bio-polyploid-tools 1.1.2 → 1.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 4611c4e04774806f9f8f265eccc992f8221a8b3cb61ae50f4323cbd68c538a33
-  data.tar.gz: f180e87cc04f0ee67cf68dffda01c1a0be6686ab02cc1cbd536d4aad4ae4e298
+  metadata.gz: 9191156e91a48ec245e181a1541d4b636b01c848b03f2b7db5f7729ddfc05421
+  data.tar.gz: '0449ab8d09b268538d3604f20b555d94be53cac35ff8d591a29c792f98df3def'
 SHA512:
-  metadata.gz: 441115704f6e6ed75b6bb40361393a5281cb256d4a9731abe1bb1056cc28d7c825232e198f4fa14c0cf4f5b4ce6b66872bfd34e01942db856a41c6945daa149a
-  data.tar.gz: 7b4a10b0268583e2459cc93d437393a7a89caa6cd201c50833203039e4f75eb204b512242c315569a09fd3be9f28db12e09db8a0550b4fbb014a15fa0bddc94c
+  metadata.gz: 1c23625ac5c1cdfc3b4d34c3a8f416f680bc42a274b983ee64938bc3ba3bd7b685ad3e9cd9c04521a8f1baf8f91b0efae27a4c5d3034a4a18b141ec10209a7ee
+  data.tar.gz: cebf5a46d0a3cce9b63ccd71451f2f2a0d4903ae3e0954d34ba48955cc148b3d232bc5612ed8a528ade86cbfbb6e216c9788126c53b7f8cfa2157785ee00533b

data/VERSION

@@ -1 +1 @@
-1.1.2
+1.2.0

data/bin/polymarker_capillary.rb

@@ -146,7 +146,7 @@ module Bio::PolyploidTools
       snp
     end
 
-    def primer_3_all_strings(target_chromosome, parental) 
+    def primer_3_all_strings(target_chromosome, parental, max_specific_primers: 20, flanking_size:500) 
       #puts target_chromosome 
       #puts parental
       #puts aligned_sequences.to_fasta
@@ -155,8 +155,11 @@ module Bio::PolyploidTools
 
       seq_original = String.new(pr.sequence)
       #puts seq_original.size.to_s << "-" << primer_3_min_seq_length.to_s
+      #puts "___"
+      #puts pr.inspect
       return primer_3_propertes if seq_original.size < primer_3_min_seq_length
-      return primer_3_propertes unless pr.snp_pos == 500
+      #puts "((("
+      return primer_3_propertes unless pr.snp_pos == flanking_size
       #puts "Sequence origina: #{ self.original}" 
       #puts pr.to_fasta
       #puts "Postion: #{pr.snp_pos}"
@@ -274,9 +277,9 @@ file.close
 exo_f = File.open(exonerate_file, "w")
 target=reference
 
-fasta_file = Bio::DB::Fasta::FastaFile.new({:fasta=>target})
+fasta_file = Bio::DB::Fasta::FastaFile.new(fasta: target)
 fasta_file.load_fai_entries
-min_identity = 95
+min_identity = 90
 found_contigs = Set.new
 
 
@@ -361,7 +364,7 @@ class Bio::DB::Primer3::Primer3Record
 end
 
 printed_counts = Hash.new(0)
-Bio::DB::Primer3::Primer3Record.parse_file(primer_3_output) do | primer3record |
+Bio::DB::Primer3::Primer3Record.parse_file(primer_3_output ) do | primer3record |
   #puts primer3record.inspect
   next if primer3record.primer_left_num_returned.to_i == 0
   

data/bio-polyploid-tools.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: bio-polyploid-tools 1.1.2 ruby lib
+# stub: bio-polyploid-tools 1.2.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "bio-polyploid-tools".freeze
-  s.version = "1.1.2"
+  s.version = "1.2.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Ricardo H.  Ramirez-Gonzalez".freeze]
-  s.date = "2020-03-18"
+  s.date = "2020-10-28"
   s.description = "Repository of tools developed at Crop Genetics in JIC to work with polyploid wheat".freeze
   s.email = "ricardo.ramirez-gonzalez@jic.ac.uk".freeze
   s.executables = ["bfr.rb".freeze, "blast_triads.rb".freeze, "blast_triads_promoters.rb".freeze, "count_variations.rb".freeze, "filter_blat_by_target_coverage.rb".freeze, "filter_exonerate_by_identity.rb".freeze, "find_best_blat_hit.rb".freeze, "find_best_exonerate.rb".freeze, "get_longest_hsp_blastx_triads.rb".freeze, "hexaploid_primers.rb".freeze, "homokaryot_primers.rb".freeze, "mafft_triads.rb".freeze, "mafft_triads_promoters.rb".freeze, "map_markers_to_contigs.rb".freeze, "marker_to_vcf.rb".freeze, "markers_in_region.rb".freeze, "mask_triads.rb".freeze, "polymarker.rb".freeze, "polymarker_capillary.rb".freeze, "polymarker_deletions.rb".freeze, "snp_position_to_polymarker.rb".freeze, "snps_between_bams.rb".freeze, "tag_stats.rb".freeze, "vcfLineToTable.rb".freeze, "vcfToPolyMarker.rb".freeze]
@@ -101,6 +101,17 @@ Gem::Specification.new do |s|
     "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",
@@ -184,29 +195,21 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/tgac/bioruby-polyploid-tools".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "3.0.8".freeze
+  s.rubygems_version = "3.1.2".freeze
   s.summary = "Tool to work with polyploids, NGS and molecular biology".freeze
 
   if s.respond_to? :specification_version then
     s.specification_version = 4
+  end
 
-    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<bio>.freeze, [">= 1.5.1"])
-      s.add_runtime_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])
-      s.add_runtime_dependency(%q<descriptive_statistics>.freeze, [">= 0"])
-      s.add_runtime_dependency(%q<systemu>.freeze, [">= 2.5.2"])
-      s.add_development_dependency(%q<shoulda>.freeze, [">= 2.10"])
-      s.add_development_dependency(%q<test-unit>.freeze, [">= 0"])
-      s.add_development_dependency(%q<juwelier>.freeze, [">= 0"])
-    else
-      s.add_dependency(%q<bio>.freeze, [">= 1.5.1"])
-      s.add_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])
-      s.add_dependency(%q<descriptive_statistics>.freeze, [">= 0"])
-      s.add_dependency(%q<systemu>.freeze, [">= 2.5.2"])
-      s.add_dependency(%q<shoulda>.freeze, [">= 2.10"])
-      s.add_dependency(%q<test-unit>.freeze, [">= 0"])
-      s.add_dependency(%q<juwelier>.freeze, [">= 0"])
-    end
+  if s.respond_to? :add_runtime_dependency then
+    s.add_runtime_dependency(%q<bio>.freeze, [">= 1.5.1"])
+    s.add_runtime_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])
+    s.add_runtime_dependency(%q<descriptive_statistics>.freeze, [">= 0"])
+    s.add_runtime_dependency(%q<systemu>.freeze, [">= 2.5.2"])
+    s.add_development_dependency(%q<shoulda>.freeze, [">= 2.10"])
+    s.add_development_dependency(%q<test-unit>.freeze, [">= 0"])
+    s.add_development_dependency(%q<juwelier>.freeze, [">= 0"])
   else
     s.add_dependency(%q<bio>.freeze, [">= 1.5.1"])
     s.add_dependency(%q<bio-samtools>.freeze, [">= 2.6.2"])

data/lib/bio/PolyploidTools/ExonContainer.rb

@@ -18,7 +18,7 @@ module Bio::PolyploidTools
     end
 
     def gene_models(path)
-      @gene_models_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
+      @gene_models_db = Bio::DB::Fasta::FastaFile.new(fasta: path)
       @gene_models_db.index
       @gene_models_path = path
     end
@@ -48,7 +48,7 @@ module Bio::PolyploidTools
 
     #Sets the reference file for the gene models
     def chromosomes(path)
-      @chromosomes_db = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
+      @chromosomes_db = Bio::DB::Fasta::FastaFile.new(fasta: path)
       @chromosomes_path = path
     end
 
@@ -72,7 +72,7 @@ module Bio::PolyploidTools
       name = opts[:name]
       path = opts[:reference_path]
       path = opts[:alig_path]
-      chromosomes[name] = Bio::DB::Fasta::FastaFile.new({:fasta=>path})
+      chromosomes[name] = Bio::DB::Fasta::FastaFile.new(fasta: path)
     end
     
     def add_snp(snp)
@@ -109,7 +109,7 @@ module Bio::PolyploidTools
       ret_str = ""
       @parents.each  do |name, bam|
         ret_str << ">#{gene_region.id}_SNP-#{snp.position}_#{name} Overlapping_exons:#{gene_region.to_s} localSNPpo:#{local_pos_in_gene+1}\n" 
-        to_print =  bam.consensus_with_ambiguities({:region=>gene_region}).to_s
+        to_print =  bam.consensus_with_ambiguities(region: gene_region).to_s
         to_print[local_pos_in_gene] = to_print[local_pos_in_gene].upcase
         ret_str << to_print << "\n"
       end

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: 1.1.2
+  version: 1.2.0
 platform: ruby
 authors:
 - Ricardo H.  Ramirez-Gonzalez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-03-18 00:00:00.000000000 Z
+date: 2020-10-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -223,6 +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
@@ -322,7 +333,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.8
+rubygems_version: 3.1.2
 signing_key: 
 specification_version: 4
 summary: Tool to work with polyploids, NGS and molecular biology