bio-polyploid-tools 0.1.0

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Files changed (92) hide show
  1. checksums.yaml +7 -0
  2. data/Gemfile +16 -0
  3. data/Gemfile.lock +67 -0
  4. data/README +21 -0
  5. data/Rakefile +61 -0
  6. data/VERSION +1 -0
  7. data/bin/bfr.rb +133 -0
  8. data/bin/count_variations.rb +36 -0
  9. data/bin/filter_blat_by_target_coverage.rb +15 -0
  10. data/bin/find_best_blat_hit.rb +32 -0
  11. data/bin/hexaploid_primers.rb +168 -0
  12. data/bin/homokaryot_primers.rb +155 -0
  13. data/bin/map_markers_to_contigs.rb +66 -0
  14. data/bin/markers_in_region.rb +42 -0
  15. data/bin/polymarker.rb +219 -0
  16. data/bin/snps_between_bams.rb +106 -0
  17. data/bio-polyploid-tools.gemspec +139 -0
  18. data/conf/defaults.rb +1 -0
  19. data/conf/primer3_config/dangle.dh +128 -0
  20. data/conf/primer3_config/dangle.ds +128 -0
  21. data/conf/primer3_config/interpretations/dangle_i.dh +131 -0
  22. data/conf/primer3_config/interpretations/dangle_i.ds +131 -0
  23. data/conf/primer3_config/interpretations/loops_i.dh +34 -0
  24. data/conf/primer3_config/interpretations/loops_i.ds +31 -0
  25. data/conf/primer3_config/interpretations/stack_i.dh +257 -0
  26. data/conf/primer3_config/interpretations/stack_i.ds +256 -0
  27. data/conf/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
  28. data/conf/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
  29. data/conf/primer3_config/interpretations/tetraloop_i.dh +79 -0
  30. data/conf/primer3_config/interpretations/tetraloop_i.ds +81 -0
  31. data/conf/primer3_config/interpretations/triloop_i.dh +21 -0
  32. data/conf/primer3_config/interpretations/triloop_i.ds +18 -0
  33. data/conf/primer3_config/interpretations/tstack2_i.dh +256 -0
  34. data/conf/primer3_config/interpretations/tstack2_i.ds +256 -0
  35. data/conf/primer3_config/interpretations/tstack_i.dh +256 -0
  36. data/conf/primer3_config/interpretations/tstack_i.ds +256 -0
  37. data/conf/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
  38. data/conf/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
  39. data/conf/primer3_config/loops.dh +30 -0
  40. data/conf/primer3_config/loops.ds +30 -0
  41. data/conf/primer3_config/stack.dh +256 -0
  42. data/conf/primer3_config/stack.ds +256 -0
  43. data/conf/primer3_config/stackmm.dh +256 -0
  44. data/conf/primer3_config/stackmm.ds +256 -0
  45. data/conf/primer3_config/tetraloop.dh +77 -0
  46. data/conf/primer3_config/tetraloop.ds +77 -0
  47. data/conf/primer3_config/triloop.dh +16 -0
  48. data/conf/primer3_config/triloop.ds +16 -0
  49. data/conf/primer3_config/tstack.dh +256 -0
  50. data/conf/primer3_config/tstack2.dh +256 -0
  51. data/conf/primer3_config/tstack2.ds +256 -0
  52. data/conf/primer3_config/tstack_tm_inf.ds +256 -0
  53. data/lib/bio/BFRTools.rb +698 -0
  54. data/lib/bio/BIOExtensions.rb +186 -0
  55. data/lib/bio/PolyploidTools/ChromosomeArm.rb +52 -0
  56. data/lib/bio/PolyploidTools/ExonContainer.rb +194 -0
  57. data/lib/bio/PolyploidTools/Marker.rb +175 -0
  58. data/lib/bio/PolyploidTools/PrimerRegion.rb +22 -0
  59. data/lib/bio/PolyploidTools/SNP.rb +681 -0
  60. data/lib/bio/PolyploidTools/SNPSequence.rb +56 -0
  61. data/lib/bio/SAMToolsExtensions.rb +284 -0
  62. data/lib/bio/db/exonerate.rb +272 -0
  63. data/lib/bio/db/fastadb.rb +164 -0
  64. data/lib/bio/db/primer3.rb +673 -0
  65. data/lib/bioruby-polyploid-tools.rb +25 -0
  66. data/test/data/BS00068396_51.fa +2 -0
  67. data/test/data/BS00068396_51_contigs.aln +1412 -0
  68. data/test/data/BS00068396_51_contigs.dnd +7 -0
  69. data/test/data/BS00068396_51_contigs.fa +8 -0
  70. data/test/data/BS00068396_51_exonerate.tab +6 -0
  71. data/test/data/BS00068396_51_genes.txt +14 -0
  72. data/test/data/LIB1716.bam +0 -0
  73. data/test/data/LIB1716.bam.bai +0 -0
  74. data/test/data/LIB1719.bam +0 -0
  75. data/test/data/LIB1719.bam.bai +0 -0
  76. data/test/data/LIB1721.bam +0 -0
  77. data/test/data/LIB1721.bam.bai +0 -0
  78. data/test/data/LIB1722.bam +0 -0
  79. data/test/data/LIB1722.bam.bai +0 -0
  80. data/test/data/S22380157.fa +16 -0
  81. data/test/data/S22380157.fa.fai +1 -0
  82. data/test/data/Test3Aspecific.csv +1 -0
  83. data/test/data/Test3Aspecific_contigs.fa +6 -0
  84. data/test/data/patological_cases5D.csv +1 -0
  85. data/test/data/short_primer_design_test.csv +10 -0
  86. data/test/data/test_primer3_error.csv +4 -0
  87. data/test/data/test_primer3_error_contigs.fa +10 -0
  88. data/test/test_bfr.rb +51 -0
  89. data/test/test_exon_container.rb +17 -0
  90. data/test/test_exonearate.rb +53 -0
  91. data/test/test_snp_parsing.rb +40 -0
  92. metadata +201 -0
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
data/conf/primer3_config/tstack.dh ADDED
@@ -0,0 +1,256 @@
1
+ 0
2
+ 0
3
+ 0
4
+ -2500
5
+ 0
6
+ 0
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+ 0
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+ -8000
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data/conf/primer3_config/tstack2.dh ADDED
@@ -0,0 +1,256 @@
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+ 0
2
+ 0
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+ -2500
5
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