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
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+ 3.6
228
+ -1.7
229
+ inf
230
+ -4.5
231
+ 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