bio-polyploid-tools 0.9.7 → 0.9.8

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -128,6 +128,11 @@ To use blast instead of exonerate, use the following command:
 
 ## Release Notes
 
+### 0.9.7 
+There was some strange issue with the numbering, so bumped to 0.9.7
+
+* Moved the arm selection function for fields in the chromosome name to the ```ChromosomeArm``` class.
+
 ### 0.8.7
 * FEATURE: ```polymarker.rb``` now also prints the total number of hits found. 
 

data/VERSION

@@ -1 +1 @@
-0.9.7
+0.9.8

data/bin/polymarker.rb

@@ -39,8 +39,7 @@ options[:min_identity] = 90
 options[:scoring] = :genome_specific
 options[:database]  = false
 options[:filter_best]  = false
-options[:max_hits] = 8
-options[:aligner] = :exonerate
+options[:aligner] = :blast
 
 
 options[:primer_3_preferences] = {
@@ -58,70 +57,56 @@ options[:primer_3_preferences] = {
 OptionParser.new do |opts|
   opts.banner = "Usage: polymarker.rb [options]"
 
-  opts.on("-a", "--arm_selection #{Bio::PolyploidTools::ChromosomeArm.getValidFunctions.join('|')}", "Function to decide the chromome arm") do |o|
-    tmp_str = o
-    arr = o.split(",")
-    if arr.size == 2
-       options[:arm_selection] = lambda do |contig_name|
-          separator, field = arr
-          field = field.to_i
-          ret = contig_name.split(separator)[field]
-          return ret
-        end
-    else
-      options[:arm_selection] = Bio::PolyploidTools::ChromosomeArm.getArmSelection(o)
-    end
-   end
-
-  opts.on("-b", "--filter_best", "If set, only keep the best alignment for each chromosome") do 
-    options[:filter_best]  = true
-  end
-
   opts.on("-c", "--contigs FILE", "File with contigs to use as database") do |o|
     options[:path_to_contigs] = o
   end
   
-  opts.on("-d", "--database PREFIX", "Path to the blast database. Only used if the aligner is blast. The default is the name of the contigs file without extension.") do |o|
-    options[:database] = o
-  end
-
-  opts.on("-e", "--exonerate_model MODEL", "Model to be used in exonerate to search for the contigs") do |o|
-     options[:model] = o
+  opts.on("-m", "--marker_list FILE", "File with the list of markers to search from") do |o|
+    options[:marker_list] = o
   end
 
   opts.on("-g", "--genomes_count INT", "Number of genomes (default 3, for hexaploid)") do |o|
     options[:genomes_count] = o.to_i
   end
-
-  opts.on("-i", "--min_identity INT", "Minimum identity to consider a hit (default 90)") do |o|
-    options[:min_identity] = o.to_i
+  
+  opts.on("-b", "--filter_best", "If set, only keep the best alignment for each chromosome") do 
+    options[:filter_best]  = true
   end
 
-  opts.on("-m", "--marker_list FILE", "File with the list of markers to search from") do |o|
-    options[:marker_list] = o
-  end
 
-  opts.on("-o", "--output FOLDER", "Output folder") do |o|
-    options[:output_folder] = o
+  opts.on("-s", "--snp_list FILE", "File with the list of snps to search from, requires --reference to get the sequence using a position") do |o|
+    options[:snp_list] = o
   end
 
-  opts.on("-p", "--primer_3_preferences FILE", "file with preferences to be sent to primer3") do |o|
-    options[:primer_3_preferences] = Bio::DB::Primer3.read_primer_preferences(o, options[:primer_3_preferences] )
+  opts.on("-t", "--mutant_list FILE", "File with the list of positions with mutation and the mutation line.\n\
+    requires --reference to get the sequence using a position") do |o|
+    options[:mutant_list] = o
   end
-
+  
   opts.on("-r", "--reference FILE", "Fasta file with the sequence for the markers (to complement --snp_list)") do |o|
     options[:reference] = o
   end
+
+  opts.on("-i", "--min_identity INT", "Minimum identity to consider a hit (default 90)") do |o|
+    options[:min_identity] = o.to_i
+  end
   
-  opts.on("-s", "--snp_list FILE", "File with the list of snps to search from, requires --reference to get the sequence using a position") do |o|
-    options[:snp_list] = o
+  opts.on("-o", "--output FOLDER", "Output folder") do |o|
+    options[:output_folder] = o
   end
-
-  opts.on("-t", "--mutant_list FILE", "File with the list of positions with mutation and the mutation line.\n\
-    requires --reference to get the sequence using a position") do |o|
-    options[:mutant_list] = o
+  
+  opts.on("-e", "--exonerate_model MODEL", "Model to be used in exonerate to search for the contigs") do |o|
+     options[:model] = o
   end
+
+  opts.on("-a", "--arm_selection #{Bio::PolyploidTools::ChromosomeArm.getValidFunctions.join('|')}", "Function to decide the chromome arm") do |o|
+    options[:arm_selection] = Bio::PolyploidTools::ChromosomeArm.getArmSelection(o)
+   end
   
+  opts.on("-p", "--primer_3_preferences FILE", "file with preferences to be sent to primer3") do |o|
+    options[:primer_3_preferences] = Bio::DB::Primer3.read_primer_preferences(o, options[:primer_3_preferences] )
+  end
+
   opts.on("-v", "--variation_free_region INT", "If present, avoid generating the common primer if there are homoeologous SNPs within the specified distance") do |o|
     options[:variation_free_region] = o.to_i
   end
@@ -130,24 +115,23 @@ OptionParser.new do |opts|
     options[:extract_found_contigs] = true
   end
 
-  opts.on("-A", "--aligner exonerate|blast", "Select the aligner to use. Default: exonerate") do |o|
-    raise "Invalid aligner" unless o == "exonerate" or o == "blast" 
-    options[:aligner] = o.to_sym
+  opts.on("-P", "--primers_to_order", "If present, save a separate file with the primers with the KASP tails")do
+    #TODO: have a string with the tails, optional. 
+    options[:primers_to_order] = true
   end
 
   opts.on("-H", "--het_dels", "If present, change the scoring to give priority to: semi-specific, specific, non-specific")  do
     options[:scoring] = :het_dels
   end
 
-  opts.on("-M", "--max_hits INT", "Maximum number of hits to consider a region as non repetitive. Markers with more than this number of hits will be ignored. (default #{options[:max_hits]})") do |o|
-    options[:max_hits] = o.to_i
+  opts.on("-A", "--aligner exonerate|blast", "Select the aligner to use. Default: exonerate") do |o|
+    raise "Invalid aligner" unless o == "exonerate" or o == "blast" 
+    options[:aligner] = o.to_sym
   end
 
-  opts.on("-P", "--primers_to_order", "If present, save a separate file with the primers with the KASP tails")do
-    #TODO: have a string with the tails, optional. 
-    options[:primers_to_order] = true
+  opts.on("-d", "--database PREFIX", "Path to the blast database. Only used if the aligner is blast. The default is the name of the contigs file without extension.") do |o|
+    options[:database] = o
   end
-
 end.parse!
 
 
@@ -312,7 +296,7 @@ def do_align(aln, exo_f, found_contigs, min_identity,fasta_file,options)
 
 end
 
-Bio::DB::Blast.align({:max_hits=>options[:max_hits], :query=>temp_fasta_query, :target=>options[:database], :model=>model}) do |aln|
+Bio::DB::Blast.align({:query=>temp_fasta_query, :target=>options[:database], :model=>model}) do |aln|
   do_align(aln, exo_f, found_contigs,min_identity, fasta_file,options)
 end if options[:aligner] == :blast
 
@@ -333,9 +317,8 @@ contigs_f.close() if options[:extract_found_contigs]
 write_status "Reading best alignment on each chromosome"
 
 
-container = Bio::PolyploidTools::ExonContainer.new
-container.flanking_size = options[:flanking_size] 
-container.max_hits = options[:max_hits]
+container= Bio::PolyploidTools::ExonContainer.new
+container.flanking_size=options[:flanking_size] 
 container.gene_models(temp_fasta_query)
 container.chromosomes(target)
 container.add_parental({:name=>snp_in})
@@ -392,7 +375,7 @@ snps.each do |snp|
 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,is_repetitive,hit_count"
+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"
 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()) }

data/bio-polyploid-tools.gemspec

@@ -2,11 +2,11 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.9.7 ruby lib
+# stub: bio-polyploid-tools 0.9.8 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "0.9.7"
+  s.version = "0.9.8"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]

data/lib/bio/PolyploidTools/ChromosomeArm.rb

@@ -1,8 +1,6 @@
 module Bio::PolyploidTools
 class ChromosomeArm
 
-
-
   @@arm_selection_functions = Hash.new;
 
   #example format: chr2A
@@ -42,11 +40,24 @@ class ChromosomeArm
   end
 
   def self.getArmSelection(name)
+    arr = name.split(",")
+    if arr.size == 2
+       @@arm_selection_functions[name.to_sym] = lambda do |contig_name|
+          separator, field = arr
+          field = field.to_i
+          ret = contig_name.split(separator)[field]
+          return ret
+        end
+    end
     @@arm_selection_functions[name.to_sym]
   end
 
   def self.getValidFunctions
-    @@arm_selection_functions.keys.map { |e| e.to_s }
+    tmp = @@arm_selection_functions.keys.map { |e| e.to_s }
+    tmp.unshift "<sep>,<index>"
+    tmp
   end
+
+
 end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.9.7
+  version: 0.9.8
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez