bio-polyploid-tools 0.7.1 → 0.7.2

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

@@ -1,8 +1,7 @@
 #bio-polyploid-tools
 
 ##Introduction
-This tools are designed to deal with polyploid wheat. The first tool is to design KASP primers, 
-making them as specific as possible. 
+This tools are designed to deal with polyploid wheat. The first tool is to design KASP primers, making them as specific as possible. 
 
 
 ##Installation
@@ -17,12 +16,9 @@ You need to have in your ```$PATH``` the following programs:
 
 The code has been developed on ruby 2.1.0, but it should work on 1.9.3 and above. 
 
-
 #PolyMarker
 
-To run poolymerker with the CSS wheat contigs, you need to unzip the 
-[reference file](ftp://ftp.ensemblgenomes.org/pub/release-25/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC2.25.dna.genome.fa.gz
-).
+To run poolymerker with the CSS wheat contigs, you need to unzip the reference file from  [ensembl](http://ftp.ensemblgenomes.org/pub/release-25/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC2.25.dna.genome.fa.gz).
 
 
 
@@ -30,9 +26,7 @@ To run poolymerker with the CSS wheat contigs, you need to unzip the
 polymarker.rb --contigs Triticum_aestivum.IWGSC2.25.dna.genome.fa --marker_list snp_list.csv --output output_folder
 ```
 
-The ```snp_list``` file must follow the convention
-```<ID>,<Chromosome>,<SEQUENCE>```
-with the SNP inside the sequence in the format [A/T]. As a reference, look at test/data/short_primer_design_test.csv
+The ```snp_list``` file must follow the convention ```ID,Chromosome,SEQUENCE``` with the SNP inside the sequence in the format [A/T]. As a reference, look at test/data/short_primer_design_test.csv
 
 If you want to use the web interface, visit the [PolyMarker webservice at TGAC](http://polymarker.tgac.ac.uk)
 
@@ -49,6 +43,7 @@ Usage: polymarker.rb [options]
     -r, --reference FILE             Fasta file with the sequence for the markers (to complement --snp_list)
     -o, --output FOLDER              Output folder
     -e, --exonerate_model MODEL      Model to be used in exonerate to search for the contigs
+    -i, --min_identity INT           Minimum identity to consider a hit (default 90)
     -a, --arm_selection arm_selection_embl|arm_selection_morex|arm_selection_first_two
                     Function to decide the chromome arm
     -p, --primer_3_preferences FILE  file with preferences to be sent to primer3
@@ -61,7 +56,7 @@ Usage: polymarker.rb [options]
 By default, the contigs and pseudomolecules from [ensembl](ftp://ftp.ensemblgenomes.org/pub/release-25/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC2.25.dna.genome.fa.gz
 ) are used. However, it is possible to use a custom reference. To define the chromosome where each contig belongs the argument ```arm_selection``` is used.  The defailt uses ids like: ```IWGSC_CSS_1AL_scaff_110```, where the third field, separated by underscores is used. A simple way to add costum references is to rename the fasta file to follow that convention. Another way is to use the option ```--arm_selection arm_selection_first_two```, where only the first two characters in each contig is used as identifier, useful when pseudomolecules are named after the chromosomes (ie: ">1A" in the fasta file). 
 
-If your contigs follow a different convention, in ```polymarker.rb``` it is possible to define new parsers, by adding at the begining, with the rest of the parsers a new lambda like:
+If your contigs follow a different convention, in the file ```polymarker.rb``` it is possible to define new parsers, by adding at the begining, with the rest of the parsers a new lambda like:
 
 ```rb
 arm_selection_functions[:arm_selection_embl] = lambda do | contig_name|
@@ -80,12 +75,15 @@ The function should return a 2 character string, when the first is the chromosom
 
 ##Release Notes
 
+###0.7.2
+* FEATURE: Added a flag ```min_identity``` to set the minimum identity to consider a hit. The default is 90
+
 ###0.7.1
 * BUGFIX: Now the parser for ```arm_selection_embl``` works with the mixture of contigs and pseudomolecules
 *  DOC: Added documentation on how to use custom references.  
 
 ###0.7.0
-* Added flag ```gebines_count``` for number of genomes, to be used on tetraploids, etc. 
+* Added flag ```genomes_count``` for number of genomes, to be used on tetraploids, etc. 
 
 ###0.6.1
 

data/VERSION

@@ -1 +1 @@
-0.7.1
+0.7.2

data/bin/polymarker.rb

@@ -61,6 +61,8 @@ options[:flanking_size] = 150;
 options[:variation_free_region] = 0 
 options[:extract_found_contigs] = false
 options[:genomes_count] = 3
+options[:min_identity] = 90
+
 options[:primer_3_preferences] = {
       :primer_product_size_range => "50-150" ,
       :primer_max_size => 25 , 
@@ -98,6 +100,10 @@ OptionParser.new do |opts|
   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("-o", "--output FOLDER", "Output folder") do |o|
     options[:output_folder] = o
@@ -123,7 +129,7 @@ OptionParser.new do |opts|
     options[:extract_found_contigs] = true
   end
 
-  opts.on("-P", "--primers_to_order")do
+  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
@@ -131,6 +137,7 @@ OptionParser.new do |opts|
   
 end.parse!
 
+
 validate_files(options)
 
 if options[:primer_3_preferences][:primer_product_size_range]
@@ -172,6 +179,8 @@ primer_3_output="#{output_folder}/primer_3_output_temp"
 exons_filename="#{output_folder}/exons_genes_and_contigs.fa"
 output_primers="#{output_folder}/primers.csv"
 output_to_order="#{output_folder}/primers_to_order.csv"
+min_identity= options[:min_identity]
+
 @status_file="#{output_folder}/status.txt"
 
 primer_3_config=File.expand_path(File.dirname(__FILE__) + '/../conf/primer3_config')
@@ -183,7 +192,7 @@ def write_status(status)
   f.close
 end
 
-min_identity= 90
+
 snps = Array.new
 
 begin

data/bio-polyploid-tools.gemspec

@@ -2,11 +2,11 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.7.1 ruby lib
+# stub: bio-polyploid-tools 0.7.2 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools"
-  s.version = "0.7.1"
+  s.version = "0.7.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.7.1
+  version: 0.7.2
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez