bio-polymarker 1.3.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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 @@
1
+ require 'bio'
2
+ require 'bio-samtools-wrapper'
3
+ require "set"
4
+ require 'systemu'
5
+ require 'json'
6
+
7
+ #require 'bio/db/exonerate'
8
+ #require 'bio/db/primer3'
9
+ #require 'bio/db/fasta'
10
+
11
+ #puts "Loading all... #{Dir[File.dirname(__FILE__) + "/bio/*/*.rb"]}"
12
+ module Bio::PolyploidTools
13
+
14
+ end
15
+ Dir[File.dirname(__FILE__) + "/bio/*.rb"].each {|file|
16
+ # puts file
17
+ require_relative file }
18
+ Dir[File.dirname(__FILE__) + "/bio/*/*.rb"].each do |file|
19
+ # $stderr.puts "loading #{file}"
20
+ require_relative file
21
+ end
22
+
23
+ require_relative File.dirname(__FILE__) + "/../conf/defaults.rb"
24
+
25
+
26
+ #require_relative "bio/BFRTools.rb"
27
+ #require_relative "bio/PolyploidTools/ExonContainer.rb"
28
+
data/test/data/7B_amplicon_test.fa ADDED
@@ -0,0 +1,12 @@
1
+ >chr7B:1000-1600
2
+ TTTCAAATGCTTGTAAGATATCTGACATCAAGGGGCGATCCCGAAAGTCATACTCGAAGC
3
+ AGCTAGGAAGGACATTCTCAACCTCTGCAGGTAAGTTGTACGGGAATATCGGTTTCTCTT
4
+ TCTTCAGGACAACCAACTGATAAATCTCGTCTGGTGATTTGCCACGCCAAGGCTGAACGC
5
+ CAGTGAACATCTCAAGAATGCTGCAGGCAAAGCCCCATGAATCTGTCTCGTAACTAATTG
6
+ 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