bio-polyploid-tools 0.6.0 → 0.6.1

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data/README.md

@@ -1,45 +1,59 @@
-bio-polyploid-tools
-===================
+#bio-polyploid-tools
 
-Introduction
--------------
+##Introduction
 This tools are designed to deal with polyploid wheat. The first tool is to design KASP primers, 
 making them as specific as possible. 
 
 
-Installation
-------------
-'gem install bio-polyploid-tools'
+##Installation
+```sh
+gem install bio-polyploid-tools
+```
+You need to have in your ```$PATH``` the following programs:
 
-You need to have in your $PATH the following programs:
-* [MAFFT]{http://mafft.cbrc.jp/alignment/software/}
-* [primer3]{http://primer3.sourceforge.net/releases.php}
-* [exonerate]{http://www.ebi.ac.uk/~guy/exonerate/} 
+* [MAFFT](http://mafft.cbrc.jp/alignment/software/)
+* [primer3](http://primer3.sourceforge.net/releases.php)
+* [exonerate](http://www.ebi.ac.uk/~guy/exonerate/) 
 
 The code has been developed on ruby 2.1.0, but it should work on 1.9.3 and above. 
 
 
-Polymarker
-----------
+#PolyMarker
 
 To run poolymerker with the CSS wheat contigs, you need to unzip the 
-reference file [Triticum_aestivum.IWGSP1.22.dna_rm.genome.fa.gz{ftp://ftp.ensemblgenomes.org/pub/release-22/plants/fasta/triticum_aestivum/dna/}. 
+(reference file)[ftp://ftp.ensemblgenomes.org/pub/release-25/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC2.25.dna.genome.fa.gz
+].
 
-polymarker.rb --contigs Triticum_aestivum.IWGSP1.22.dna_rm.genome.fa --marker_list snp_list.csv --output output_folder
+
+
+```sh
+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
 
-Notes
------
+If you want to use the web interface, visit the [PolyMarker webservice at TGAC](http://polymarker.tgac.ac.uk)
+
+##Release Notes
+
+###0.6.1
+
+
+* polymarker.rb now validates that all the files exist. 
+* BUGFIX: A reference was required even when it was not used to generate contigs. 
+
+#Notes
+
 
 * If the SNP is in a gap in the alignment to the chromosomes, it is ignored. 
 
 BUG: Blocks with NNNs are picked and treated as semi-specific. 
 BUG: If the name of the reference have space, the ID is not chopped. ">gene_1 (G12A)" shouls be treated as ">gene_1". 
-TODO: If reading from a reference file, only get one reference to align when the region is queried several times
 TODO: Add a parameter file to configure the alignments. 
 TODO: Produce primers for products of different sizes
 
 
+
+

data/VERSION

@@ -1 +1 @@
-0.6.0
+0.6.1

data/bin/polymarker.rb

@@ -28,6 +28,19 @@ arm_selection_functions[:arm_selection_morex] = lambda do | contig_name |
   return ret
 end
 
+def validate_files(o)
+
+  [
+    o[:path_to_contigs], 
+    o[:marker_list], 
+    o[:snp_list], 
+    o[:mutant_list],
+    o[:reference]
+  ].flatten.compact.each do |f|  
+        raise IOError "Unable to read #{f}" unless File.exists? f 
+    end
+end 
+
 options = {}
 options[:path_to_contigs] = "/tgac/references/external/projects/iwgsc/css/IWGSC_CSS_all_scaff_v1.fa"
 options[:chunks] = 1
@@ -104,6 +117,8 @@ OptionParser.new do |opts|
   
 end.parse!
 
+validate_files(options)
+
 if options[:primer_3_preferences][:primer_product_size_range]
   range = options[:primer_3_preferences][:primer_product_size_range]
   range_arr = range.split("-")
@@ -267,7 +282,7 @@ write_status "Reading best alignment on each chromosome"
 container= Bio::PolyploidTools::ExonContainer.new
 container.flanking_size=options[:flanking_size] 
 container.gene_models(temp_fasta_query)
-container.chromosomes(fasta_reference)
+container.chromosomes(target)
 container.add_parental({:name=>snp_in})
 container.add_parental({:name=>original_name})
 snps.each do |snp|

data/bio-polyploid-tools.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 0.6.0 ruby lib
+# stub: bio-polyploid-tools 0.6.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools"
-  s.version = "0.6.0"
+  s.version = "0.6.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Ricardo H.  Ramirez-Gonzalez"]
-  s.date = "2015-02-15"
+  s.date = "2015-03-05"
   s.description = "Repository of tools developed in TGAC and Crop Genetics in JIC to work with polyploid wheat"
   s.email = "ricardo.ramirez-gonzalez@tgac.ac.uk"
   s.executables = ["bfr.rb", "count_variations.rb", "filter_blat_by_target_coverage.rb", "find_best_blat_hit.rb", "find_best_exonerate.rb", "hexaploid_primers.rb", "homokaryot_primers.rb", "map_markers_to_contigs.rb", "markers_in_region.rb", "polymarker.rb", "snp_position_to_polymarker.rb", "snps_between_bams.rb"]

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.6.0
+  version: 0.6.1
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-02-15 00:00:00.000000000 Z
+date: 2015-03-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio