference_path, :bam=>path.realpath.to_s)
       @parental_1_path = path
 
     end 
@@ -61,7 +61,7 @@ module Bio::BFRTools
       raise BFRToolsException.new("Unable to open #{path}") unless path.readable? or path.directory?        
 
       @parental_2_name = @name = opts[:name] ? opts[:name] : path.basename(".bam").to_s
-      @parental_2_sam =  Bio::DB::Sam.new({:fasta=>@reference_path, :bam=>path.realpath.to_s})
+      @parental_2_sam =  Bio::DB::Sam.new(fasta: @reference_path, :bam=>path.realpath.to_s)
       @parental_2_path = path
     end
 
@@ -72,7 +72,7 @@ module Bio::BFRTools
       raise BFRToolsException.new("Unable to open #{path}") unless path.readable? or path.directory?        
 
       @bulk_1_name =  opts[:name] ? opts[:name] : path.basename(".bam").to_s
-      @bulk_1_sam =  Bio::DB::Sam.new({:fasta=>@reference_path, :bam=>path.realpath.to_s})
+      @bulk_1_sam =  Bio::DB::Sam.new(fasta: @reference_path, :bam=>path.realpath.to_s)
       @bulk_1_path = path
     end 
 
@@ -83,7 +83,7 @@ module Bio::BFRTools
       raise BFRToolsException.new("Unable to open #{path}") unless path.readable? or path.directory?        
 
       @bulk_2_name =  opts[:name] ? opts[:name] : path.basename(".bam").to_s
-      @bulk_2_sam =  Bio::DB::Sam.new({:fasta=>@reference_path, :bam=>path.realpath.to_s})
+      @bulk_2_sam =  Bio::DB::Sam.new(fasta: @reference_path, :bam=>path.realpath.to_s)
       @bulk_2_path = path
     end     
 

data/lib/bio/PolyploidTools/SNP.rb

@@ -409,7 +409,7 @@ module Bio::PolyploidTools
       total_candidates += pr.almost_crhomosome_specific_intron.size
 
       skip_specific = total_candidates > max_specific_primers
-
+      #puts "skip_specific: #{skip_specific}: #{total_candidates} > #{max_specific_primers}"
       pr.chromosome_specific.each do |pos|
         break if skip_specific
         args = {:name =>"#{gene}:#{original}#{position}#{snp} #{original_name} chromosome_specific exon #{@snp_type} #{chromosome}", :left_pos => pr.snp_pos, :right_pos => pos, :sequence=>seq_original}

data/lib/bio/db/primer3.rb

@@ -34,13 +34,17 @@ module Bio::DB::Primer3
 
   def self.run(opts={})
     puts "Primer3.run running..."
-
+    timeout = 600
     f_in=opts[:in]
     f_out=opts[:out]
+    timeout = opts[:timeout] if opts[:timeout]
     opts.delete(:in)
     opts.delete(:out)
     primer_3_in = File.read(f_in)
-    status = systemu "primer3_core", 0=>primer_3_in, 1=>stdout='', 2=>stderr=''
+    status = systemu "primer3_core", 0=>primer_3_in, 1=>stdout='', 2=>stderr='' do |cid|
+      sleep timeout
+      Process.kill 9, cid
+    end
     # $stderr.puts cmdline
     if status.exitstatus == 0
       File.open(f_out, 'w') { |f| f.write(stdout) }

data/test/data/7B_marker_test.txt

@@ -0,0 +1 @@
+RAC875_c8221_649,7B,CGTACAATTTACCTGCAGAGGTTGAGAATGTCCTTTCTAGCTGCTTTGAG[T/C]ACGACTTTCGGGATCGCCCCTTGATGTCAGATATCTTACAAGCATTTGAA

data/test/test_bfr.rb

@@ -26,12 +26,12 @@ class TestPolyploidTools < Test::Unit::TestCase
     @f2_b=data_path + "/LIB1719.bam"
     
     @bfr_path=data_path + "/bfr_out_test.csv"
-    @fasta_db = Bio::DB::Fasta::FastaFile.new({:fasta=>@ref})
+    @fasta_db = Bio::DB::Fasta::FastaFile.new(fasta: @ref)
     @fasta_db.load_fai_entries
-    @bam_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@a})
-    @bam_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@b})
-    @bam_f2_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_a})
-    @bam_f2_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_b})
+    @bam_a =  Bio::DB::Sam.new(fasta: @ref, bam: @a)
+    @bam_b =  Bio::DB::Sam.new(fasta: @ref, bam: @b)
+    @bam_f2_a =  Bio::DB::Sam.new(fasta: @ref, bam: @f2_a)
+    @bam_f2_b =  Bio::DB::Sam.new(fasta: @ref, bam: @f2_b)
    # puts "SETUP"
   end
   
@@ -49,8 +49,8 @@ class TestPolyploidTools < Test::Unit::TestCase
     
     #puts @bam_a.methods
     ref_seq=@fasta_db.fetch_sequence(region)
-    reg_a = @bam_a.fetch_region({:region=>region,  :min_cov=>min_cov, :A=>1})
-    reg_b = @bam_b.fetch_region({:region=>region,  :min_cov=>min_cov, :A=>1})
+    reg_a = @bam_a.fetch_region(region: region,  min_cov: min_cov, A: 1)
+    reg_b = @bam_b.fetch_region(region: region,  min_cov: min_cov, A: 1)
     cons_1 = reg_a.consensus
     cons_2 = reg_b.consensus
     
@@ -85,10 +85,10 @@ class TestPolyploidTools < Test::Unit::TestCase
     container = Bio::BFRTools::BFRContainer.new
     
     container.reference @ref
-    container.parental_1  ( {:path => @a } )
-    container.parental_2  ( {:path => @b } )
-    container.bulk_1 ( {:path => @f2_a  })
-    container.bulk_2 ( {:path => @f2_b  })
+    container.parental_1( path:  @a )
+    container.parental_2( path:  @b )
+    container.bulk_1( path:  @f2_a  )
+    container.bulk_2( path:  @f2_b  )
 
     i = -1
 

data/test/test_integration.rb

@@ -0,0 +1,76 @@
+$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
+$: << File.expand_path('.')
+path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
+
+tmp_verb = $VERBOSE
+$VERBOSE=nil
+#puts path
+require path
+require 'bio-samtools'
+require "test/unit"
+$VERBOSE=tmp_verb
+
+
+class TestInregration < Test::Unit::TestCase
+
+  
+  #Set up the paths
+  def setup
+    @data_path= File.expand_path(File.dirname(__FILE__)   + '/data/' )
+    
+    @ref="#{@data_path}/7B_amplicon_test_reference.fa"
+    @amplicon = "#{@data_path}/7B_amplicon_test.fa"
+    @genomes_count = 3
+    @output_folder="#{@data_path}/test_out"
+    @bin=File.expand_path(File.dirname(__FILE__) + '/../bin')
+    @marker = "#{@data_path}/7B_marker_test.txt"
+    FileUtils.rm_r(@output_folder, force: true) if Dir.exist? @output_folder
+
+    cmd = "makeblastdb -in #{@ref} -dbtype nucl "
+    #status, stdout, stderr = 
+    systemu cmd
+    # @ref=data_path + '/S22380157.fa'
+    # @a=data_path + "/LIB1721.bam"
+    # @b=data_path + "/LIB1722.bam"
+    # @f2_a=data_path + "/LIB1716.bam"
+    # @f2_b=data_path + "/LIB1719.bam"
+    
+    # @bfr_path=data_path + "/bfr_out_test.csv"
+    # @fasta_db = Bio::DB::Fasta::FastaFile.new({:fasta=>@ref})
+    # @fasta_db.load_fai_entries
+    # @bam_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@a})
+    # @bam_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@b})
+    # @bam_f2_a =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_a})
+    # @bam_f2_b =  Bio::DB::Sam.new({:fasta=>@ref, :bam=>@f2_b})
+   # puts "SETUP"
+
+  end
+  
+  def teardown
+    FileUtils.rm_r(@output_folder, force: true) if Dir.exist? @output_folder
+    Dir.glob("#{@ref}.n*").each do |file| 
+      #puts file 
+      File.delete(file)
+    end
+  end
+  
+  def test_amplicon_primers
+    cmd = "ruby #{@bin}/polymarker_capillary.rb --reference #{@ref} --sequences #{@amplicon}  --genomes_count #{@genomes_count}  --output #{@output_folder} --database #{@ref}"
+    status, stdout, stderr = systemu cmd
+    assert_equal(status.exitstatus, 0, "Failed running '#{cmd}'\nSTDOUT:\n#{stdout}\nSTDERR\n#{stderr}")
+   
+  end
+
+  def test_deletion_primers
+    cmd = "ruby #{@bin}/polymarker_deletions.rb --reference #{@ref} --sequences #{@amplicon}  --genomes_count #{@genomes_count}  --output #{@output_folder} --database #{@ref}"
+    status, stdout, stderr = systemu cmd
+     assert_equal(status.exitstatus, 0, "Failed running '#{cmd}'\nSTDOUT:\n#{stdout}\nSTDERR\n#{stderr}")
+  end
+
+  def test_polymerker
+    cmd = "ruby ./bin/polymarker.rb -m #{@marker} -c #{@ref} --extract_found_contigs  -A blast -a nrgene --output #{@output_folder}"
+    status, stdout, stderr = systemu cmd
+     assert_equal(status.exitstatus, 0, "Failed running '#{cmd}'\nSTDOUT:\n#{stdout}\nSTDERR\n#{stderr}")
+  end
+
+end

data/test/test_snp_parsing.rb

@@ -27,7 +27,7 @@ class TestSNPparsing < Test::Unit::TestCase
   def test_mutant_snp
 
     ref=@data + "/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa"
-    fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>ref})
+    fasta_reference_db = Bio::DB::Fasta::FastaFile.new(fasta: ref)
     fasta_reference_db.index
     fasta_reference_db.load_fai_entries 
     
@@ -49,7 +49,7 @@ class TestSNPparsing < Test::Unit::TestCase
 
   def test_vcf_line
     ref=@data + "/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa"
-    fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>ref})
+    fasta_reference_db = Bio::DB::Fasta::FastaFile.new(fasta: ref)
     
     fasta_reference_db.load_fai_entries 
     vcf="IWGSC_CSS_1AL_scaff_1455974	127	test_snp	C	T	135.03	.	"
@@ -85,7 +85,7 @@ class TestSNPparsing < Test::Unit::TestCase
   def test_reference_snp
 
     ref=@data + "/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa"
-    fasta_reference_db = Bio::DB::Fasta::FastaFile.new({:fasta=>ref})
+    fasta_reference_db = Bio::DB::Fasta::FastaFile.new(fasta: ref)
     
     fasta_reference_db.load_fai_entries 
     

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 1.2.0
+  version: 1.2.1
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
-autorequire: 
+autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-10-28 00:00:00.000000000 Z
+date: 2021-05-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -227,13 +227,7 @@ files:
 - test/data/7B_amplicon_test.fa.fai
 - test/data/7B_amplicon_test_reference.fa
 - test/data/7B_amplicon_test_reference.fa.fai
-- test/data/7B_amplicon_test_reference.fa.ndb
-- test/data/7B_amplicon_test_reference.fa.nhr
-- test/data/7B_amplicon_test_reference.fa.nin
-- test/data/7B_amplicon_test_reference.fa.not
-- test/data/7B_amplicon_test_reference.fa.nsq
-- test/data/7B_amplicon_test_reference.fa.ntf
-- test/data/7B_amplicon_test_reference.fa.nto
+- test/data/7B_marker_test.txt
 - test/data/BS00068396_51.fa
 - test/data/BS00068396_51_blast.tab
 - test/data/BS00068396_51_contigs.aln
@@ -263,6 +257,13 @@ files:
 - test/data/PST130_7067.csv
 - test/data/PST130_7067.fa
 - test/data/PST130_7067.fa.fai
+- test/data/PST130_7067.fa.ndb
+- test/data/PST130_7067.fa.nhr
+- test/data/PST130_7067.fa.nin
+- test/data/PST130_7067.fa.not
+- test/data/PST130_7067.fa.nsq
+- test/data/PST130_7067.fa.ntf
+- test/data/PST130_7067.fa.nto
 - test/data/PST130_reverse_primer.csv
 - test/data/S22380157.fa
 - test/data/S22380157.fa.fai
@@ -312,13 +313,14 @@ files:
 - test/test_blast.rb
 - test/test_exon_container.rb
 - test/test_exonearate.rb
+- test/test_integration.rb
 - test/test_snp_parsing.rb
 - test/test_wrong_selection.sh
 homepage: http://github.com/tgac/bioruby-polyploid-tools
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
+post_install_message:
 rdoc_options: []
 require_paths:
 - lib
@@ -333,8 +335,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.2
-signing_key: 
+rubygems_version: 3.1.4
+signing_key:
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology
 test_files: []