bio-polyploid-tools 0.7.0 → 0.7.1

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

@@ -21,8 +21,8 @@ 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
-].
+[reference file](ftp://ftp.ensemblgenomes.org/pub/release-25/plants/fasta/triticum_aestivum/dna/Triticum_aestivum.IWGSC2.25.dna.genome.fa.gz
+).
 
 
 
@@ -30,14 +30,63 @@ 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>
+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)
 
+The available command line arguments are: 
+
+```
+Usage: polymarker.rb [options]
+    -c, --contigs FILE               File with contigs to use as database
+    -m, --marker_list FILE           File with the list of markers to search from
+    -g, --genomes_count INT          Number of genomes (default 3, for hexaploid)
+    -s, --snp_list FILE              File with the list of snps to search from, requires --reference to get the sequence using a position
+    -t, --mutant_list FILE           File with the list of positions with mutation and the mutation line.
+    requires --reference to get the sequence using a position
+    -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
+    -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
+    -v, --variation_free_region INT  If present, avoid generating the common primer if there are homoeologous SNPs within the specified distance (not tested)
+    -x, --extract_found_contigs      If present, save in a separate file the contigs with matches. Useful to debug.
+    -P, --primers_to_order			 If present, saves a file named primers_to_order which contains the KASP tails
+```
+
+###Custom reference sequences. 
+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:
+
+```rb
+arm_selection_functions[:arm_selection_embl] = lambda do | contig_name|
+  arr = contig_name.split('_')
+  ret = "U"
+  ret = arr[2][0,2] if arr.size >= 3
+  ret = "3B" if arr.size == 2 and arr[0] == "v443"
+  ret = arr[0][0,2] if arr.size == 1   
+  return ret
+end
+```
+
+The function should return a 2 character string, when the first is the chromosome number and the second the chromosome group. The symbol in the hash is the name to be used in the argument ```--arm_selection```.  If you want your parser to be added to the distribution, feel free to fork and make a pull request. 
+
+
+
 ##Release Notes
 
+###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. 
+
 ###0.6.1
 
 
@@ -49,10 +98,10 @@ If you want to use the web interface, visit the [PolyMarker webservice at TGAC](
 
 * 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: Add a parameter file to configure the alignments. 
-TODO: Produce primers for products of different sizes
+* 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: Add a parameter file to configure the alignments. 
+* TODO: Produce primers for products of different sizes. This can probably be done with the primer_3_preferences option, but hasn't been tested. 
 
 
 

data/VERSION

@@ -1 +1 @@
-0.7.0
+0.7.1

data/bin/polymarker.rb

@@ -17,9 +17,18 @@ arm_selection_functions[:arm_selection_first_two] = lambda do | contig_name |
   ret = contig_name[0,2]       
   return ret
 end
-#Function to parse stuff like: IWGSC_CSS_1AL_scaff_110
+
+#Function to parse stuff like: "IWGSC_CSS_1AL_scaff_110"
+#Or the first two characters in the contig name, to deal with 
+#pseudomolecules that start with headers like: "1A"
+#And with the cases when 3B is named with the prefix: v443
 arm_selection_functions[:arm_selection_embl] = lambda do | contig_name|
-  ret = contig_name.split('_')[2][0,2]
+  
+  arr = contig_name.split('_')
+  ret = "U"
+  ret = arr[2][0,2] if arr.size >= 3
+  ret = "3B" if arr.size == 2 and arr[0] == "v443"
+  ret = arr[0][0,2] if arr.size == 1   
   return ret
 end
 

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 0.7.0 ruby lib
+# stub: bio-polyploid-tools 0.7.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools"
-  s.version = "0.7.0"
+  s.version = "0.7.1"
 
   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 = "2015-05-08"
+  s.date = "2015-05-28"
   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", "filter_exonerate_by_identity.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"]
@@ -129,7 +129,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/tgac/bioruby-polyploid-tools"
   s.licenses = ["MIT"]
-  s.rubygems_version = "2.2.1"
+  s.rubygems_version = "2.4.7"
   s.summary = "Tool to work with polyploids, NGS and molecular biology"
 
   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: 0.7.0
+  version: 0.7.1
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-08 00:00:00.000000000 Z
+date: 2015-05-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -228,7 +228,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.1
+rubygems_version: 2.4.7
 signing_key: 
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology