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
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+ inf
232
+ inf
233
+ inf
234
+ -11.7
235
+ inf
236
+ -6.2
237
+ inf
238
+ -15.8
239
+ inf
240
+ inf
241
+ inf
242
+ -7
243
+ -5.3
244
+ -1.5
245
+ 0.2
246
+ inf
247
+ inf
248
+ inf
249
+ 0.9
250
+ inf
251
+ 16.3
252
+ inf
253
+ -10.8
254
+ inf
255
+ inf
256
+ inf
data/conf/primer3_config/tetraloop.dh ADDED
@@ -0,0 +1,77 @@
1
+ AAAAAT 500
2
+ AAAACT 700
3
+ AAACAT 1000
4
+ ACTTGT 0
5
+ AGAAAT -1100
6
+ AGAGAT -1100
7
+ AGATAT -1500
8
+ AGCAAT -1600
9
+ AGCGAT -1100
10
+ AGCTTT 200
11
+ AGGAAT -1100
12
+ AGGGAT -1100
13
+ AGGGGT 500
14
+ AGTAAT -1600
15
+ AGTGAT -1100
16
+ AGTTCT 800
17
+ ATTCGT -200
18
+ ATTTGT 0
19
+ ATTTTT -500
20
+ CAAAAG 500
21
+ CAAACG 700
22
+ CAACAG 1000
23
+ CAACCG 0
24
+ CCTTGG 0
25
+ CGAAAG -1100
26
+ CGAGAG -1100
27
+ CGATAG -1500
28
+ CGCAAG -1600
29
+ CGCGAG -1100
30
+ CGCTTG 200
31
+ CGGAAG -1100
32
+ CGGGAG -1000
33
+ CGGGGG 500
34
+ CGTAAG -1600
35
+ CGTGAG -1100
36
+ CGTTCG 800
37
+ CTTCGG -200
38
+ CTTTGG 0
39
+ CTTTTG -500
40
+ GAAAAC 500
41
+ GAAACC 700
42
+ GAACAC 1000
43
+ GCTTGC 0
44
+ GGAAAC -1100
45
+ GGAGAC -1100
46
+ GGATAC -1600
47
+ GGCAAC -1600
48
+ GGCGAC -1100
49
+ GGCTTC 200
50
+ GGGAAC -1100
51
+ GGGGAC -1100
52
+ GGGGGC 500
53
+ GGTAAC -1600
54
+ GGTGAC -1100
55
+ GGTTCC 800
56
+ GTTCGC -200
57
+ GTTTGC 0
58
+ GTTTTC -500
59
+ TAAAAA 500
60
+ TAAACA 700
61
+ TAACAA 1000
62
+ TCTTGA 0
63
+ TGAAAA -1100
64
+ TGAGAA -1100
65
+ TGATAA -1600
66
+ TGCAAA -1600
67
+ TGCGAA -1100
68
+ TGCTTA 200
69
+ TGGAAA -1100
70
+ TGGGAA -1100
71
+ TGGGGA 500
72
+ TGTAAA -1600
73
+ TGTGAA -1100
74
+ TGTTCA 800
75
+ TTTCGA -200
76
+ TTTTGA 0
77
+ TTTTTA -500
data/conf/primer3_config/tetraloop.ds ADDED
@@ -0,0 +1,77 @@
1
+ AAAAAT -650
2
+ AAAACT 1610
3
+ AAACAT 1610
4
+ ACTTGT 4190
5
+ AGAAAT 1610
6
+ AGAGAT 1610
7
+ AGATAT 1610
8
+ AGCAAT 1610
9
+ AGCGAT 1610
10
+ AGCTTT 1610
11
+ AGGAAT 1610
12
+ AGGGAT 1610
13
+ AGGGGT 640
14
+ AGTAAT 1610
15
+ AGTGAT 1610
16
+ AGTTCT 1610
17
+ ATTCGT 1610
18
+ ATTTGT 1610
19
+ ATTTTT 1610
20
+ CAAAAG -1290
21
+ CAAACG 0
22
+ CAACAG 0
23
+ CAACCG 0
24
+ CCTTGG 2570
25
+ CGAAAG 0
26
+ CGAGAG 0
27
+ CGATAG 0
28
+ CGCAAG 0
29
+ CGCGAG 0
30
+ CGCTTG 0
31
+ CGGAAG 0
32
+ CGGGAG 0
33
+ CGGGGG -970
34
+ CGTAAG 0
35
+ CGTGAG 0
36
+ CGTTCG 0
37
+ CTTCGG 0
38
+ CTTTGG 0
39
+ CTTTTG 0
40
+ GAAAAC -3230
41
+ GAAACC 0
42
+ GAACAC 0
43
+ GCTTGC 2570
44
+ GGAAAC 0
45
+ GGAGAC 0
46
+ GGATAC 0
47
+ GGCAAC 0
48
+ GGCGAC 0
49
+ GGCTTC 0
50
+ GGGAAC 0
51
+ GGGGAC 0
52
+ GGGGGC -970
53
+ GGTAAC 0
54
+ GGTGAC 0
55
+ GGTTCC 0
56
+ GTTCGC 0
57
+ GTTTGC 0
58
+ GTTTTC 0
59
+ TAAAAA 320
60
+ TAAACA 1610
61
+ TAACAA 1610
62
+ TCTTGA 4190
63
+ TGAAAA 1610
64
+ TGAGAA 1610
65
+ TGATAA 1610
66
+ TGCAAA 1610
67
+ TGCGAA 1610
68
+ TGCTTA 1610
69
+ TGGAAA 1610
70
+ TGGGAA 1610
71
+ TGGGGA 640
72
+ TGTAAA 1610
73
+ TGTGAA 1610
74
+ TGTTCA 1610
75
+ TTTCGA 1610
76
+ TTTTGA 1610
77
+ TTTTTA 1610
data/conf/primer3_config/triloop.dh ADDED
@@ -0,0 +1,16 @@
1
+ AGAAT -1500
2
+ AGCAT -1500
3
+ AGGAT -1500
4
+ AGTAT -1500
5
+ CGAAG -2000
6
+ CGCAG -2000
7
+ CGGAG -2000
8
+ CGTAG -2000
9
+ GGAAC -2000
10
+ GGCAC -2000
11
+ GGGAC -2000
12
+ GGTAC -2000
13
+ TGAAA -1500
14
+ TGCAA -1500
15
+ TGGAA -1500
16
+ TGTAA -1500
data/conf/primer3_config/triloop.ds ADDED
@@ -0,0 +1,16 @@
1
+ AGAAT 0
2
+ AGCAT 0
3
+ AGGAT 0
4
+ AGTAT 0
5
+ CGAAG 0
6
+ CGCAG 0
7
+ CGGAG 0
8
+ CGTAG 0
9
+ GGAAC 0
10
+ GGCAC 0
11
+ GGGAC 0
12
+ GGTAC 0
13
+ TGAAA 0
14
+ TGCAA 0
15
+ TGGAA 0
16
+ TGTAA 0