bio-polyploid-tools 0.10.1 → 1.2.0

data/lib/bio/db/blast.rb

@@ -82,7 +82,7 @@ module Bio::DB::Blast
 		max_target_seqs = 6 #TODO: Actually add this as an argument to PolyMarker. 
 		max_target_seqs = opts[:max_hits] * 2 if opts[:max_hits]
 		cmdline = "blastn -max_target_seqs #{max_target_seqs} -query #{query} -db #{target} -outfmt '6 qseqid qstart qend qframe sseqid sstart send sframe score pident qlen slen qseq sseq'"
-
+		#puts cmdline
 		status, stdout, stderr = systemu cmdline
 		if status.exitstatus == 0
 			alns = Array.new unless block_given?

data/lib/bio/db/primer3.rb

@@ -30,7 +30,6 @@ module Bio::DB::Primer3
     opts.each do |key,value|
       file.puts "#{key.to_s.upcase}=#{value}\n"
     end
-    # file.puts "="
   end
 
   def self.run(opts={})
@@ -129,12 +128,12 @@ module Bio::DB::Primer3
       @values << snp_type
       if primer3_line_1 and primer3_line_2
         #Block that searches both if both pairs have a TM
-        primer_2 = primer3_line_2.left_primer_with_coordinates(primer3_line_1.left_coordinates, primer3_line_1.orientation)
-        primer_2_tm = find_left_primer_temp(primer_2)
-        primer_1 = primer3_line_1.left_primer_with_coordinates(primer3_line_2.left_coordinates, primer3_line_2.orientation) 
+        primer_1    = primer3_line_1.left_primer_with_coordinates(primer3_line_2.left_coordinates, primer3_line_2.orientation) 
         primer_1_tm = find_left_primer_temp(primer_1)
-        #  $stderr.puts primer_1
-        #  $stderr.puts primer_2
+
+        primer_2    = primer3_line_2.left_primer_with_coordinates(primer3_line_1.left_coordinates, primer3_line_1.orientation)
+        primer_2_tm = find_left_primer_temp(primer_2)
+
         if primer3_line_1 < primer3_line_2 and primer_2_tm != "NA"
           @values << primer3_line_1.left_primer
           @values << primer_2
@@ -159,7 +158,7 @@ module Bio::DB::Primer3
           @values << primer3_line_2.best_pair.product_size
         else
 
-          first_candidate = find_primer_pair_first
+          first_candidate  = find_primer_pair_first
           second_candidate = find_primer_pair_second
 
           if first_candidate
@@ -183,7 +182,7 @@ module Bio::DB::Primer3
             @values << first_candidate.best_pair.left.tm 
             @values << primer_2_tm
             @values << first_candidate.best_pair.right.tm
-            @values << "first" 
+            @values << "first-" 
             @values << first_candidate.best_pair.product_size
           elsif  second_candidate 
             #puts "B"
@@ -195,7 +194,7 @@ module Bio::DB::Primer3
             @values << primer_1_tm
             @values << second_candidate.best_pair.left.tm
             @values << second_candidate.best_pair.right.tm
-            @values << "second"
+            @values << "second-"
             @values << second_candidate.best_pair.product_size
           elsif  first_candidate 
             #puts "C"
@@ -207,7 +206,7 @@ module Bio::DB::Primer3
             @values << primer_2_tm
             @values << first_candidate.best_pair.left.tm
             @values << first_candidate.best_pair.right.tm
-            @values << "first"
+            @values << "first/"
             @values << first_candidate.best_pair.product_size
           end
         end
@@ -277,7 +276,6 @@ module Bio::DB::Primer3
     end
 
     def orientation
-      puts "insideOrientation: #{self.values[11]}"
       return self.values[11] if self.values[11]&& self.values[11] != nil 
       return 'unknown'
     end
@@ -385,7 +383,7 @@ module Bio::DB::Primer3
           @primer3_line_1 = primer3record if not @primer3_line_1  or @primer3_line_1 > primer3record
         when primer3record.line == @line_2
           primers_line_2 << primer3record
-          @primer3_line_2 = primer3record if not @primer3_line_2 or @primer3_line_2 > primer3record
+          @primer3_line_2 = primer3record if not @primer3_line_2  or @primer3_line_2 > primer3record
         else
           raise Primer3Exception.new "#{primer3record.line} is not recognized (#{line_1}, #{line_2})"
         end
@@ -508,9 +506,7 @@ module Bio::DB::Primer3
     def left_primer_with_coordinates(coordinates, other_orientation)
 
       seq = self.sequence_template
-      #puts "Left coordinates: #{seq}"
-      seq = Primer3Record.reverse_complement_string(seq) if self.orientation != other_orientation
-
+      seq = Primer3Record.reverse_complement_string(seq) if self.orientation != other_orientation    
       seq[coordinates[0],coordinates[1]] 
     end
 
@@ -807,9 +803,9 @@ module Bio::DB::Primer3
       str = ""
       snp_hash.each do |k, snp|  
         if snp.found_primers?
-          str << snp.gene << snp.original << "\t" << tail_a << snp.first_primer << "\n"
-          str << snp.gene << snp.snp      << "\t" << tail_b << snp.second_primer << "\n"
-          str << snp.gene                 << "\t"           << snp.common_primer << "\n"
+          str << snp.gene << snp.original << "_1st\t" << tail_a << snp.first_primer  << "\n"
+          str << snp.gene << snp.snp      << "_2nd\t" << tail_b << snp.second_primer << "\n"
+          str << snp.gene                 << "_common\t"        << snp.common_primer << "\n"
         end
       end
       return str

data/test/data/7B_amplicon_test.fa

@@ -0,0 +1,12 @@
+>chr7B:1000-1600
+TTTCAAATGCTTGTAAGATATCTGACATCAAGGGGCGATCCCGAAAGTCATACTCGAAGC
+AGCTAGGAAGGACATTCTCAACCTCTGCAGGTAAGTTGTACGGGAATATCGGTTTCTCTT
+TCTTCAGGACAACCAACTGATAAATCTCGTCTGGTGATTTGCCACGCCAAGGCTGAACGC
+CAGTGAACATCTCAAGAATGCTGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTG
+GACCTCTGATGTTTGGTTGCCACTGCTCTGGGGCCATGTAATTTGGAGTTCCAAGTCTTT
+GGATAAGCTCTGGGTTTGGCAGCGACAGTCCAAACAGCAAGGATGGAATCCCAAAATCCC
+CCAGCACAGCATGGTCATGGTCATCAAGGAGAAAATTGCAAGGTTTGAGATTAAGAACAA
+ATATTCCCCTGGAGTGTAGGTCTAGCACACCACGCGCCAAATCGGCGCCGTATCTGCAAA
+TTACAGGAAATAATAAAAATATGTACCACTCAAGAAAACATCCTCTAAACAGAGCATCAT
+AAGCATTCTCAAAAGTCAACCAGGATAATGTGCCTGCACTAAGGTGATGAAGGATATCTG
+C

data/test/data/7B_amplicon_test.fa.fai

@@ -0,0 +1 @@
+chr7B:1000-1600	601	17	60	61

data/test/data/7B_amplicon_test_reference.fa

@@ -0,0 +1,110 @@
+>chr7A
+CTTCCTGCTGCTGAACTTTCTGAGGATCACCGCCCTGATCGGAGACGCTGGCGACCTTTC
+GACTCCTTGGCCTTGTGATGCTCTTGCCGACAAAGATACCTAGCTTCATAGCAGTAAAGA
+AACCTATGGCGATGAACAGAGGCCTCACCACCCAATGGAAGTCCTCGAGGTGCTCATACT
+TCTTCACAACCCCATCGCACTTGTCGAAGCTCACCACCTCCACCTCTGAAGGGTCGGCCA
+AGCAGCTGCACACTTCGCCAAGGCTGAATTTGCCAGGGAAGGTCACAACAAGGCATCCAT
+TCGAGAGTATCTGTGAAATACGGCCTGTGGCAAACACTCCGCCTCTCTTTCGCGGCCATT
+CAAACCGGGGGCTTGATGTGTTAGTTCTCAGCCTCACAAATTGTCCCACGCAGTAGGCTT
+CGGCCATTTGCAGATCTGAATATTCCCCCTTCCAGAGGGTGTCCATTCCTATTAAACCAA
+CATACACGGTGCCATTACGGTCAATGCTATGAAGAATTCCGACCTGAGACCGCTTCTTGT
+CTTCCTCCCTAAGCCTTACCCAGTCTCCGGCAGCGAAACCATAGGTCACCCTCTCCACTG
+TCGAGGAATGGACCTTCAAAGGGTCATGTATTCCATGGACTCGTACAAGAATGTAGCTAT
+CACGTTCTCCATCCTCCTCCATGCCAACTATGGTTCCATCAGGAATTTCCATTGTTTCAG
+GAGTACAAGAGTTTTTAACCTTTCTCGAGCGGACCTTGTCACCAACTTGCAGCTTATCCT
+TAAAGTGTGACCAATTAGTGTGACTTGGCACTACTGCCCTTGGGTTTTCAGAACTATCCC
+AGCCATTGTTGTCATAATCCACATCTTTAGCACTGAAGAAATGAAAAAAGAAAACAAATT
+TAGGAAAGAACTATGGTAAAATCACCCATCTGATGGCAGTTTAACCAAATACTGCAAGTT
+GATAAGGCAGAAGTAGAAAGAGAGTTTTAGCATGTTACCTTTCAAATGCTTGCAAGATAT
+CTGACATCAAGGGGCGATCCCGAAAGTCGTACTCAAAGCAGCTAGAAAGGACATTCTCAA
+CCTCTGCAGGTAAGTTGTATGGGAATATCGGTTTCTCTTTCTTCAGGACAACCAACTGAT
+AAATTTCATCTGGTGATTTGCCACGCCAAGGCTGAACGCCACTGAACATCTCAAGAATGC
+TGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTGGACCTCTGATGTTTGGTTGCC
+ATTGCTCTGGGGCCATGTAATTTGGAGTCCCAAGTCTTTGGATAAGCTCTGGGTTTGGCA
+GAGAAAGTCCAAACAGCAAGGATGGAATCCCAAAATCCCCCAGCACAGCATGGTCATGGT
+CATCAAGGAGAAAATTGCAAGGCTTGAGATTAAGAACAAATATTCCCCTGGAGTGTAGGT
+CTAGCACACCACGCGCCAAATCGGCACCATATCTGCAAGTTATAAGAATTCATAAAAATA
+TGTATTACTACTCAAGAAAATATCTTCTAAACAGAGCATCATAAGCATTCTCAAAAGTCA
+ACAGGATAATGTGCCTGTACTAAGGTCATAAACTATATCTGCCAGTTAATCAATCAACAC
+GTTCACTGGTAGAAAGTTGGAAACTGCATGCTTAGGTGACACTTCATCTAAAAAAAATGT
+ATATTTGTCTCTGATAAATTGTATTCTTAAGATAAGCCGACGAACACTCAGAGTATTCAG
+AACATCAAATATGTTCAAAACTGTGGAGACTTCCACAATACCTTAAAACATCCGACAAAG
+GGAGCCTTCCACCTTTAAGCCGAGCCATCTTGTCCCCGATGGATCCTTCATAAAACTTCA
+TCGCTATGCAAAGCTGAAAATCCATGAAACAAAAATTAAGCCACAACGCCATCTTTCATT
+CACAGGTGACCCAACAGCAAGGCTTTGCCAGACAAAAACATACCCTCCCATTCTGCGTTG
+AGATGCCATGTAGGAAGCAGACATTGCCCAGGCCCTGGCATTTGCCGAACACCTCGTCGA
+ACCTCGCCGAGAACACCTGCAGCTGGTCGTCCCTGACCGGGTGCATCATCTTCACGGCG
+>chr7B
+GTGCACTTCTTGCTGCTGAACTTTCTGAGGATCGGCACCCTGATCGGAGACGCTGGCGAC
+CTTTCGACTCCTTGGCCTTGTGATGCTCTTCCCGACGAACACACCTAGCTTCATAGCAGT
+AAAGAAACCTATGGCGATGAACAGAGGTCTTACCGCCCAATGGAAGTCCTCGAGGTGCTC
+ATACTTCTTCACAACCCCCTCGCACTTGTCGAAGCTCACCACCTCCACCTCAGAAGGGTC
+GGCCAAGCAGCTGCACACTTCGCCAAGGCTCAACTTGCCAGGGAAGGTCACAACAAGGCA
+TCCATTCGAGAGTATCTGTGAAATACGGCCTGTGGCAAACACCCCGCCTCTCTTTCGCTG
+CCATTCGAACCGCGGGCTTGAAGTGTTGGTTCTCAGCCTCACAAATTGTCCCACACAGTA
+GGCTTCGGCCATTTGCAGATCTGAATATTCCCCCTTCCAGAGGGTGTCCATTCCTATCAA
+ACCAACATACACGGTGCCATTGCGGTCGATGCTATGAAGAATTCCGACCTCAGACCGCTT
+CTTGTCTTCCTCCCTGAGCCTTACCCAGTATCCGGCAGCGAAACCATAGGTCACCCTCTC
+CACTGTCGAGGAACGGACCTTCAAAGGGTCATGTATTGCATGGACTCGTACAAGAATGTT
+GCTATCACGTTCTCCATCCTCCATGCCAACTATGGTCCCATCAGGGATTTCCATTGTTTC
+AGGAGTACAAGAGTTTTTAACCTTTCTCGAGCGGACCTTGTCCCCAACTTGCAGCTTATC
+CTTGAAGTGTGACCAGTTAGTGTGACTTGGTGCTACTGCCCTTGGGTTTTCAGAACTGTC
+CCAGCCATTGTTGTCATAATCCACATCTTTAGCACTGAAGAAAGGAAAAAAAAACAAATT
+TAGGGAAGTAACATGGTAAAATCACCCATCCAATGGCAGTTTAACCAAATAGTGCAAGTT
+GATAAGGCAGAAGTAGAAAGAGAGTTTTAGCATGTTACCTTTCAAATGCTTGTAAGATAT
+CTGACATCAAGGGGCGATCCCGAAAGTCATACTCGAAGCAGCTAGGAAGGACATTCTCAA
+CCTCTGCAGGTAAGTTGTACGGGAATATCGGTTTCTCTTTCTTCAGGACAACCAACTGAT
+AAATCTCGTCTGGTGATTTGCCACGCCAAGGCTGAACGCCAGTGAACATCTCAAGAATGC
+TGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTGGACCTCTGATGTTTGGTTGCC
+ACTGCTCTGGGGCCATGTAATTTGGAGTTCCAAGTCTTTGGATAAGCTCTGGGTTTGGCA
+GCGACAGTCCAAACAGCAAGGATGGAATCCCAAAATCCCCCAGCACAGCATGGTCATGGT
+CATCAAGGAGAAAATTGCAAGGTTTGAGATTAAGAACAAATATTCCCCTGGAGTGTAGGT
+CTAGCACACCACGCGCCAAATCGGCGCCGTATCTGCAAATTACAGGAAATAATAAAAATA
+TGTACCACTCAAGAAAACATCCTCTAAACAGAGCATCATAAGCATTCTCAAAAGTCAACC
+AGGATAATGTGCCTGCACTAAGGTGATGAAGGATATCTGCCAGTTAATCAACCAACACGT
+TCACTGGTAGAAAGTTGGAAACTGCATGCTTAGGTGACAATTCATCTAAAAAAACTGTAT
+ATTTGCCTCTGGTAAACTGTATTCTTAAGATAAGCCGACAAACATTCAGTATTCAGAACA
+TCAATATGTACAGAACTGTGGAGACTTCCACCATACCTTAAAACATCTGACAAAGGGAGC
+CTTCCACCTTTAAGCCGAGCCATCTTGTCCCCGACGGATCCTTCGTAAAACTTCATCGCT
+ATGCAAAGCTGAAAATCCATGAAACAAAAATTAAGCCACAGCACCATCTTTCATTCACAG
+GTGACCCAACAGCAAGGCTATGCCAGACAGAGAACATACCCTCCCATTCTGCGTCGAGAT
+GCCATGTAGGAAGCAGACATTGCCCAGGCCCTGGCACTTGCCGAACACCTCGTCGAACCT
+CGCCGAGAACACCTGCAGCTGGTCGTCCCTGACCGGGTGCAGCATCTTCACAGCGACCTC
+G
+>chr7D
+GTTGTGCACTTCTTGCTGCTGAACTTTCTGAGGATCGGCACCCTGATCAGAGACGCTGGC
+GACCTTTCGACTCCTTGGCCTTGTGATGCTCTTCCCAACAAAGACACCTAGCTTCATAGC
+AGTAAAGAAACCTATGGCAATGAACAGAGGCCTCACCGCCCAATGGAAGTCCTCGAGGTG
+CTCATACTTCTTCACAACGCCCTCGCACTTGTCGAAGCTCACCACCTCCACCTCTGAAGG
+GTCGGCCAAGCAGCTGCACACTTCGCCAAGGCTGAATTTGCCAGGGAAGGTCACAGCAAG
+GCATCCATTCGAGAGTATCTGTGAAATACGGCCTATGGCGAACACTCCGCCTCTCTTTCG
+CGGCCATTCAAACCGGGGGCTTGAAGTGTTAGTTCTGAGCCTCACAAATTGTCCCATGCA
+GTAGGCTTCGGCCATTTGCAGATCTGAATATTCCCCCTTCCACAGGGTGTCCATTCCTAT
+CAAACCAACATACACGGTGCCATTACGGTCAATGCTATGAAGAATTCCGACCTGAGACCG
+CTTCTTGTCTTCCTCCCTAAGCCTTACCCAGTCTCCGGCAGCGAAACCATAGGTCACCCT
+CTCCACTGCTGAGGAACGGACCTTCAGAGGGTCATGTATTCCATGGACTCGTACAAGAAT
+GTAGCTATCGCGTTCTCCATCCTCCATGCCAACTATGGTTCCATCAGGGATTTCCATTGT
+TTCAGGAGTACAAGAGTTTTTAACCTTTCTCGAGCGGACCTTGTCACCAACTTGCAGCTT
+ATCCTTGAAGTGTGACCAATTAGTGTGACTTGGCACTACTGCCCTTGGGTTTTCAGAACT
+ATCCCAGCCATTGTTGTCATAATCCACATCTTTAGCACTGAAGAAATGAAAAAAGAAAAC
+AAATTTAGGGAAGAACCATAGTAAATCACCCATCCAATGGCAGTTTAACCAAATACTGCA
+AGTTGATAAGGTAGAAGAAGAGAGTTTTAGCATGTTACCTTTCAAATGCTTGTAAGATAT
+CTGACATCAAGGGGCGATCCCGAAAGTCGTACTCAAAGCAGCTAGAAAGGACATTCTCAA
+CCTCTGCAGGTAAATTGTACGGGAATATCGGTTTCTCTTTCTTCAGGACAACCAACTGAT
+AAATCTCGTCTGGTGATTTGCCACGCCAAGGCTGAACGCCACTGAACATCTCAAGAATGC
+TGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTGGACCTCTGATGTTTGGTTGCC
+ATTGCTCTGGGGCCATGTAATTTGGAGTCCCAAGTCTTTGGATAAGCTCTGGGTTTGGCA
+GCGACAGCCCAAACAGCAAGGATGGAATCCCAAAATCCCCCAACACAGCATGGTCATGAT
+CATCAAGGAGAAAATTACAAGGCTTGAGATTAAGAACAAATATTCCCCTGGAGTGTAGGT
+CCAGCACACCACGTGCCAAATCAGCGCCATATCTGCAAGTTATAAGAATTCATAAAAATA
+TGTACTACTCCAAACAGAGCATCATAAGCATTCTCAAAAGTCAACAGGATCATTTGCCTG
+CACTAAGGTGATAAACTAGATCTGCCAGTTAATCAATCAACACGTTCACTGGTAGAAAGT
+TGGAAACTGCATGCTTAGGTGACACTTCATCTAAAAAACTGTATATTTGCCTCTGTGGTA
+AACTGTATTCTTAAGATAAGCCGACGAACATTCAGTATTCAGGACATCAAATATGTTCAA
+AACTGTGGAGACTTCCACCATACCTTAAAACATCTGACAAAGGGAGCCTTCCACCTTTAA
+GCCGAGCCATCTTGTCCCCGACGGATCCTTCATAGAACTTCATCACTATGCAAAGCTGAA
+AATCCATGAAACAAAAATTAAGCCACAACGCCATCTTTCATTCACAGGCGACCCAACAGC
+AAGGCTATGCCAGACAAAAACATACCCTCCCATTCTGCGTCGAGATGCCATGTAGGAAGC
+AGACATTGCCCAGGCCCTGGCATTTGCCAAACACCTCGTCGAACCTCGCCGAGAACACCT
+GCAGCTGGTCGTCCCTGACCGGGTGCAGCATCTTCACGGCGACCTCGTGGTACCGGTCAT
+A

data/test/data/7B_amplicon_test_reference.fa.fai

@@ -0,0 +1,3 @@
+chr7A	2099	7	60	61
+chr7B	2101	2148	60	61
+chr7D	2101	4292	60	61

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-polyploid-tools
 version: !ruby/object:Gem::Version
-  version: 0.10.1
+  version: 1.2.0
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-03-28 00:00:00.000000000 Z
+date: 2020-10-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -120,7 +120,6 @@ executables:
 - filter_exonerate_by_identity.rb
 - find_best_blat_hit.rb
 - find_best_exonerate.rb
-- find_homoeologue_variations.rb
 - get_longest_hsp_blastx_triads.rb
 - hexaploid_primers.rb
 - homokaryot_primers.rb
@@ -132,6 +131,7 @@ executables:
 - mask_triads.rb
 - polymarker.rb
 - polymarker_capillary.rb
+- polymarker_deletions.rb
 - snp_position_to_polymarker.rb
 - snps_between_bams.rb
 - tag_stats.rb
@@ -139,14 +139,13 @@ executables:
 - vcfToPolyMarker.rb
 extensions: []
 extra_rdoc_files:
-- README
 - README.md
 files:
 - ".travis.yml"
 - Gemfile
-- README
 - README.md
 - Rakefile
+- SECURITY.md
 - VERSION
 - bin/bfr.rb
 - bin/blast_triads.rb
@@ -156,7 +155,6 @@ files:
 - bin/filter_exonerate_by_identity.rb
 - bin/find_best_blat_hit.rb
 - bin/find_best_exonerate.rb
-- bin/find_homoeologue_variations.rb
 - bin/get_longest_hsp_blastx_triads.rb
 - bin/hexaploid_primers.rb
 - bin/homokaryot_primers.rb
@@ -168,6 +166,7 @@ files:
 - bin/mask_triads.rb
 - bin/polymarker.rb
 - bin/polymarker_capillary.rb
+- bin/polymarker_deletions.rb
 - bin/snp_position_to_polymarker.rb
 - bin/snps_between_bams.rb
 - bin/tag_stats.rb
@@ -224,6 +223,17 @@ files:
 - lib/bio/db/exonerate.rb
 - lib/bio/db/primer3.rb
 - lib/bioruby-polyploid-tools.rb
+- test/data/7B_amplicon_test.fa
+- test/data/7B_amplicon_test.fa.fai
+- test/data/7B_amplicon_test_reference.fa
+- test/data/7B_amplicon_test_reference.fa.fai
+- test/data/7B_amplicon_test_reference.fa.ndb
+- test/data/7B_amplicon_test_reference.fa.nhr
+- test/data/7B_amplicon_test_reference.fa.nin
+- test/data/7B_amplicon_test_reference.fa.not
+- test/data/7B_amplicon_test_reference.fa.nsq
+- test/data/7B_amplicon_test_reference.fa.ntf
+- test/data/7B_amplicon_test_reference.fa.nto
 - test/data/BS00068396_51.fa
 - test/data/BS00068396_51_blast.tab
 - test/data/BS00068396_51_contigs.aln
@@ -323,8 +333,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.7
+rubygems_version: 3.1.2
 signing_key: 
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology

data/README

@@ -1,21 +0,0 @@
-= bio-polyploid-tools
-
-== Introduction
-This tools are designed to deal with polyploid wheat. The first tool is to design KASPer primers, making them as specific as possible. 
-
-
-== Installation
-'gem install bio-polyploid-tools'
-
-
-== Notes
-
-* If the SNP is in a gap in the alignmetn to the chromosomes, it is ignored. 
-
-BUG: Sometimes the primers are reversed (the first comes second)
-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 file to tweak the alignments. 
-
-