bio-polymarker 1.3.2

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Files changed (177) hide show
  1. checksums.yaml +7 -0
  2. data/.travis.yml +24 -0
  3. data/Gemfile +23 -0
  4. data/README.md +205 -0
  5. data/Rakefile +61 -0
  6. data/SECURITY.md +16 -0
  7. data/VERSION +1 -0
  8. data/bin/bfr.rb +128 -0
  9. data/bin/blast_triads.rb +166 -0
  10. data/bin/blast_triads_promoters.rb +192 -0
  11. data/bin/count_variations.rb +36 -0
  12. data/bin/filter_blat_by_target_coverage.rb +69 -0
  13. data/bin/filter_exonerate_by_identity.rb +38 -0
  14. data/bin/find_best_blat_hit.rb +33 -0
  15. data/bin/find_best_exonerate.rb +17 -0
  16. data/bin/get_longest_hsp_blastx_triads.rb +66 -0
  17. data/bin/hexaploid_primers.rb +168 -0
  18. data/bin/homokaryot_primers.rb +183 -0
  19. data/bin/mafft_triads.rb +120 -0
  20. data/bin/mafft_triads_promoters.rb +403 -0
  21. data/bin/map_markers_to_contigs.rb +66 -0
  22. data/bin/marker_to_vcf.rb +241 -0
  23. data/bin/markers_in_region.rb +42 -0
  24. data/bin/mask_triads.rb +169 -0
  25. data/bin/polymarker.rb +410 -0
  26. data/bin/polymarker_capillary.rb +443 -0
  27. data/bin/polymarker_deletions.rb +350 -0
  28. data/bin/snp_position_to_polymarker.rb +101 -0
  29. data/bin/snps_between_bams.rb +107 -0
  30. data/bin/tag_stats.rb +75 -0
  31. data/bin/vcfLineToTable.rb +56 -0
  32. data/bin/vcfToPolyMarker.rb +82 -0
  33. data/bio-polymarker.gemspec +227 -0
  34. data/conf/defaults.rb +1 -0
  35. data/conf/primer3_config/dangle.dh +128 -0
  36. data/conf/primer3_config/dangle.ds +128 -0
  37. data/conf/primer3_config/interpretations/dangle_i.dh +131 -0
  38. data/conf/primer3_config/interpretations/dangle_i.ds +131 -0
  39. data/conf/primer3_config/interpretations/loops_i.dh +34 -0
  40. data/conf/primer3_config/interpretations/loops_i.ds +31 -0
  41. data/conf/primer3_config/interpretations/stack_i.dh +257 -0
  42. data/conf/primer3_config/interpretations/stack_i.ds +256 -0
  43. data/conf/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
  44. data/conf/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
  45. data/conf/primer3_config/interpretations/tetraloop_i.dh +79 -0
  46. data/conf/primer3_config/interpretations/tetraloop_i.ds +81 -0
  47. data/conf/primer3_config/interpretations/triloop_i.dh +21 -0
  48. data/conf/primer3_config/interpretations/triloop_i.ds +18 -0
  49. data/conf/primer3_config/interpretations/tstack2_i.dh +256 -0
  50. data/conf/primer3_config/interpretations/tstack2_i.ds +256 -0
  51. data/conf/primer3_config/interpretations/tstack_i.dh +256 -0
  52. data/conf/primer3_config/interpretations/tstack_i.ds +256 -0
  53. data/conf/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
  54. data/conf/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
  55. data/conf/primer3_config/loops.dh +30 -0
  56. data/conf/primer3_config/loops.ds +30 -0
  57. data/conf/primer3_config/stack.dh +256 -0
  58. data/conf/primer3_config/stack.ds +256 -0
  59. data/conf/primer3_config/stackmm.dh +256 -0
  60. data/conf/primer3_config/stackmm.ds +256 -0
  61. data/conf/primer3_config/tetraloop.dh +77 -0
  62. data/conf/primer3_config/tetraloop.ds +77 -0
  63. data/conf/primer3_config/triloop.dh +16 -0
  64. data/conf/primer3_config/triloop.ds +16 -0
  65. data/conf/primer3_config/tstack.dh +256 -0
  66. data/conf/primer3_config/tstack2.dh +256 -0
  67. data/conf/primer3_config/tstack2.ds +256 -0
  68. data/conf/primer3_config/tstack_tm_inf.ds +256 -0
  69. data/lib/bio/BFRTools.rb +465 -0
  70. data/lib/bio/BIOExtensions.rb +153 -0
  71. data/lib/bio/PolyploidTools/ChromosomeArm.rb +63 -0
  72. data/lib/bio/PolyploidTools/ExonContainer.rb +245 -0
  73. data/lib/bio/PolyploidTools/Marker.rb +175 -0
  74. data/lib/bio/PolyploidTools/Mask.rb +116 -0
  75. data/lib/bio/PolyploidTools/NoSNPSequence.rb +292 -0
  76. data/lib/bio/PolyploidTools/PrimerRegion.rb +30 -0
  77. data/lib/bio/PolyploidTools/SNP.rb +804 -0
  78. data/lib/bio/PolyploidTools/SNPMutant.rb +86 -0
  79. data/lib/bio/PolyploidTools/SNPSequence.rb +55 -0
  80. data/lib/bio/db/blast.rb +114 -0
  81. data/lib/bio/db/exonerate.rb +333 -0
  82. data/lib/bio/db/primer3.rb +820 -0
  83. data/lib/bio-polymarker.rb +28 -0
  84. data/test/data/7B_amplicon_test.fa +12 -0
  85. data/test/data/7B_amplicon_test.fa.fai +1 -0
  86. data/test/data/7B_amplicon_test_reference.fa +110 -0
  87. data/test/data/7B_amplicon_test_reference.fa.fai +3 -0
  88. data/test/data/7B_marker_test.txt +1 -0
  89. data/test/data/BS00068396_51.fa +2 -0
  90. data/test/data/BS00068396_51_blast.tab +4 -0
  91. data/test/data/BS00068396_51_contigs.aln +1412 -0
  92. data/test/data/BS00068396_51_contigs.dnd +7 -0
  93. data/test/data/BS00068396_51_contigs.fa +8 -0
  94. data/test/data/BS00068396_51_contigs.fa.fai +4 -0
  95. data/test/data/BS00068396_51_contigs.fa.nhr +0 -0
  96. data/test/data/BS00068396_51_contigs.fa.nin +0 -0
  97. data/test/data/BS00068396_51_contigs.fa.nsq +0 -0
  98. data/test/data/BS00068396_51_contigs.nhr +0 -0
  99. data/test/data/BS00068396_51_contigs.nin +0 -0
  100. data/test/data/BS00068396_51_contigs.nsq +0 -0
  101. data/test/data/BS00068396_51_exonerate.tab +6 -0
  102. data/test/data/BS00068396_51_for_polymarker.txt +1 -0
  103. data/test/data/BS00068396_51_genes.txt +14 -0
  104. data/test/data/IWGSC_CSS_1AL_scaff_1455974.fa +112 -0
  105. data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa +2304 -0
  106. data/test/data/IWGSC_CSS_1AL_scaff_1455974_aln_contigs.fa.fai +11 -0
  107. data/test/data/LIB1716.bam +0 -0
  108. data/test/data/LIB1716.bam.bai +0 -0
  109. data/test/data/LIB1719.bam +0 -0
  110. data/test/data/LIB1719.bam.bai +0 -0
  111. data/test/data/LIB1721.bam +0 -0
  112. data/test/data/LIB1721.bam.bai +0 -0
  113. data/test/data/LIB1722.bam +0 -0
  114. data/test/data/LIB1722.bam.bai +0 -0
  115. data/test/data/PST130_7067.csv +1 -0
  116. data/test/data/PST130_7067.fa +2 -0
  117. data/test/data/PST130_7067.fa.fai +1 -0
  118. data/test/data/PST130_7067.fa.ndb +0 -0
  119. data/test/data/PST130_7067.fa.nhr +0 -0
  120. data/test/data/PST130_7067.fa.nin +0 -0
  121. data/test/data/PST130_7067.fa.not +0 -0
  122. data/test/data/PST130_7067.fa.nsq +0 -0
  123. data/test/data/PST130_7067.fa.ntf +0 -0
  124. data/test/data/PST130_7067.fa.nto +0 -0
  125. data/test/data/PST130_reverse_primer.csv +1 -0
  126. data/test/data/S22380157.fa +16 -0
  127. data/test/data/S22380157.fa.fai +1 -0
  128. data/test/data/S22380157.vcf +67 -0
  129. data/test/data/S58861868/LIB1716.bam +0 -0
  130. data/test/data/S58861868/LIB1716.sam +651 -0
  131. data/test/data/S58861868/LIB1719.bam +0 -0
  132. data/test/data/S58861868/LIB1719.sam +805 -0
  133. data/test/data/S58861868/LIB1721.bam +0 -0
  134. data/test/data/S58861868/LIB1721.sam +1790 -0
  135. data/test/data/S58861868/LIB1722.bam +0 -0
  136. data/test/data/S58861868/LIB1722.sam +1271 -0
  137. data/test/data/S58861868/S58861868.fa +16 -0
  138. data/test/data/S58861868/S58861868.fa.fai +1 -0
  139. data/test/data/S58861868/S58861868.vcf +76 -0
  140. data/test/data/S58861868/header.txt +9 -0
  141. data/test/data/S58861868/merged.bam +0 -0
  142. data/test/data/S58861868/merged_reheader.bam +0 -0
  143. data/test/data/S58861868/merged_reheader.bam.bai +0 -0
  144. data/test/data/Test3Aspecific.csv +2 -0
  145. data/test/data/Test3Aspecific_contigs.fa +6 -0
  146. data/test/data/bfr_out_test.csv +5 -0
  147. data/test/data/chr1A_C1145499T/chr1A_C1145499T.csv +1 -0
  148. data/test/data/chr1A_G540414846C/chr1A_G540414846C.csv +1 -0
  149. data/test/data/chr1A_G540414846C/chr1A_G540414846C.fa +2 -0
  150. data/test/data/chr1A_T517634750C/chr1A_T517634750C.csv +1 -0
  151. data/test/data/chr2D_C112180134A/chr2D_C112180134A.csv +1 -0
  152. data/test/data/chr4D_C14473543T/chr4D_C14473543T.csv +1 -0
  153. data/test/data/chr4D_C14473543T/chr4D_C14473543T.fa +2 -0
  154. data/test/data/headerMergeed.txt +9 -0
  155. data/test/data/headerS2238015 +1 -0
  156. data/test/data/mergedLibs.bam +0 -0
  157. data/test/data/mergedLibsReheader.bam +0 -0
  158. data/test/data/mergedLibsSorted.bam +0 -0
  159. data/test/data/mergedLibsSorted.bam.bai +0 -0
  160. data/test/data/patological_cases5D.csv +1 -0
  161. data/test/data/primer_3_input_header_test +5 -0
  162. data/test/data/short_primer_design_test.csv +10 -0
  163. data/test/data/some_tests/some_tests.csv +201 -0
  164. data/test/data/test_from_mutant.csv +3 -0
  165. data/test/data/test_iselect.csv +196 -0
  166. data/test/data/test_iselect_reference.fa +1868 -0
  167. data/test/data/test_iselect_reference.fa.fai +934 -0
  168. data/test/data/test_primer3_error.csv +4 -0
  169. data/test/data/test_primer3_error_contigs.fa +10 -0
  170. data/test/test_bfr.rb +135 -0
  171. data/test/test_blast.rb +47 -0
  172. data/test/test_exon_container.rb +17 -0
  173. data/test/test_exonearate.rb +48 -0
  174. data/test/test_integration.rb +76 -0
  175. data/test/test_snp_parsing.rb +121 -0
  176. data/test/test_wrong_selection.sh +5 -0
  177. metadata +356 -0
data/lib/bio-polymarker.rb ADDED
@@ -0,0 +1,28 @@
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+ require 'bio'
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+ require 'bio-samtools-wrapper'
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+ require "set"
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+ require 'systemu'
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+ require 'json'
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+
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+ #require 'bio/db/exonerate'
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+ #require 'bio/db/primer3'
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+ #require 'bio/db/fasta'
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+
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+ #puts "Loading all... #{Dir[File.dirname(__FILE__) + "/bio/*/*.rb"]}"
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+ module Bio::PolyploidTools
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+
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+ end
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+ Dir[File.dirname(__FILE__) + "/bio/*.rb"].each {|file|
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+ # puts file
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+ require_relative file }
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+ Dir[File.dirname(__FILE__) + "/bio/*/*.rb"].each do |file|
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+ # $stderr.puts "loading #{file}"
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+ require_relative file
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+ end
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+
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+ require_relative File.dirname(__FILE__) + "/../conf/defaults.rb"
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+
25
+
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+ #require_relative "bio/BFRTools.rb"
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+ #require_relative "bio/PolyploidTools/ExonContainer.rb"
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+
data/test/data/7B_amplicon_test.fa ADDED
@@ -0,0 +1,12 @@
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+ >chr7B:1000-1600
2
+ TTTCAAATGCTTGTAAGATATCTGACATCAAGGGGCGATCCCGAAAGTCATACTCGAAGC
3
+ AGCTAGGAAGGACATTCTCAACCTCTGCAGGTAAGTTGTACGGGAATATCGGTTTCTCTT
4
+ TCTTCAGGACAACCAACTGATAAATCTCGTCTGGTGATTTGCCACGCCAAGGCTGAACGC
5
+ CAGTGAACATCTCAAGAATGCTGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTG
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+ GACCTCTGATGTTTGGTTGCCACTGCTCTGGGGCCATGTAATTTGGAGTTCCAAGTCTTT
7
+ GGATAAGCTCTGGGTTTGGCAGCGACAGTCCAAACAGCAAGGATGGAATCCCAAAATCCC
8
+ CCAGCACAGCATGGTCATGGTCATCAAGGAGAAAATTGCAAGGTTTGAGATTAAGAACAA
9
+ ATATTCCCCTGGAGTGTAGGTCTAGCACACCACGCGCCAAATCGGCGCCGTATCTGCAAA
10
+ TTACAGGAAATAATAAAAATATGTACCACTCAAGAAAACATCCTCTAAACAGAGCATCAT
11
+ AAGCATTCTCAAAAGTCAACCAGGATAATGTGCCTGCACTAAGGTGATGAAGGATATCTG
12
+ C
data/test/data/7B_amplicon_test.fa.fai ADDED
@@ -0,0 +1 @@
1
+ chr7B:1000-1600 601 17 60 61
data/test/data/7B_amplicon_test_reference.fa ADDED
@@ -0,0 +1,110 @@
1
+ >chr7A
2
+ CTTCCTGCTGCTGAACTTTCTGAGGATCACCGCCCTGATCGGAGACGCTGGCGACCTTTC
3
+ GACTCCTTGGCCTTGTGATGCTCTTGCCGACAAAGATACCTAGCTTCATAGCAGTAAAGA
4
+ AACCTATGGCGATGAACAGAGGCCTCACCACCCAATGGAAGTCCTCGAGGTGCTCATACT
5
+ TCTTCACAACCCCATCGCACTTGTCGAAGCTCACCACCTCCACCTCTGAAGGGTCGGCCA
6
+ AGCAGCTGCACACTTCGCCAAGGCTGAATTTGCCAGGGAAGGTCACAACAAGGCATCCAT
7
+ TCGAGAGTATCTGTGAAATACGGCCTGTGGCAAACACTCCGCCTCTCTTTCGCGGCCATT
8
+ CAAACCGGGGGCTTGATGTGTTAGTTCTCAGCCTCACAAATTGTCCCACGCAGTAGGCTT
9
+ CGGCCATTTGCAGATCTGAATATTCCCCCTTCCAGAGGGTGTCCATTCCTATTAAACCAA
10
+ CATACACGGTGCCATTACGGTCAATGCTATGAAGAATTCCGACCTGAGACCGCTTCTTGT
11
+ CTTCCTCCCTAAGCCTTACCCAGTCTCCGGCAGCGAAACCATAGGTCACCCTCTCCACTG
12
+ TCGAGGAATGGACCTTCAAAGGGTCATGTATTCCATGGACTCGTACAAGAATGTAGCTAT
13
+ CACGTTCTCCATCCTCCTCCATGCCAACTATGGTTCCATCAGGAATTTCCATTGTTTCAG
14
+ GAGTACAAGAGTTTTTAACCTTTCTCGAGCGGACCTTGTCACCAACTTGCAGCTTATCCT
15
+ TAAAGTGTGACCAATTAGTGTGACTTGGCACTACTGCCCTTGGGTTTTCAGAACTATCCC
16
+ AGCCATTGTTGTCATAATCCACATCTTTAGCACTGAAGAAATGAAAAAAGAAAACAAATT
17
+ TAGGAAAGAACTATGGTAAAATCACCCATCTGATGGCAGTTTAACCAAATACTGCAAGTT
18
+ GATAAGGCAGAAGTAGAAAGAGAGTTTTAGCATGTTACCTTTCAAATGCTTGCAAGATAT
19
+ CTGACATCAAGGGGCGATCCCGAAAGTCGTACTCAAAGCAGCTAGAAAGGACATTCTCAA
20
+ CCTCTGCAGGTAAGTTGTATGGGAATATCGGTTTCTCTTTCTTCAGGACAACCAACTGAT
21
+ AAATTTCATCTGGTGATTTGCCACGCCAAGGCTGAACGCCACTGAACATCTCAAGAATGC
22
+ TGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTGGACCTCTGATGTTTGGTTGCC
23
+ ATTGCTCTGGGGCCATGTAATTTGGAGTCCCAAGTCTTTGGATAAGCTCTGGGTTTGGCA
24
+ GAGAAAGTCCAAACAGCAAGGATGGAATCCCAAAATCCCCCAGCACAGCATGGTCATGGT
25
+ CATCAAGGAGAAAATTGCAAGGCTTGAGATTAAGAACAAATATTCCCCTGGAGTGTAGGT
26
+ CTAGCACACCACGCGCCAAATCGGCACCATATCTGCAAGTTATAAGAATTCATAAAAATA
27
+ TGTATTACTACTCAAGAAAATATCTTCTAAACAGAGCATCATAAGCATTCTCAAAAGTCA
28
+ ACAGGATAATGTGCCTGTACTAAGGTCATAAACTATATCTGCCAGTTAATCAATCAACAC
29
+ GTTCACTGGTAGAAAGTTGGAAACTGCATGCTTAGGTGACACTTCATCTAAAAAAAATGT
30
+ ATATTTGTCTCTGATAAATTGTATTCTTAAGATAAGCCGACGAACACTCAGAGTATTCAG
31
+ AACATCAAATATGTTCAAAACTGTGGAGACTTCCACAATACCTTAAAACATCCGACAAAG
32
+ GGAGCCTTCCACCTTTAAGCCGAGCCATCTTGTCCCCGATGGATCCTTCATAAAACTTCA
33
+ TCGCTATGCAAAGCTGAAAATCCATGAAACAAAAATTAAGCCACAACGCCATCTTTCATT
34
+ CACAGGTGACCCAACAGCAAGGCTTTGCCAGACAAAAACATACCCTCCCATTCTGCGTTG
35
+ AGATGCCATGTAGGAAGCAGACATTGCCCAGGCCCTGGCATTTGCCGAACACCTCGTCGA
36
+ ACCTCGCCGAGAACACCTGCAGCTGGTCGTCCCTGACCGGGTGCATCATCTTCACGGCG
37
+ >chr7B
38
+ GTGCACTTCTTGCTGCTGAACTTTCTGAGGATCGGCACCCTGATCGGAGACGCTGGCGAC
39
+ CTTTCGACTCCTTGGCCTTGTGATGCTCTTCCCGACGAACACACCTAGCTTCATAGCAGT
40
+ AAAGAAACCTATGGCGATGAACAGAGGTCTTACCGCCCAATGGAAGTCCTCGAGGTGCTC
41
+ ATACTTCTTCACAACCCCCTCGCACTTGTCGAAGCTCACCACCTCCACCTCAGAAGGGTC
42
+ GGCCAAGCAGCTGCACACTTCGCCAAGGCTCAACTTGCCAGGGAAGGTCACAACAAGGCA
43
+ TCCATTCGAGAGTATCTGTGAAATACGGCCTGTGGCAAACACCCCGCCTCTCTTTCGCTG
44
+ CCATTCGAACCGCGGGCTTGAAGTGTTGGTTCTCAGCCTCACAAATTGTCCCACACAGTA
45
+ GGCTTCGGCCATTTGCAGATCTGAATATTCCCCCTTCCAGAGGGTGTCCATTCCTATCAA
46
+ ACCAACATACACGGTGCCATTGCGGTCGATGCTATGAAGAATTCCGACCTCAGACCGCTT
47
+ CTTGTCTTCCTCCCTGAGCCTTACCCAGTATCCGGCAGCGAAACCATAGGTCACCCTCTC
48
+ CACTGTCGAGGAACGGACCTTCAAAGGGTCATGTATTGCATGGACTCGTACAAGAATGTT
49
+ GCTATCACGTTCTCCATCCTCCATGCCAACTATGGTCCCATCAGGGATTTCCATTGTTTC
50
+ AGGAGTACAAGAGTTTTTAACCTTTCTCGAGCGGACCTTGTCCCCAACTTGCAGCTTATC
51
+ CTTGAAGTGTGACCAGTTAGTGTGACTTGGTGCTACTGCCCTTGGGTTTTCAGAACTGTC
52
+ CCAGCCATTGTTGTCATAATCCACATCTTTAGCACTGAAGAAAGGAAAAAAAAACAAATT
53
+ TAGGGAAGTAACATGGTAAAATCACCCATCCAATGGCAGTTTAACCAAATAGTGCAAGTT
54
+ GATAAGGCAGAAGTAGAAAGAGAGTTTTAGCATGTTACCTTTCAAATGCTTGTAAGATAT
55
+ CTGACATCAAGGGGCGATCCCGAAAGTCATACTCGAAGCAGCTAGGAAGGACATTCTCAA
56
+ CCTCTGCAGGTAAGTTGTACGGGAATATCGGTTTCTCTTTCTTCAGGACAACCAACTGAT
57
+ AAATCTCGTCTGGTGATTTGCCACGCCAAGGCTGAACGCCAGTGAACATCTCAAGAATGC
58
+ TGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTGGACCTCTGATGTTTGGTTGCC
59
+ ACTGCTCTGGGGCCATGTAATTTGGAGTTCCAAGTCTTTGGATAAGCTCTGGGTTTGGCA
60
+ GCGACAGTCCAAACAGCAAGGATGGAATCCCAAAATCCCCCAGCACAGCATGGTCATGGT
61
+ CATCAAGGAGAAAATTGCAAGGTTTGAGATTAAGAACAAATATTCCCCTGGAGTGTAGGT
62
+ CTAGCACACCACGCGCCAAATCGGCGCCGTATCTGCAAATTACAGGAAATAATAAAAATA
63
+ TGTACCACTCAAGAAAACATCCTCTAAACAGAGCATCATAAGCATTCTCAAAAGTCAACC
64
+ AGGATAATGTGCCTGCACTAAGGTGATGAAGGATATCTGCCAGTTAATCAACCAACACGT
65
+ TCACTGGTAGAAAGTTGGAAACTGCATGCTTAGGTGACAATTCATCTAAAAAAACTGTAT
66
+ ATTTGCCTCTGGTAAACTGTATTCTTAAGATAAGCCGACAAACATTCAGTATTCAGAACA
67
+ TCAATATGTACAGAACTGTGGAGACTTCCACCATACCTTAAAACATCTGACAAAGGGAGC
68
+ CTTCCACCTTTAAGCCGAGCCATCTTGTCCCCGACGGATCCTTCGTAAAACTTCATCGCT
69
+ ATGCAAAGCTGAAAATCCATGAAACAAAAATTAAGCCACAGCACCATCTTTCATTCACAG
70
+ GTGACCCAACAGCAAGGCTATGCCAGACAGAGAACATACCCTCCCATTCTGCGTCGAGAT
71
+ GCCATGTAGGAAGCAGACATTGCCCAGGCCCTGGCACTTGCCGAACACCTCGTCGAACCT
72
+ CGCCGAGAACACCTGCAGCTGGTCGTCCCTGACCGGGTGCAGCATCTTCACAGCGACCTC
73
+ G
74
+ >chr7D
75
+ GTTGTGCACTTCTTGCTGCTGAACTTTCTGAGGATCGGCACCCTGATCAGAGACGCTGGC
76
+ GACCTTTCGACTCCTTGGCCTTGTGATGCTCTTCCCAACAAAGACACCTAGCTTCATAGC
77
+ AGTAAAGAAACCTATGGCAATGAACAGAGGCCTCACCGCCCAATGGAAGTCCTCGAGGTG
78
+ CTCATACTTCTTCACAACGCCCTCGCACTTGTCGAAGCTCACCACCTCCACCTCTGAAGG
79
+ GTCGGCCAAGCAGCTGCACACTTCGCCAAGGCTGAATTTGCCAGGGAAGGTCACAGCAAG
80
+ GCATCCATTCGAGAGTATCTGTGAAATACGGCCTATGGCGAACACTCCGCCTCTCTTTCG
81
+ CGGCCATTCAAACCGGGGGCTTGAAGTGTTAGTTCTGAGCCTCACAAATTGTCCCATGCA
82
+ GTAGGCTTCGGCCATTTGCAGATCTGAATATTCCCCCTTCCACAGGGTGTCCATTCCTAT
83
+ CAAACCAACATACACGGTGCCATTACGGTCAATGCTATGAAGAATTCCGACCTGAGACCG
84
+ CTTCTTGTCTTCCTCCCTAAGCCTTACCCAGTCTCCGGCAGCGAAACCATAGGTCACCCT
85
+ CTCCACTGCTGAGGAACGGACCTTCAGAGGGTCATGTATTCCATGGACTCGTACAAGAAT
86
+ GTAGCTATCGCGTTCTCCATCCTCCATGCCAACTATGGTTCCATCAGGGATTTCCATTGT
87
+ TTCAGGAGTACAAGAGTTTTTAACCTTTCTCGAGCGGACCTTGTCACCAACTTGCAGCTT
88
+ ATCCTTGAAGTGTGACCAATTAGTGTGACTTGGCACTACTGCCCTTGGGTTTTCAGAACT
89
+ ATCCCAGCCATTGTTGTCATAATCCACATCTTTAGCACTGAAGAAATGAAAAAAGAAAAC
90
+ AAATTTAGGGAAGAACCATAGTAAATCACCCATCCAATGGCAGTTTAACCAAATACTGCA
91
+ AGTTGATAAGGTAGAAGAAGAGAGTTTTAGCATGTTACCTTTCAAATGCTTGTAAGATAT
92
+ CTGACATCAAGGGGCGATCCCGAAAGTCGTACTCAAAGCAGCTAGAAAGGACATTCTCAA
93
+ CCTCTGCAGGTAAATTGTACGGGAATATCGGTTTCTCTTTCTTCAGGACAACCAACTGAT
94
+ AAATCTCGTCTGGTGATTTGCCACGCCAAGGCTGAACGCCACTGAACATCTCAAGAATGC
95
+ TGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTGGACCTCTGATGTTTGGTTGCC
96
+ ATTGCTCTGGGGCCATGTAATTTGGAGTCCCAAGTCTTTGGATAAGCTCTGGGTTTGGCA
97
+ GCGACAGCCCAAACAGCAAGGATGGAATCCCAAAATCCCCCAACACAGCATGGTCATGAT
98
+ CATCAAGGAGAAAATTACAAGGCTTGAGATTAAGAACAAATATTCCCCTGGAGTGTAGGT
99
+ CCAGCACACCACGTGCCAAATCAGCGCCATATCTGCAAGTTATAAGAATTCATAAAAATA
100
+ TGTACTACTCCAAACAGAGCATCATAAGCATTCTCAAAAGTCAACAGGATCATTTGCCTG
101
+ CACTAAGGTGATAAACTAGATCTGCCAGTTAATCAATCAACACGTTCACTGGTAGAAAGT
102
+ TGGAAACTGCATGCTTAGGTGACACTTCATCTAAAAAACTGTATATTTGCCTCTGTGGTA
103
+ AACTGTATTCTTAAGATAAGCCGACGAACATTCAGTATTCAGGACATCAAATATGTTCAA
104
+ AACTGTGGAGACTTCCACCATACCTTAAAACATCTGACAAAGGGAGCCTTCCACCTTTAA
105
+ GCCGAGCCATCTTGTCCCCGACGGATCCTTCATAGAACTTCATCACTATGCAAAGCTGAA
106
+ AATCCATGAAACAAAAATTAAGCCACAACGCCATCTTTCATTCACAGGCGACCCAACAGC
107
+ AAGGCTATGCCAGACAAAAACATACCCTCCCATTCTGCGTCGAGATGCCATGTAGGAAGC
108
+ AGACATTGCCCAGGCCCTGGCATTTGCCAAACACCTCGTCGAACCTCGCCGAGAACACCT
109
+ GCAGCTGGTCGTCCCTGACCGGGTGCAGCATCTTCACGGCGACCTCGTGGTACCGGTCAT
110
+ A
data/test/data/7B_amplicon_test_reference.fa.fai ADDED
@@ -0,0 +1,3 @@
1
+ chr7A 2099 7 60 61
2
+ chr7B 2101 2148 60 61
3
+ chr7D 2101 4292 60 61
data/test/data/7B_marker_test.txt ADDED
@@ -0,0 +1 @@
1
+ RAC875_c8221_649,7B,CGTACAATTTACCTGCAGAGGTTGAGAATGTCCTTTCTAGCTGCTTTGAG[T/C]ACGACTTTCGGGATCGCCCCTTGATGTCAGATATCTTACAAGCATTTGAA
data/test/data/BS00068396_51.fa ADDED
@@ -0,0 +1,2 @@
1
+ >BS00068396_51
2
+ CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA
data/test/data/BS00068396_51_blast.tab ADDED
@@ -0,0 +1,4 @@
1
+ BS00068396_51 1 101 1 2AS_5222932 3015 2915 -1 99 99.010 101 6364 CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTATATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA
2
+ BS00068396_51 1 101 1 2DS_5334799 6813 6913 1 99 99.010 101 7226 CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTACATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA
3
+ BS00068396_51 1 101 1 2BS_5245544 4550 4651 1 87 95.098 101 8836 CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAG-TCGTGTGAACAACTGAAATTTGAGCGCCACAA CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTACATGCAGGATCTTGATTAGATCATGTGAACATTTGAAATTTGAGCGCCACAA
4
+ BS00068396_51 101 1 -1 2BS_5163353 7425 7324 -1 87 95.098 101 11974 CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTACATGCAGGATCTTGATTAGATCATGTGAACATTTGAAATTTGAGCGCCACAA CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAYATGCAGGATCTTGATTAG-TCGTGTGAACAACTGAAATTTGAGCGCCACAA