bio-bwa 0.2.0

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  1. data/.document +5 -0
  2. data/Gemfile +15 -0
  3. data/Gemfile.lock +28 -0
  4. data/LICENSE.txt +35 -0
  5. data/README.rdoc +33 -0
  6. data/Rakefile +56 -0
  7. data/VERSION +1 -0
  8. data/bio-bwa.gemspec +152 -0
  9. data/doc/Bio.html +93 -0
  10. data/doc/Bio/BWA.html +2884 -0
  11. data/doc/Bio/BWA/Library.html +229 -0
  12. data/doc/_index.html +119 -0
  13. data/doc/class_list.html +36 -0
  14. data/doc/css/common.css +1 -0
  15. data/doc/css/full_list.css +53 -0
  16. data/doc/css/style.css +310 -0
  17. data/doc/file.LICENSE.html +88 -0
  18. data/doc/file.README.html +119 -0
  19. data/doc/file_list.html +41 -0
  20. data/doc/frames.html +13 -0
  21. data/doc/index.html +119 -0
  22. data/doc/js/app.js +203 -0
  23. data/doc/js/full_list.js +149 -0
  24. data/doc/js/jquery.js +154 -0
  25. data/doc/method_list.html +171 -0
  26. data/doc/top-level-namespace.html +88 -0
  27. data/ext/COPYING +674 -0
  28. data/ext/ChangeLog +3864 -0
  29. data/ext/NEWS +555 -0
  30. data/ext/README +29 -0
  31. data/ext/bamlite.c +155 -0
  32. data/ext/bamlite.h +94 -0
  33. data/ext/bntseq.c +303 -0
  34. data/ext/bntseq.h +80 -0
  35. data/ext/bwa.1 +562 -0
  36. data/ext/bwape.c +807 -0
  37. data/ext/bwase.c +686 -0
  38. data/ext/bwase.h +27 -0
  39. data/ext/bwaseqio.c +222 -0
  40. data/ext/bwt.c +250 -0
  41. data/ext/bwt.h +105 -0
  42. data/ext/bwt_gen/Makefile +23 -0
  43. data/ext/bwt_gen/QSufSort.c +496 -0
  44. data/ext/bwt_gen/QSufSort.h +40 -0
  45. data/ext/bwt_gen/bwt_gen.c +1547 -0
  46. data/ext/bwt_gen/bwt_gen.h +105 -0
  47. data/ext/bwt_lite.c +94 -0
  48. data/ext/bwt_lite.h +29 -0
  49. data/ext/bwtaln.c +345 -0
  50. data/ext/bwtaln.h +150 -0
  51. data/ext/bwtgap.c +264 -0
  52. data/ext/bwtgap.h +38 -0
  53. data/ext/bwtindex.c +186 -0
  54. data/ext/bwtio.c +77 -0
  55. data/ext/bwtmisc.c +269 -0
  56. data/ext/bwtsw2.h +51 -0
  57. data/ext/bwtsw2_aux.c +650 -0
  58. data/ext/bwtsw2_chain.c +107 -0
  59. data/ext/bwtsw2_core.c +594 -0
  60. data/ext/bwtsw2_main.c +100 -0
  61. data/ext/cs2nt.c +191 -0
  62. data/ext/is.c +218 -0
  63. data/ext/khash.h +506 -0
  64. data/ext/kseq.h +208 -0
  65. data/ext/ksort.h +269 -0
  66. data/ext/kstring.c +35 -0
  67. data/ext/kstring.h +46 -0
  68. data/ext/kvec.h +90 -0
  69. data/ext/main.c +63 -0
  70. data/ext/main.h +29 -0
  71. data/ext/mkrf_conf.rb +49 -0
  72. data/ext/qualfa2fq.pl +27 -0
  73. data/ext/simple_dp.c +162 -0
  74. data/ext/simpletest.c +23 -0
  75. data/ext/solid2fastq.pl +111 -0
  76. data/ext/stdaln.c +1072 -0
  77. data/ext/stdaln.h +162 -0
  78. data/ext/utils.c +82 -0
  79. data/ext/utils.h +54 -0
  80. data/lib/bio-bwa.rb +7 -0
  81. data/lib/bio/bwa.rb +312 -0
  82. data/lib/bio/bwa/library.rb +42 -0
  83. data/test/data/testdata.fa +602 -0
  84. data/test/data/testdata.long.fa +175 -0
  85. data/test/data/testdata.short.fa +2 -0
  86. data/test/helper.rb +18 -0
  87. data/test/test_bio-bwa_basic.rb +62 -0
  88. data/test/test_bio-bwa_make_index.rb +42 -0
  89. data/test/test_bio-bwa_run_aln.rb +49 -0
  90. data/test/test_bio-bwa_sam_conversion.rb +49 -0
  91. metadata +218 -0
@@ -0,0 +1,175 @@
1
+ >NM_204276
2
+ GCGCCGCGGGAGCGCGCAGTTCGGTGTGGCTGTGCCGTGCCCGCGGGGAGCCCCGCGCTT
3
+ GGGGCGATGCTGCGGTCCCGGAGCGCTCCCGGGGGCCGGAGGGAGGTTTGCCAACAAGTG
4
+ TTCCAGTGAGATAAAAAAATGGCTTACAAATCTGGGAAAAGACCTACTTTCTTTGAAGTA
5
+ TTTAAGGCGCATTGTAGCGATTCAGACTTGGGGCCTGTAAGTCTTGACTGGTTTGAAGAG
6
+ CTCAGCTCAGAAGCACCTCCGTATGAGCCTAAGTTGTTAGGAGAACCTGAGGGTCCCATT
7
+ GGATGGTTTGATCAAACTTTTAAAACTCCAAAGGCAAAATCTTCTACGGACAGCCAGTTG
8
+ GCATCAACTCCACTGATTTTTAAAGAACAGAATACAATGCCGCCTTTTTCTTCTCCTGGA
9
+ AAAGAATTGGATCAGAAAAAAATGGAAACAAGCAGAGAGAATTTGCTAAGTCCAAGTATG
10
+ GCAGGAAGAAAGACAGATCAAGAAAATCAAATACTCGCTTCTCCTCATGGTATCTGCCAC
11
+ AACTACACTGCTGCTAGTCCAGCTATTGTAAGGAATCCTTGCAGAACACCACAGGGAAGT
12
+ AATATACCTGGACCATATGGAAGCTTGTTTTGCACACCAAAATTCTTGGAGATCCCAACT
13
+ CCGAAACGGATTTCTGAAAGTCTGGGAGCAGAAGTGGATCCAGAAATGTCCTGGACAAGT
14
+ TCTTTAGCTACTCCTCCTACACTTGGTGTGACAGTGATAATAGCTAGAGAGAATGATTCT
15
+ ATTTCTGGAGCAAAGCAGCAGGATGAAAGAGCTGAGATAGTTTTGCACAACTTTTTATCT
16
+ GAAGATGATGGATATACTGCAAAGAATGATACAAGTCTGCTGTCCATACCAGAGACGGTA
17
+ AAACTAAATGCTAGAGATGACATAAAAGATCTTGAGTCAGAAGTGTTAGATGGTTTATTT
18
+ GGTGAGACAAATAGCTTTGAGGATTCATTCAACTTGCCTGCTGAATCCAGTGGAATTCTG
19
+ TTGTCGCCACGTGCTCTGGATGCAATAGAGAAATGTGAAATAAAAATAGATGAAGCACAA
20
+ GAAAAGAGTGATGTTCTTTCAGAGCAACATAGGAGAAGAAAGTCTACCATTTCACAGGAG
21
+ GTGAAAGCTGCTAACTGGACTGAAAAAAGCTGCTGTGTTGAAGTGAAGGATTCTATAATC
22
+ CAGAACACCAATGAAGATATCATGGATAGTAAAGACAACTGCTTACTAGGGCGTGAAAAG
23
+ GAATTGGAGTATCTTAGGATTGCAGGAAACTTGCAAGATAATAGAACACAGAAATCATCT
24
+ GTGAATGAGAAGCTTGTGAAAGATGTGCTGTCTTCATCAAGCCAGTGGTCTCAGCTGAAC
25
+ TTGTCTGGTCTTGATGTAACTCATCTGGAAATGTCTATATGTAGCTCTCCACAGTCTGAC
26
+ TCATGTAGAGAGAAAGGTTTAGAAGAGAAGTCAGTACTGATGACCAAGGATGATGCTGTA
27
+ GAAACATCTTTACTGAATACTTCAGGCTTGAGAAATGCACAGGAGCTCTCAAGTGCCAGT
28
+ TTGTCAGAAAATGGCAGTGATACGAAAATATCTAAAAACAACCCAATGTCAGAAATAACT
29
+ CCAGTAAAACCTGTGTGTGCAAGTCCGAAGTTGGTAAAAGGATATGCACATGAGGAGGTT
30
+ TCCGGAATGAGCTTTTTAAACTGTAGTTCTTTTTTAATTGAAAGTACAAATGTCATGGAG
31
+ TATTCTGTAGTCTACAACAGCACTTTTTCCACGCATTTAAAAGCAACTTCGCAATCTGTG
32
+ GTAACTGATGTTCTTTCTCACCCTCTTATATGTAGTGCTGCATCTCCAGATAATTGCAGT
33
+ GACCTACATTTAAGAAATAGTGAAAAAACTCTTAGGAAATCTAACTTTAAAAGCCTAAAT
34
+ ATGTTATCCAGATTGAGGAAGAAATCCAAGAGATTTATTTATACAATAAATAATACTTTA
35
+ GTGTATCAGGAAGAAAATGTGCAGAAAGAAGTAACCTCTGAATCACCTGATAATCCTGTA
36
+ TTAACACATTTGGAATCTGATTTACATGAATTTAAAGATTGTCAGGTGGCCACAGATGGT
37
+ AACCAAGACTGCTTGCTTTCGGCTGAGAGGCAATCAAATATCAAAGAAAATAATTTAAAC
38
+ ACTCTTACCATAAAGGTAGATATAATGGATAACTCATCTGATAATTCTGTCAACAATAGG
39
+ CTGAAACAAGAGCTGAGTGAGTCAGGGAAAAATGCAAGAGAGTATCAACCTGCTACCTCA
40
+ TTTAAATGCTTAAAAGCTTCTCATACTGAGAGTGAAGACACAACAGATTGTTTAAACAGT
41
+ GGAAGAATTTCAAATATAAAACATAAGGTACTAACTTCGGCATACCTAATGGCAAGAAGG
42
+ CATTCCAGATTGTTTCCTGAAGACTGTTGCTTAAGGAAAGGCAAGAATGATACATATACC
43
+ GTTTCTAATGTGAACAGTCGAGCTGCTGTACCTCGGAGCCCTAAAGGACAGCCTCCACAG
44
+ TCCTCTCCTAGTTGTAGTGATTGCTTGATTGATATGCGCCATGGCACTGCGTTTGTGACA
45
+ AACAGCAAGTTCAATAATACTTTGAGTCACATCAAGTTTGGCATGAACAGAGTCAGTAGT
46
+ AACTCTTGCAATAAAATATCGGCTGATAAAAGACGTGCTTCAGATCAGTTGTCAGTAGCT
47
+ GAATGTAGGGAAATAGTTGCACCTTTGGGAATAAACTGCTTAGAAAACAATAGTACTAGC
48
+ TTAAAACAACGGGGAAAAGAAGATGTAGATGAAAATCAAGAAACACTCTCTATTAAAAGC
49
+ AGTGAAAACCCTCAAGCAGCTGCTTGGAATAACGAATCTATAGAGGTTGCTGAAGAATTC
50
+ TTGGATTGTATAGATAATTCTTTGAATGAAGTAGTTTCTGAAGAAGATAGACAAGTAGCA
51
+ CCTGTGTATTTCAACACAAAGCCAATTGAAAGCCTAGAACATAAAGGGAAATCATCAGGA
52
+ GATCTTAACGCATGCAGTTCAAGTTTGAGCTTTGGTGGCTTCCAGACTGCTTCCAATAAG
53
+ CAGATTAAATTCTCAGAAAGCAGCATAGCGAAAGGCAAAATGCTGTTCAAAGATATTGAA
54
+ AATGAATTCTTTGAAGCCTCTTCCATGGAAAGAGTCAGAAATTTTTCAAATCGAGTTCAA
55
+ AAGGAGAATATATTTTCCTCAGATTTGGAAAGCAAAACAGGCAGTACTTCATCTGGTTTG
56
+ CAGACAAGGTGTATGCAATATATTCCACGTAAAGTTGATTTATGTAAAAACTCGCCTAGA
57
+ AATCAACTATCTGTGCAAGAACCAAATCAGTCTTTGACAGCAAGCCAAGAAGCTGAAATT
58
+ GCTGAACTTTCTAATATCTTGGAAGAAACGGGTAGCCAGTTTGAATTCACACAATTTAGA
59
+ AAGCAAAGTAACATGATACAAAGTCACATTCAGCAGTTTGGAGCAACGAATGTGGAAAAT
60
+ GCTTCTGAAGCAGGGGAAGATACTAATTTCTATAGCACTCTTAAATCTGAAAATCATGTA
61
+ ATAAATGACGAGTATTGCAGTAAGttgaaaaatgaaaatgaatgtaaaatggtagaatat
62
+ gaaaaagaagacacagtggtttttcataaaaataaaagaaaaGTTACTTTTACTAACTTG
63
+ GACAGAAATGAAAGTAGAATATCCAGCCATGAGAGCTGTCCGGTACCTTTACGGGACAGC
64
+ TTTTCTAATTTTGTAGGATTTACTTCAGCTGGAGGTAAAAAAATAAATATTTGTAAGGCA
65
+ GCTTTGACCAGATCTGCAGAGCTTTTCAAGGACTTGGATGATGATAACTTTTTGTTTAAA
66
+ TCTTCTGGAACTAATACCAGATGCTGCAATTCAGATGGGCATGTATCTTCTAACTGGAAT
67
+ TTTCTCAGATGCCAGACAAAAGAAGATGAAGGAGGAATACTTTGTGTTCCAAACATAAAA
68
+ AGCGTAGGTCCCATTTCCCACCATTCAGAGAAAAAATATGCAGAAAATATTAGTTCACCA
69
+ TGTAAGGAAAATACAGAAAACTGGACAGAAATATTAAGTGATAATGTTGATTTCAGTTGT
70
+ ACTAATGGTGGATATTCTGCCTCTGGAATGAGAAACAGTCCGTCATCCTTTAAAAAACCT
71
+ CACCAGAACTGTAAAAATTCTGATCAGTTTCTGAATCAAGGAAACAGCGAAGTTGAAGGT
72
+ TGTTTGCAAGAAGACACTTCATATCTGATTTGTCTAGGAGATAATATTACTAGTGCAGAA
73
+ GAACATGATTTAAATGTTTCAGATGAAATGGAAAACCTGTCCCCTAATCAGAAAGAAGAC
74
+ AGAAAGCAGGAAGATGAGCATTTGCTGCTAAACCGTCAAGCTGCAGACACTGATGCTGTA
75
+ TCCATTTCTGATTCATCGTTCCGTAGTTCTCTACGTGATCTCAACGTACAATGTGGGGAA
76
+ AGAGATACAGATGTTTCAGAGAAATCTAGTAAACAAAAGACAAATAGTGTCAGTGTGGAA
77
+ GGAGAAGACTCCACCTATAAGAACCTGTTTGTGAGTGAAAGTGAGATTAAAATAGGCTCT
78
+ AACCAACGTCATCAAGTACCTTCCGAGCAAGAGATGGATGTTGACAAAAACAAAGTTAAG
79
+ GGAACTTATCTGACTGGTTTCTGTACTGCTAGTGGCAAGAAAATAACAATTGCTGATGGA
80
+ TTTTTGGCTAAAGCTGAAGAGTTTTTTTCAGAAAATAATGTTGATTTAGGAAAAGATGAT
81
+ AATGATTGTTTTGAGGACTGCTTAAGAAAATGTAATAAAAGCTATGTTAAAGACCGTGAC
82
+ TTATGTATGGACAGTACTGCTCATTGTGATGCAGATGTACTTAATTTTAAAGATAAGCTT
83
+ ATTCCTCAAGAACCTGGGGACCGACTAAAGCAGACAATAGAGGAGAGTCCCATTATACAA
84
+ GCTGTTAATCATGACAGCATTAAAGTGGGTGCATTTATTAATGTGGATGAAGATTGTGAA
85
+ AGAAATTTGGCAGCTCCATGTGCAAATAAGGAAGCTTATGTCAGACCTGGAAAGTCAGAA
86
+ GTAGAATCTCTTCCTGTACATGGGAACAATTCTTTAAGTAGAACTCTTTTGCTTGAAGAC
87
+ AGAAAACAGTTTGCAGAGAGAGATGTGGAATACTCAGCAACAAAGAGGGATAATTCAGAA
88
+ AGCAAACCTGACTCTTCTCTGAAGTGTGCTACATCTCTGCATTTAACAAAGGTGTCGAGT
89
+ CACCTTGCAGATAATTCTGTGCCTGGTGGTATTATTCAGACTGTATCTGCTGAGGATAGT
90
+ TGCAAGTCTAATCAGTCCTTCCTCTTACCTCGTGGTAGTGTTCCAAGAAGTACCTCACCT
91
+ TATCTGAACTGCGGCAATAAGGAGATTGACTTAAAACGTTTAAATGAACCTTGTTCCAAT
92
+ ACAGACAGTTTCACAAATACTGTAGATAATGCTCACCAAGAACAGTCTGAATTTGATCTT
93
+ CCTGAAGATGAAACTAATTTAACCTGCTTACAGGAAACATCACTTAATGCTGAAAGTCAA
94
+ AAGAGTGATCTGAAACAAGTGTTCAGTACAGCAAAAGGTAAAGCAGTCTCTGTTTCAGAA
95
+ AGTGCATTAGCAAGCATCAGACAAATGTTTCAAACAGACTGTGATGCATCTGTAAAATCT
96
+ GAAATTGAGACTAAATCAGGAACTAATCAAACAGCAATTGCTGGAAGTTCATCTTTCAGC
97
+ ATTCATGCTGGGGGTCCTGGTTTTGCTACATTTTTAGATACTAGAAAAAGTGAGATGAAT
98
+ GTGGCTGCACCTCATTTTATTAATGGAAATGGGAATCTTATTGAAAACAATCACCAAGGC
99
+ GCAAACATGTTTGCAGATGCAGATTCTGTTCCAGGTTTTCAGATGCAATGCTTTGAGCAG
100
+ AAGAGTAAGCTTTTAGGACACTTTCCTGTGCCAGATAAGCAGATGGAGCAGTCAGGTCCT
101
+ TCAGGCAACCTTGGGTTTTTCAGTACGGCAAGTGGGAAGCCTGTGCAACTATCAGAAGAG
102
+ TCGCTAAAGAAAGCTAGACAGCTCTTTTCTGAAATGGAAGGTAGCCATTCATCAGGGCTA
103
+ CAAGATGCACATTTGCTTGAAGACGTTGAGAAATCCACAAACCATGGTGAAGTATTTCCT
104
+ AGAGAAATGCAGCTACTGCTGCCAAGAGGGAAGGAGAATGCCAGCACGGATAAGATTTCA
105
+ AGTCCTGCTTTGGGGTTCAGCACTGCAAGTGGAAAGCAAGTGACCATCTCTGAAAGTGCC
106
+ TATCAGAAAGCAAAGGCAATTTTAAAGGAAGCAGATGGCTTTTTAAGCAGTGAGCTTGGT
107
+ GTTACAAATGAACTTTGTGAAATTAAAGAGAGTGGTCAACATGCAGAATATTTAACTGGT
108
+ AAAGTAATTTCAGAATCCAAAACTGAAAAAAGCTGCAGTGAGGAGCTTGACTTGAAAAGC
109
+ ATTCACCCTGAAAAAATGAAGTCTTTGCCAAGCACTCACCGTGTCAAAATTACTGAGTAT
110
+ GTACCACATAGTAAGAGAAACAGCCAGTCAGCACCATTTAAAAATAGCTTTGAGCAAGAA
111
+ GAGACCAGATTTTTCAGAAAAGGAGAGCTGAATCTGGGGATAAAAGCAGAGTCTGAATCA
112
+ GATTTATGCAGTGCTACATCTAAAGCAGAAATAAACATTTTCCAAACTCCAAAAGACTAC
113
+ TTGAAAACAGAGGCTGTAGAAAGTGCAAAAGCCTTTATGGAAGATGATCTTTCGGATTCT
114
+ GGAGTCCAGGTCAAGTCTGCACAGTCCTTTGGCAAAATGTCAGATAACTTTCAAAACAAG
115
+ CCCTTTGGGAAGAGACACTTGGATGAAAAAGACTCACATGGAGAACCTCCAATTAAAAGA
116
+ CAGCTACTGCTTGAATTTGAGAAGATGAAGATTCCCCCCAAATCTGTGAAACCTTTGAAA
117
+ AGCACTCCTGATGGCATTTTCAAAGACAGAAGAAAATTTATGTACCACGTCCCTTTAAAA
118
+ CCAGTAACTTGTCGACCTTTGGGGACTACTAAGGAACGACAAGAAGTCAGGAACCCTACA
119
+ CTTACTCTTCCTGATCAAGACTTGAAAGGATTTAAATCTATACCTGCCGTTTTTCAGCAC
120
+ TGTGCCCTACGGCAGTCTTCAAGTGGTGCTTCAGGGCTTTTTACTCCACATAAGGCCGTG
121
+ GCCAAGGATAGCGAGGAAACAAGAAGTTTGTGCAAGTCAGGCAAAGCTGTTAAAACTTTT
122
+ GTTCCACCCTTCAAAACCAAGCTGACACTTTCTACAGGTGAACAAGGCGGCAGCAAGAGA
123
+ TGTCACTCACCAATCAGAAACAGTGTGATGGAGGAGAGGGAATTAAATCAAATCCCAGTT
124
+ GAACAAAATAGTGCTGAAGCTCGGGATCACCAGTCCTGCATCCTGCATGCAGCGGTCACT
125
+ GACATAGAAAATGACAATTTAGTTACAAGCAACATGATGGCAAATCTCCACTGTGCTAGA
126
+ GATCTACAGGAAATGAGAATTAAAAAGAAATATAGGCAAAATATTAGCCCACAGCCAGGC
127
+ AGCCTTTATGTCACTAAAACATCTGCAAGAAATAGAATCTCTTTGAAAACTGCAGTTGAA
128
+ GAGGAAACACCCAGTTTTCATTCTACAGAAAAGCTTTACACATACGGAGTTTCAAAACAT
129
+ TGCATACAAGTTAACAGCACAAATGCAGAATCATTTCAGTTTCTCATTGAAGAATTTTTC
130
+ AGTAAGGAGTATTTATTAGCAGGAAATGGGATACAACTTGCTGATGGAGGATGGCTGATA
131
+ CCTACAGATGAGGGAAAGGCTGGAAAAAAGGAATTTTACAGGGCTCTCTGCGATACTCCT
132
+ GGTGTGGATCCCAAGCTAATAACAGAGGCCTGGGTTTACAATCATTATAGGTGGATTGTA
133
+ TGGAAACTGGCAGCCATGGAAGTGTGTTTTCCACATAAATTTGCTAACAGATGCTTGACA
134
+ CCAGAAACAGTACTGTTGCAGTTGAAATATAGGTATGACTTGGAAATCGATAAAAGTAAA
135
+ CGATCAGCAATCAAAAAAATAACAGAGAGAGATGATGCAGCAGGTAAAACACTTGTGCTG
136
+ TGTGTTTCTAAAGTCCTATCACTGAACACTGCTGTATCTCCTAGTAATAGTAATAACAAC
137
+ ACGGAAGGTGAAAAAGCAGCAGCAATAATTGAAGTTACTGATGGCTGGTATGGGATTAGA
138
+ GCTCTTTTGGATCCACCTCTCAAAGCTTTCTTACATAGAAGAAGGCTGACTGTTGGTCAG
139
+ AAGATCATAGTGCATGGAGCAGAACTTATTGGCTCTCCAAATGGATGTACGCCACTGGAA
140
+ GCCCCAGATTCCCTTATGCTAAAGATTGCAGCAAACAGCACGCGATGCGCACGGTGGTAC
141
+ ACAAAGCTGGGATTTCATCGGGACCCCAGACCTTTCCCTTTGCCTCTGTCATCACTTTAC
142
+ AGTGAGGGTGGTACAGTGGGCTGCATTGATGTGGTTGTCCAAAGAACTTATCCTATTCAG
143
+ TGGATGGAAAAGACATCAGCTGGCTCATATGTGTTTCGTAACAGCCGAGCTGAAGAAAGG
144
+ GAAGCTGCCAAGCATGCGGAGGATCAACAAAAGAAACTGGAAGCTCTATTTGCAAAAATT
145
+ CAAGCAGAATTTGAAAAGCACGAAGAGAGAAATTGCAGAAGAGCACCAAGGTCACGCATA
146
+ GTCACAAGGCAGCAAATCCATAATTTGCAAGATGGTGCAGAACTTTATGAAGCAATTCAG
147
+ AATGCAGCTGATCCCAGTTATATGGAGGGATATCTCAGTGAAGATCAGTTAAAAGCTCTG
148
+ AATGCTCACAAGCAGCTGATGAACGATAAAAAACAAACTCGGATACGGGAAGAATTCAAG
149
+ AAGGCTGTCGAGTCTGCAGAACAGGAAAAACATGGTTTTTCCAAAAGGGATGTGTCTACT
150
+ GTATGGAAATTATTTGTGATAGACTATAGAAAGCAAGAAAAACATAGAGGAGTGATCCTG
151
+ AGTATCTGGCGTCCACTGCTGGATGTGTGTTCACTGCTGAAGGAAGGCAGTCGGTACAGA
152
+ ATCTGCCAGCTGTCAACATCGCAGTCCAAAGGAAGATCAGACTCAACTAACGTACAGTTA
153
+ TCAGCAACAAAGAAAACTCGGTATCTACAACTATCAGTCTCACAGAAGATGCTGCAGCAG
154
+ AttttttttCCAAGAAAGGCTCTCAAATTCACCAGCCTGTTGGATCCTTCTTATCAGCCA
155
+ CCATGTGCCGAAGTTGATGTAGTTGGAGTTGTAATATCCATTAGCAGGACAGGATTCTCT
156
+ AACATGGTTTATTTATCTGATGAAAGCTATAATCTTGTGGCAATAAAAATCTGGGCAGAT
157
+ CTCCGGCATTTTGCTATCGAAGATATCGTTGTCCGCTGTTCGTTCATTGCTGCAAGCAAC
158
+ CTTCAGTGGCAGTCTGAATTCAGATCAGAAATTCCTGTGCTGTTGGCCGGAGATCTTTCT
159
+ GCATTCTCAGCTAGCCCAAAGGAAAACCATCTTCAAGAGAAGTTTAATGAACTGCGAAGG
160
+ ATGATAGAGAATGTGGACTCCTTTTGCTCTGATGCAGAAAGTAAATTGATGAATTTGCTA
161
+ CAAAGAAATTGCTCACTTACACCCATTTTACCTAAGAGATGTGGTTTGGAATGCTCTTCT
162
+ CCTTCCTGCAACTCAGGCCTTTATGCAGAAGATAGAAGTTCGATCTCTTCCAAAATTGAA
163
+ ACGAAGCATCCAAGCCCCTTGTCAGCTAGCACACCAAATACAAAGCTTTTCCCACAAGGC
164
+ TCAGCAATAACGCCTTCATCTGCTGTAAGTAGTGAGAACCATCCCAGAAACAGCAAAAAG
165
+ AGAAAAGCAGTGGACTTCCTCAGCTGCATACCTGCCCCTCCACCACTGACACCGCTCTGT
166
+ TCCATCATTTCTCCATCTTTAAAAAAGGCATTTCAGCCTCCGCGACGTTTGGGCTCACAG
167
+ CATAGCAAGTTATCAAAAGAAACAAACCCAAACGCTGGTTGTGTCACCCCCAGTAGAAGA
168
+ CTGAGAGAAGCTGTCCAGCTTCCTGATAATGACCTGGTTGCTGATGAAGAACTTGCAATG
169
+ ATTAATACACAAGCACTCATAAATACTGTACCGGAAGAAAAGAAGATGGATTATGTAAAT
170
+ GAAGACAGTACAAGGGCTACTAACTTATCTGGTGATACAAGAGCTACTAATTTATCTCGT
171
+ GATATGAGGGCTCCTAATTTATCTGGTGATCTTTCATCCAAAAATAGTTCCAGATCTGCT
172
+ AAGGAAGCAAACAGTTCATTGAAAAGCAGTTCTGAAGGAGCTGATGCTCTCCAGAAGGAC
173
+ ACAGAGGAACCTGAGGGTTCGTTATCAATCCGCAGAGTGCTGCAAAGGCGCAAATCCCGC
174
+ AAATGCTACTAGATGCACATGTACAGTACTGTGTATATTTCAAATTTAAATGTTTTTACT
175
+ TTGTACATTAAAGCCTGATTGTAATAAAGTTACATTACAAAATTCAT
@@ -0,0 +1,2 @@
1
+ >short
2
+ GCTTCTGAAGCAGGGGAAGATACTAATTTCTATAGCACTCTTAAATCTGAAAATCATGTA
data/test/helper.rb ADDED
@@ -0,0 +1,18 @@
1
+ require 'rubygems'
2
+ require 'bundler'
3
+ begin
4
+ Bundler.setup(:default, :development)
5
+ rescue Bundler::BundlerError => e
6
+ $stderr.puts e.message
7
+ $stderr.puts "Run `bundle install` to install missing gems"
8
+ exit e.status_code
9
+ end
10
+ require 'test/unit'
11
+ require 'shoulda'
12
+
13
+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
14
+ $LOAD_PATH.unshift(File.dirname(__FILE__))
15
+ require 'bio-bwa'
16
+
17
+ class Test::Unit::TestCase
18
+ end
@@ -0,0 +1,62 @@
1
+
2
+ $:<<"."
3
+ require 'test/helper'
4
+ require 'digest/md5'
5
+
6
+ class TestBioBwa < Test::Unit::TestCase
7
+
8
+ def setup
9
+ @testdata = File.join("test","data","testdata")
10
+ end
11
+
12
+ def test_1bwa_fa2pac
13
+ Bio::BWA.fa2pac(:file_in => "#{@testdata}.fa",:prefix => @testdata)
14
+ md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.pac","rb") {|f| f.read})
15
+ assert_equal("31ab6686d10cf980b9fc910854a38a7a",md5)
16
+ end
17
+
18
+
19
+ def test_2pac2bwt
20
+ out = "#{@testdata}.bwt"
21
+ Bio::BWA.pac2bwt(:file_in => "#{@testdata}.pac",:file_out => out)
22
+ md5 = Digest::MD5::hexdigest(File.open(out,"rb") {|f| f.read})
23
+ assert_equal("3c5e20c123ed8ab961287933e9734e70",md5)
24
+ end
25
+
26
+ def test_4bwtupdate
27
+ out = File.join("test","data","testdata.bwt")
28
+ FileUtils.cp out,"#{@testdata}.updated.bwt"
29
+ Bio::BWA.bwtupdate(:file_in => "#{@testdata}.updated.bwt")
30
+ md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.updated.bwt","rb") {|f| f.read})
31
+ assert_equal("4f7ee2b68fade083421d8fd93bf024ec",md5)
32
+ FileUtils.rm(out)
33
+ end
34
+
35
+ def test_3pac_rev
36
+ out = File.join("test","data","out.rev.pac")
37
+ Bio::BWA.pac_rev(:file_in => "#{@testdata}.pac",:file_out => out)
38
+ md5 = Digest::MD5::hexdigest(File.open(out,"rb") {|f| f.read})
39
+ assert_equal("879cd21435a314f672c7de6d13977d69",md5)
40
+ FileUtils.rm(out)
41
+ end
42
+
43
+ def test_5bwt2sa
44
+ out = File.join("test","data","out.sa")
45
+ bwt = File.join("test","data","testdata.updated.bwt")
46
+ Bio::BWA.bwt2sa(:file_in => bwt,:file_out => out)
47
+ md5 = Digest::MD5::hexdigest(File.open(out,"rb") {|f| f.read})
48
+ assert_equal("948d0ebf6176f61de3ecdc8c085ae88a",md5)
49
+ FileUtils.rm(out)
50
+ FileUtils.rm(bwt)
51
+ FileUtils.rm("#{@testdata}.pac")
52
+ FileUtils.rm("#{@testdata}.amb")
53
+ FileUtils.rm("#{@testdata}.ann")
54
+ end
55
+
56
+ def test_no_method
57
+ assert_raise NoMethodError do
58
+ Bio::BWA.fake_method("some_file")
59
+ end
60
+ end
61
+
62
+ end
@@ -0,0 +1,42 @@
1
+
2
+ $:<<"."
3
+ require 'test/helper'
4
+ require 'digest/md5'
5
+
6
+ class TestBwaIndex < Test::Unit::TestCase
7
+
8
+ def setup
9
+ @testdata = File.join("test","data","testdata")
10
+ end
11
+
12
+ def test_make_index_colorspace
13
+ out = File.join("test","data","out")
14
+ Bio::BWA.make_index(:file_in=>"#{@testdata}.fa",:a => 'is',:prefix => "#{out}", :c => true)
15
+ md5_rbwt = Digest::MD5::hexdigest(File.open("#{out}.rbwt","rb") {|f| f.read})
16
+ md5_rpac = Digest::MD5::hexdigest(File.open("#{out}.rpac","rb") {|f| f.read})
17
+ md5_bwt = Digest::MD5::hexdigest(File.open("#{out}.bwt","rb") {|f| f.read})
18
+ md5_pac = Digest::MD5::hexdigest(File.open("#{out}.pac","rb") {|f| f.read})
19
+ md5_sa = Digest::MD5::hexdigest(File.open("#{out}.sa","rb") {|f| f.read})
20
+ assert_equal("6d6fd723604377dc5d6ad6c0f4f1cdf6",md5_rbwt)
21
+ assert_equal("64838ba5ad44f662266853ebc9451191",md5_rpac)
22
+ assert_equal("12fb7007102154f4bc428ea01a99a6ea",md5_bwt)
23
+ assert_equal("8cb0c5f86a5b927c233e3d5268f01f6a",md5_pac)
24
+ assert_equal("95711a0e5c06419017a02c73d12b99a2",md5_sa)
25
+ FileUtils.rm Dir.glob(out+".*")
26
+ end
27
+
28
+ def test_make_index
29
+ Bio::BWA.make_index(:file_in=>"#{@testdata}.fa",:a => 'is',:prefix => "#{@testdata}")
30
+ md5_bwt = Digest::MD5::hexdigest(File.open("#{@testdata}.bwt","rb") {|f| f.read})
31
+ md5_pac = Digest::MD5::hexdigest(File.open("#{@testdata}.pac","rb") {|f| f.read})
32
+ assert_equal("4f7ee2b68fade083421d8fd93bf024ec",md5_bwt)
33
+ assert_equal("31ab6686d10cf980b9fc910854a38a7a",md5_pac)
34
+ end
35
+
36
+ def test_errors
37
+ assert_raise ArgumentError do
38
+ Bio::BWA.make_index(:a => 'is',:prefix => "foo", :c => true)
39
+ end
40
+ end
41
+
42
+ end
@@ -0,0 +1,49 @@
1
+ $:<<"."
2
+ require 'test/helper'
3
+ require 'digest/md5'
4
+
5
+ class TestBioBwa < Test::Unit::TestCase
6
+
7
+ def setup
8
+ @testdata = File.join("test","data","testdata")
9
+ end
10
+
11
+ def test_short_read_alignment
12
+ assert_nothing_raised do
13
+ Bio::BWA.short_read_alignment(:prefix=>"#{@testdata}",:file_in=>"#{@testdata}.fa",:file_out=>"#{@testdata}.sai")
14
+ end
15
+ md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.sai","rb") {|f| f.read})
16
+ assert_equal("56793f4473805683a7d494808c19f79e",md5)
17
+ end
18
+
19
+ def test_long_read_alignment
20
+ assert_nothing_raised do
21
+ Bio::BWA.long_read_alignment(:prefix=>"#{@testdata}",:file_in=>"#{@testdata}.fa", :file_out=>"#{@testdata}.bwasw")
22
+ end
23
+ md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.bwasw","rb") {|f| f.read})
24
+ assert_equal("f569b0dfa7482d468bc68eb8151fb117",md5)
25
+ FileUtils.rm("#{@testdata}.bwasw")
26
+ end
27
+
28
+ def test_simple_SW
29
+ if RUBY_PLATFORM != 'java' then # the method redirect STDOUT to a file and this test does not pass in JRuby
30
+ assert_nothing_raised do
31
+ Bio::BWA.simple_SW(:long_seq=>"#{@testdata}.long.fa",:short_seq=>"#{@testdata}.short.fa",:f => true,:file_out => "#{@testdata}.stdsw")
32
+ end
33
+ md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.stdsw","rb") {|f| f.read})
34
+ assert_equal("cedb41d4ba3581111fbcefec6063dc86",md5)
35
+ FileUtils.rm("#{@testdata}.stdsw")
36
+ end
37
+ end
38
+
39
+ def test_errors
40
+ assert_raise ArgumentError do
41
+ Bio::BWA.long_read_alignment(:prefix=>"#{@testdata}",:file_out=>"#{@testdata}.fa")
42
+ end
43
+
44
+ assert_raise ArgumentError do
45
+ Bio::BWA.long_read_alignment(:prefix=>"#{@testdata}",:file_in=>"#{@testdata}.fa", :file_out=>"#{@testdata}.bwasw", :unknown_parameter => "foo")
46
+ end
47
+ end
48
+
49
+ end
@@ -0,0 +1,49 @@
1
+ $:<<"."
2
+ require 'test/helper'
3
+ require 'digest/md5'
4
+
5
+ class TestBioBwa < Test::Unit::TestCase
6
+
7
+ def setup
8
+ @testdata = File.join("test","data","testdata")
9
+ end
10
+
11
+ def test_sai_to_sam_single
12
+ assert_nothing_raised do
13
+ Bio::BWA.sai_to_sam_single(:prefix=>"#{@testdata}",:sai=>"#{@testdata}.sai",:fastq=>"#{@testdata}.fa",:file_out => "#{@testdata}.sam")
14
+ end
15
+ md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.sam","rb") {|f| f.read})
16
+ assert_equal("5c523ae7bf18656190fa0bcd8944bd14",md5)
17
+ FileUtils.rm("#{@testdata}.sam")
18
+ end
19
+
20
+ def test_sai_to_sam_paired
21
+ assert_nothing_raised do
22
+ Bio::BWA.sai_to_sam_paired(:prefix=>"#{@testdata}",:sai=>["#{@testdata}.sai","#{@testdata}.sai"],:fastq=>["#{@testdata}.fa","#{@testdata}.fa"],:file_out => "#{@testdata}.sampe")
23
+ end
24
+ md5 = Digest::MD5::hexdigest(File.open("#{@testdata}.sampe","rb") {|f| f.read})
25
+ assert_equal("8c3847bade0a19e5de77c274355fe154",md5)
26
+ FileUtils.rm("#{@testdata}.sampe")
27
+ end
28
+
29
+ def test_zomg_cleanup
30
+ assert_nothing_raised do
31
+ list = Dir.glob("#{@testdata}.*")
32
+ list.delete("#{@testdata}.fa")
33
+ list.delete("#{@testdata}.long.fa")
34
+ list.delete("#{@testdata}.short.fa")
35
+ list.each {|l| FileUtils.rm(l)}
36
+ end
37
+ end
38
+
39
+ def test_errors
40
+ assert_raise ArgumentError do
41
+ Bio::BWA.sai_to_sam_single(:prefix=>"#{@testdata}",:fastq=>"#{@testdata}.fa",:file_out => "#{@testdata}.sam")
42
+ end
43
+
44
+ assert_raise ArgumentError do
45
+ Bio::BWA.sai_to_sam_paired(:prefix=>"#{@testdata}",:sai=>"#{@testdata}.sai",:fastq=>["#{@testdata}.fa","#{@testdata}.fa"],:file_out => "#{@testdata}.sampe")
46
+ end
47
+ end
48
+
49
+ end
metadata ADDED
@@ -0,0 +1,218 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: bio-bwa
3
+ version: !ruby/object:Gem::Version
4
+ prerelease:
5
+ version: 0.2.0
6
+ platform: ruby
7
+ authors:
8
+ - Francesco Strozzi
9
+ autorequire:
10
+ bindir: bin
11
+ cert_chain: []
12
+
13
+ date: 2011-03-22 00:00:00 +01:00
14
+ default_executable:
15
+ dependencies:
16
+ - !ruby/object:Gem::Dependency
17
+ name: shoulda
18
+ requirement: &id001 !ruby/object:Gem::Requirement
19
+ none: false
20
+ requirements:
21
+ - - ">="
22
+ - !ruby/object:Gem::Version
23
+ version: "0"
24
+ type: :development
25
+ prerelease: false
26
+ version_requirements: *id001
27
+ - !ruby/object:Gem::Dependency
28
+ name: bundler
29
+ requirement: &id002 !ruby/object:Gem::Requirement
30
+ none: false
31
+ requirements:
32
+ - - ~>
33
+ - !ruby/object:Gem::Version
34
+ version: 1.0.0
35
+ type: :development
36
+ prerelease: false
37
+ version_requirements: *id002
38
+ - !ruby/object:Gem::Dependency
39
+ name: jeweler
40
+ requirement: &id003 !ruby/object:Gem::Requirement
41
+ none: false
42
+ requirements:
43
+ - - ~>
44
+ - !ruby/object:Gem::Version
45
+ version: 1.5.2
46
+ type: :development
47
+ prerelease: false
48
+ version_requirements: *id003
49
+ - !ruby/object:Gem::Dependency
50
+ name: rcov
51
+ requirement: &id004 !ruby/object:Gem::Requirement
52
+ none: false
53
+ requirements:
54
+ - - ">="
55
+ - !ruby/object:Gem::Version
56
+ version: "0"
57
+ type: :development
58
+ prerelease: false
59
+ version_requirements: *id004
60
+ - !ruby/object:Gem::Dependency
61
+ name: bio
62
+ requirement: &id005 !ruby/object:Gem::Requirement
63
+ none: false
64
+ requirements:
65
+ - - ">="
66
+ - !ruby/object:Gem::Version
67
+ version: 1.4.1
68
+ type: :development
69
+ prerelease: false
70
+ version_requirements: *id005
71
+ - !ruby/object:Gem::Dependency
72
+ name: ffi
73
+ requirement: &id006 !ruby/object:Gem::Requirement
74
+ none: false
75
+ requirements:
76
+ - - ">="
77
+ - !ruby/object:Gem::Version
78
+ version: 1.0.5
79
+ type: :development
80
+ prerelease: false
81
+ version_requirements: *id006
82
+ description: Ruby binding for BWA mapping software, built using Ruby-FFI library
83
+ email: francesco.strozzi@gmail.com
84
+ executables: []
85
+
86
+ extensions:
87
+ - ext/mkrf_conf.rb
88
+ extra_rdoc_files:
89
+ - LICENSE.txt
90
+ - README.rdoc
91
+ files:
92
+ - .document
93
+ - Gemfile
94
+ - Gemfile.lock
95
+ - LICENSE.txt
96
+ - README.rdoc
97
+ - Rakefile
98
+ - VERSION
99
+ - bio-bwa.gemspec
100
+ - doc/Bio.html
101
+ - doc/Bio/BWA.html
102
+ - doc/Bio/BWA/Library.html
103
+ - doc/_index.html
104
+ - doc/class_list.html
105
+ - doc/css/common.css
106
+ - doc/css/full_list.css
107
+ - doc/css/style.css
108
+ - doc/file.LICENSE.html
109
+ - doc/file.README.html
110
+ - doc/file_list.html
111
+ - doc/frames.html
112
+ - doc/index.html
113
+ - doc/js/app.js
114
+ - doc/js/full_list.js
115
+ - doc/js/jquery.js
116
+ - doc/method_list.html
117
+ - doc/top-level-namespace.html
118
+ - ext/COPYING
119
+ - ext/ChangeLog
120
+ - ext/NEWS
121
+ - ext/README
122
+ - ext/bamlite.c
123
+ - ext/bamlite.h
124
+ - ext/bntseq.c
125
+ - ext/bntseq.h
126
+ - ext/bwa.1
127
+ - ext/bwape.c
128
+ - ext/bwase.c
129
+ - ext/bwase.h
130
+ - ext/bwaseqio.c
131
+ - ext/bwt.c
132
+ - ext/bwt.h
133
+ - ext/bwt_gen/Makefile
134
+ - ext/bwt_gen/QSufSort.c
135
+ - ext/bwt_gen/QSufSort.h
136
+ - ext/bwt_gen/bwt_gen.c
137
+ - ext/bwt_gen/bwt_gen.h
138
+ - ext/bwt_lite.c
139
+ - ext/bwt_lite.h
140
+ - ext/bwtaln.c
141
+ - ext/bwtaln.h
142
+ - ext/bwtgap.c
143
+ - ext/bwtgap.h
144
+ - ext/bwtindex.c
145
+ - ext/bwtio.c
146
+ - ext/bwtmisc.c
147
+ - ext/bwtsw2.h
148
+ - ext/bwtsw2_aux.c
149
+ - ext/bwtsw2_chain.c
150
+ - ext/bwtsw2_core.c
151
+ - ext/bwtsw2_main.c
152
+ - ext/cs2nt.c
153
+ - ext/is.c
154
+ - ext/khash.h
155
+ - ext/kseq.h
156
+ - ext/ksort.h
157
+ - ext/kstring.c
158
+ - ext/kstring.h
159
+ - ext/kvec.h
160
+ - ext/main.c
161
+ - ext/main.h
162
+ - ext/mkrf_conf.rb
163
+ - ext/qualfa2fq.pl
164
+ - ext/simple_dp.c
165
+ - ext/simpletest.c
166
+ - ext/solid2fastq.pl
167
+ - ext/stdaln.c
168
+ - ext/stdaln.h
169
+ - ext/utils.c
170
+ - ext/utils.h
171
+ - lib/bio-bwa.rb
172
+ - lib/bio/bwa.rb
173
+ - lib/bio/bwa/library.rb
174
+ - test/data/testdata.fa
175
+ - test/data/testdata.long.fa
176
+ - test/data/testdata.short.fa
177
+ - test/helper.rb
178
+ - test/test_bio-bwa_basic.rb
179
+ - test/test_bio-bwa_make_index.rb
180
+ - test/test_bio-bwa_run_aln.rb
181
+ - test/test_bio-bwa_sam_conversion.rb
182
+ has_rdoc: true
183
+ homepage: http://github.com/fstrozzi/bioruby-bwa
184
+ licenses:
185
+ - MIT/GPLv3
186
+ post_install_message:
187
+ rdoc_options: []
188
+
189
+ require_paths:
190
+ - lib
191
+ required_ruby_version: !ruby/object:Gem::Requirement
192
+ none: false
193
+ requirements:
194
+ - - ">="
195
+ - !ruby/object:Gem::Version
196
+ hash: -1510626449413692226
197
+ segments:
198
+ - 0
199
+ version: "0"
200
+ required_rubygems_version: !ruby/object:Gem::Requirement
201
+ none: false
202
+ requirements:
203
+ - - ">="
204
+ - !ruby/object:Gem::Version
205
+ version: "0"
206
+ requirements: []
207
+
208
+ rubyforge_project:
209
+ rubygems_version: 1.6.2
210
+ signing_key:
211
+ specification_version: 3
212
+ summary: Ruby binding for BWA mapping software
213
+ test_files:
214
+ - test/helper.rb
215
+ - test/test_bio-bwa_basic.rb
216
+ - test/test_bio-bwa_make_index.rb
217
+ - test/test_bio-bwa_run_aln.rb
218
+ - test/test_bio-bwa_sam_conversion.rb