bio-polyploid-tools 0.5.2 → 0.6.0

data/test/data/test_from_mutant.csv

@@ -0,0 +1,3 @@
+seqid,library,position,wt_base,mut_base
+IWGSC_CSS_1AL_scaff_1455974,Kronos2281,127,C,T
+IWGSC_CSS_1AL_scaff_5678297,Kronos2132,1375,C,T

data/test/test_snp_parsing.rb

@@ -10,6 +10,7 @@ class TestPolyploidTools < Test::Unit::TestCase
 
   #Set up the paths
   def setup
+    @data = File.expand_path(File.dirname(__FILE__) + "/data")
     
   end
   
@@ -37,5 +38,31 @@ class TestPolyploidTools < Test::Unit::TestCase
     assert(snp.template_sequence == "CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA", "#{snp.template_sequence}!=CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA")
     #true
   end
+
+  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.load_fai_entries 
+    
+    snp = Bio::PolyploidTools::SNPMutant.parse("IWGSC_CSS_1AL_scaff_1455974,Kronos2281,127,C,T")
+    assert_equal(snp.gene , "1AL_1455974_Kronos2281_127", "The original name was not parsed: #{snp.gene}")
+    assert_equal(snp.contig, "IWGSC_CSS_1AL_scaff_1455974")
+    assert_equal(snp.chromosome, "1A", "The chromosome wasnt parsed: #{snp.chromosome}")
+    assert_equal(snp.position, 127, "The position is not parsed: #{snp.position}")
+    
+    region = fasta_reference_db.index.region_for_entry(snp.contig).get_full_region
+    snp.full_sequence = fasta_reference_db.fetch_sequence(region)
+
+    assert_equal(snp.template_sequence, "actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctcYttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaaga")
+    assert_equal(snp.sequence_original, "actcgatcgtcagcacccgctggaacttggggaacgtcttgaacgccgcaagcaccggggcgtcctctgactgtatgagcacgcgctgcttacaggtctc[C/T]ttgtcgtacccggacttgacaagcgctttggagaccgcatccaccacgtcaaggcttctggctataaggtacgtagcatgctgcactcggtaggtacaaga")
+    assert_equal(snp.position, 101)
+    assert_equal(snp.original, "C")
+    assert_equal(snp.snp, "T")
+    
+    
+  end
+
   
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.5.2
+  version: 0.6.0
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-28 00:00:00.000000000 Z
+date: 2015-02-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -162,6 +162,7 @@ files:
 - lib/bio/PolyploidTools/Marker.rb
 - lib/bio/PolyploidTools/PrimerRegion.rb
 - lib/bio/PolyploidTools/SNP.rb
+- lib/bio/PolyploidTools/SNPMutant.rb
 - lib/bio/PolyploidTools/SNPSequence.rb
 - lib/bio/db/exonerate.rb
 - lib/bio/db/primer3.rb
@@ -172,6 +173,8 @@ files:
 - test/data/BS00068396_51_contigs.fa
 - test/data/BS00068396_51_exonerate.tab
 - test/data/BS00068396_51_genes.txt
+- test/data/IWGSC_CSS_1AL_scaff_1455974.fa
+- test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa
 - test/data/LIB1716.bam
 - test/data/LIB1716.bam.bai
 - test/data/LIB1719.bam
@@ -192,6 +195,7 @@ files:
 - test/data/patological_cases5D.csv
 - test/data/primer_3_input_header_test
 - test/data/short_primer_design_test.csv
+- test/data/test_from_mutant.csv
 - test/data/test_iselect.csv
 - test/data/test_iselect_reference.fa
 - test/data/test_iselect_reference.fa.fai