qu-cmdwrapper 1.0.0

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 (67) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +17 -0
  3. data/Gemfile +5 -0
  4. data/LICENSE.txt +22 -0
  5. data/README.md +32 -0
  6. data/Rakefile +1 -0
  7. data/lib/qu/cmdwrapper.rb +10 -0
  8. data/lib/qu/cmdwrapper/cmd.rb +109 -0
  9. data/lib/qu/cmdwrapper/ext_bin/linux/32/faToTwoBit +0 -0
  10. data/lib/qu/cmdwrapper/ext_bin/linux/32/ntdpal +0 -0
  11. data/lib/qu/cmdwrapper/ext_bin/linux/32/ntthal +0 -0
  12. data/lib/qu/cmdwrapper/ext_bin/linux/32/oligotm +0 -0
  13. data/lib/qu/cmdwrapper/ext_bin/linux/32/primer3_core +0 -0
  14. data/lib/qu/cmdwrapper/ext_bin/linux/32/twoBitToFa +0 -0
  15. data/lib/qu/cmdwrapper/ext_bin/linux/64/faToTwoBit +0 -0
  16. data/lib/qu/cmdwrapper/ext_bin/linux/64/ntdpal +0 -0
  17. data/lib/qu/cmdwrapper/ext_bin/linux/64/ntthal +0 -0
  18. data/lib/qu/cmdwrapper/ext_bin/linux/64/oligotm +0 -0
  19. data/lib/qu/cmdwrapper/ext_bin/linux/64/primer3_core +0 -0
  20. data/lib/qu/cmdwrapper/ext_bin/linux/64/twoBitToFa +0 -0
  21. data/lib/qu/cmdwrapper/ext_bin/mac/32/faToTwoBit +0 -0
  22. data/lib/qu/cmdwrapper/ext_bin/mac/32/ntthal +0 -0
  23. data/lib/qu/cmdwrapper/ext_bin/mac/32/oligotm +0 -0
  24. data/lib/qu/cmdwrapper/ext_bin/mac/32/primer3_core +0 -0
  25. data/lib/qu/cmdwrapper/ext_bin/mac/32/twoBitToFa +0 -0
  26. data/lib/qu/cmdwrapper/ext_bin/mac/64/faToTwoBit +0 -0
  27. data/lib/qu/cmdwrapper/ext_bin/mac/64/ntthal +0 -0
  28. data/lib/qu/cmdwrapper/ext_bin/mac/64/oligotm +0 -0
  29. data/lib/qu/cmdwrapper/ext_bin/mac/64/primer3_core +0 -0
  30. data/lib/qu/cmdwrapper/ext_bin/mac/64/twoBitToFa +0 -0
  31. data/lib/qu/cmdwrapper/primer3_config/dangle.dh +128 -0
  32. data/lib/qu/cmdwrapper/primer3_config/dangle.ds +128 -0
  33. data/lib/qu/cmdwrapper/primer3_config/interpretations/dangle_i.dh +131 -0
  34. data/lib/qu/cmdwrapper/primer3_config/interpretations/dangle_i.ds +131 -0
  35. data/lib/qu/cmdwrapper/primer3_config/interpretations/loops_i.dh +34 -0
  36. data/lib/qu/cmdwrapper/primer3_config/interpretations/loops_i.ds +31 -0
  37. data/lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.dh +257 -0
  38. data/lib/qu/cmdwrapper/primer3_config/interpretations/stack_i.ds +256 -0
  39. data/lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.dh +257 -0
  40. data/lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.ds +256 -0
  41. data/lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.dh +79 -0
  42. data/lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.ds +81 -0
  43. data/lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.dh +21 -0
  44. data/lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.ds +18 -0
  45. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.dh +256 -0
  46. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack2_i.ds +256 -0
  47. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_i.dh +256 -0
  48. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_i.ds +256 -0
  49. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_tm_inf_i.dh +256 -0
  50. data/lib/qu/cmdwrapper/primer3_config/interpretations/tstack_tm_inf_i.ds +256 -0
  51. data/lib/qu/cmdwrapper/primer3_config/loops.dh +30 -0
  52. data/lib/qu/cmdwrapper/primer3_config/loops.ds +30 -0
  53. data/lib/qu/cmdwrapper/primer3_config/stack.dh +256 -0
  54. data/lib/qu/cmdwrapper/primer3_config/stack.ds +256 -0
  55. data/lib/qu/cmdwrapper/primer3_config/stackmm.dh +256 -0
  56. data/lib/qu/cmdwrapper/primer3_config/stackmm.ds +256 -0
  57. data/lib/qu/cmdwrapper/primer3_config/tetraloop.dh +77 -0
  58. data/lib/qu/cmdwrapper/primer3_config/tetraloop.ds +77 -0
  59. data/lib/qu/cmdwrapper/primer3_config/triloop.dh +16 -0
  60. data/lib/qu/cmdwrapper/primer3_config/triloop.ds +16 -0
  61. data/lib/qu/cmdwrapper/primer3_config/tstack.dh +256 -0
  62. data/lib/qu/cmdwrapper/primer3_config/tstack2.dh +256 -0
  63. data/lib/qu/cmdwrapper/primer3_config/tstack2.ds +256 -0
  64. data/lib/qu/cmdwrapper/primer3_config/tstack_tm_inf.ds +256 -0
  65. data/lib/qu/cmdwrapper/version.rb +5 -0
  66. data/qu-cmdwrapper.gemspec +24 -0
  67. metadata +137 -0
data/lib/qu/cmdwrapper/primer3_config/interpretations/stackmm_i_mm.ds ADDED
@@ -0,0 +1,256 @@
1
+ AA_AA inf
2
+ AA_AC inf
3
+ AA_AG inf
4
+ AA_AT 12.9
5
+ AA_CA inf
6
+ AA_CC inf
7
+ AA_CG inf
8
+ AA_CT 20.2
9
+ AA_GA inf
10
+ AA_GC inf
11
+ AA_GG inf
12
+ AA_GT 7.4
13
+ AA_TA 1.7
14
+ AA_TC 4.6
15
+ AA_TG -2.3
16
+ AA_TT inf
17
+ AC_AA inf
18
+ AC_AC inf
19
+ AC_AG -9.8
20
+ AC_AT inf
21
+ AC_CA inf
22
+ AC_CC inf
23
+ AC_CG -3.8
24
+ AC_CT inf
25
+ AC_GA inf
26
+ AC_GC inf
27
+ AC_GG 3.2
28
+ AC_GT inf
29
+ AC_TA 14.6
30
+ AC_TC -4.4
31
+ AC_TG inf
32
+ AC_TT 0.2
33
+ AG_AA inf
34
+ AG_AC -4.2
35
+ AG_AG inf
36
+ AG_AT inf
37
+ AG_CA inf
38
+ AG_CC 0.6
39
+ AG_CG inf
40
+ AG_CT inf
41
+ AG_GA inf
42
+ AG_GC -13.2
43
+ AG_GG inf
44
+ AG_GT inf
45
+ AG_TA -2.3
46
+ AG_TC inf
47
+ AG_TG -9.5
48
+ AG_TT 0.9
49
+ AT_AA 1.7
50
+ AT_AC inf
51
+ AT_AG inf
52
+ AT_AT inf
53
+ AT_CA 14.6
54
+ AT_CC inf
55
+ AT_CG inf
56
+ AT_CT inf
57
+ AT_GA -2.3
58
+ AT_GC inf
59
+ AT_GG inf
60
+ AT_GT inf
61
+ AT_TA inf
62
+ AT_TC -6.2
63
+ AT_TG -8.3
64
+ AT_TT -10.8
65
+ CA_AA inf
66
+ CA_AC inf
67
+ CA_AG inf
68
+ CA_AT 8.0
69
+ CA_CA inf
70
+ CA_CC inf
71
+ CA_CG inf
72
+ CA_CT 16.4
73
+ CA_GA -4.2
74
+ CA_GC 3.7
75
+ CA_GG -2.3
76
+ CA_GT inf
77
+ CA_TA inf
78
+ CA_TC inf
79
+ CA_TG inf
80
+ CA_TT 0.7
81
+ CC_AA inf
82
+ CC_AC inf
83
+ CC_AG 14.2
84
+ CC_AT inf
85
+ CC_CA inf
86
+ CC_CC inf
87
+ CC_CG 8.9
88
+ CC_CT inf
89
+ CC_GA -0.6
90
+ CC_GC -7.2
91
+ CC_GG -19.9
92
+ CC_GT -4.5
93
+ CC_TA inf
94
+ CC_TC inf
95
+ CC_TG 13.5
96
+ CC_TT inf
97
+ CG_AA inf
98
+ CG_AC 3.7
99
+ CG_AG inf
100
+ CG_AT inf
101
+ CG_CA inf
102
+ CG_CC -7.2
103
+ CG_CG inf
104
+ CG_CT inf
105
+ CG_GA -13.2
106
+ CG_GC inf
107
+ CG_GG -15.3
108
+ CG_GT -11.7
109
+ CG_TA inf
110
+ CG_TC -6.1
111
+ CG_TG inf
112
+ CG_TT inf
113
+ CT_AA 4.6
114
+ CT_AC inf
115
+ CT_AG inf
116
+ CT_AT inf
117
+ CT_CA -4.4
118
+ CT_CC inf
119
+ CT_CG inf
120
+ CT_CT inf
121
+ CT_GA inf
122
+ CT_GC -6.1
123
+ CT_GG -8.0
124
+ CT_GT -15.8
125
+ CT_TA -6.2
126
+ CT_TC inf
127
+ CT_TG inf
128
+ CT_TT inf
129
+ GA_AA inf
130
+ GA_AC inf
131
+ GA_AG inf
132
+ GA_AT 0.7
133
+ GA_CA -9.8
134
+ GA_CC 14.2
135
+ GA_CG -1.0
136
+ GA_CT inf
137
+ GA_GA inf
138
+ GA_GC inf
139
+ GA_GG inf
140
+ GA_GT 3.6
141
+ GA_TA inf
142
+ GA_TC inf
143
+ GA_TG inf
144
+ GA_TT -5.3
145
+ GC_AA inf
146
+ GC_AC inf
147
+ GC_AG -1.0
148
+ GC_AT inf
149
+ GC_CA -3.8
150
+ GC_CC 8.9
151
+ GC_CG inf
152
+ GC_CT 5.4
153
+ GC_GA inf
154
+ GC_GC inf
155
+ GC_GG -15.8
156
+ GC_GT inf
157
+ GC_TA inf
158
+ GC_TC inf
159
+ GC_TG -12.3
160
+ GC_TT inf
161
+ GG_AA inf
162
+ GG_AC -2.3
163
+ GG_AG inf
164
+ GG_AT inf
165
+ GG_CA 3.2
166
+ GG_CC -19.9
167
+ GG_CG -15.8
168
+ GG_CT 10.4
169
+ GG_GA inf
170
+ GG_GC -15.3
171
+ GG_GG inf
172
+ GG_GT inf
173
+ GG_TA inf
174
+ GG_TC 80
175
+ GG_TG inf
176
+ GG_TT 16.3
177
+ GT_AA 23
178
+ GT_AC inf
179
+ GT_AG inf
180
+ GT_AT inf
181
+ GT_CA inf
182
+ GT_CC 13.5
183
+ GT_CG -12.3
184
+ GT_CT -8.4
185
+ GT_GA -9.5
186
+ GT_GC inf
187
+ GT_GG inf
188
+ GT_GT inf
189
+ GT_TA -8.3
190
+ GT_TC inf
191
+ GT_TG 9.5
192
+ GT_TT inf
193
+ TA_AA 12.9
194
+ TA_AC 8.0
195
+ TA_AG 0.7
196
+ TA_AT inf
197
+ TA_CA inf
198
+ TA_CC inf
199
+ TA_CG inf
200
+ TA_CT 0.7
201
+ TA_GA inf
202
+ TA_GC inf
203
+ TA_GG inf
204
+ TA_GT -1.7
205
+ TA_TA inf
206
+ TA_TC inf
207
+ TA_TG inf
208
+ TA_TT -1.5
209
+ TC_AA 20.2
210
+ TC_AC 16.4
211
+ TC_AG inf
212
+ TC_AT 0.7
213
+ TC_CA inf
214
+ TC_CC inf
215
+ TC_CG 5.4
216
+ TC_CT inf
217
+ TC_GA inf
218
+ TC_GC inf
219
+ TC_GG 10.4
220
+ TC_GT inf
221
+ TC_TA inf
222
+ TC_TC inf
223
+ TC_TG -8.4
224
+ TC_TT inf
225
+ TG_AA 7.4
226
+ TG_AC inf
227
+ TG_AG 3.6
228
+ TG_AT -1.7
229
+ TG_CA inf
230
+ TG_CC -4.5
231
+ TG_CG inf
232
+ TG_CT inf
233
+ TG_GA inf
234
+ TG_GC -11.7
235
+ TG_GG inf
236
+ TG_GT -6.2
237
+ TG_TA inf
238
+ TG_TC -15.8
239
+ TG_TG inf
240
+ TG_TT inf
241
+ TT_AA inf
242
+ TT_AC -7
243
+ TT_AG -5.3
244
+ TT_AT -1.5
245
+ TT_CA 0.2
246
+ TT_CC inf
247
+ TT_CG inf
248
+ TT_CT inf
249
+ TT_GA 0.9
250
+ TT_GC inf
251
+ TT_GG 16.3
252
+ TT_GT inf
253
+ TT_TA -10.8
254
+ TT_TC inf
255
+ TT_TG inf
256
+ TT_TT inf
data/lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.dh ADDED
@@ -0,0 +1,79 @@
1
+ /* tetraloop bonuses for GNRA and GNAB kcal/mol*(-10) */
2
+
3
+ AAAAAT -5
4
+ AAAACT -7
5
+ AAACAT -10
6
+ ACTTGT 0
7
+ AGAAAT 11
8
+ AGAGAT 11
9
+ AGATAT 15
10
+ AGCAAT 16
11
+ AGCGAT 11
12
+ AGCTTT -2
13
+ AGGAAT 11
14
+ AGGGAT 11
15
+ AGGGGT -5
16
+ AGTAAT 16
17
+ AGTGAT 11
18
+ AGTTCT -8
19
+ ATTCGT 2
20
+ ATTTGT 0
21
+ ATTTTT 5
22
+ CAAAAG -5
23
+ CAAACG -7
24
+ CAACAG -10
25
+ CAACCG 0
26
+ CCTTGG 0
27
+ CGAAAG 11
28
+ CGAGAG 11
29
+ CGATAG 15
30
+ CGCAAG 16
31
+ CGCGAG 11
32
+ CGCTTG -2
33
+ CGGAAG 11
34
+ CGGGAG 10
35
+ CGGGGG -5
36
+ CGTAAG 16
37
+ CGTGAG 11
38
+ CGTTCG -8
39
+ CTTCGG 2
40
+ CTTTGG 0
41
+ CTTTTG 5
42
+ GAAAAC -5
43
+ GAAACC -7
44
+ GAACAC -10
45
+ GCTTGC 0
46
+ GGAAAC 11
47
+ GGAGAC 11
48
+ GGATAC 16
49
+ GGCAAC 16
50
+ GGCGAC 11
51
+ GGCTTC -2
52
+ GGGAAC 11
53
+ GGGGAC 11
54
+ GGGGGC -5
55
+ GGTAAC 16
56
+ GGTGAC 11
57
+ GGTTCC -8
58
+ GTTCGC 2
59
+ GTTTGC 0
60
+ GTTTTC 5
61
+ TAAAAA -5
62
+ TAAACA -7
63
+ TAACAA -10
64
+ TCTTGA 0
65
+ TGAAAA 11
66
+ TGAGAA 11
67
+ TGATAA 16
68
+ TGCAAA 16
69
+ TGCGAA 11
70
+ TGCTTA -2
71
+ TGGAAA 11
72
+ TGGGAA 11
73
+ TGGGGA -5
74
+ TGTAAA 16
75
+ TGTGAA 11
76
+ TGTTCA -8
77
+ TTTCGA 2
78
+ TTTTGA 0
79
+ TTTTTA 5
data/lib/qu/cmdwrapper/primer3_config/interpretations/tetraloop_i.ds ADDED
@@ -0,0 +1,81 @@
1
+ /*
2
+ VIIDE
3
+ */
4
+
5
+ AAAAAT 6.5
6
+ AAAACT -16.1
7
+ AAACAT -16.1
8
+ ACTTGT -41.9
9
+ AGAAAT -16.1
10
+ AGAGAT -16.1
11
+ AGATAT -16.1
12
+ AGCAAT -16.1
13
+ AGCGAT -16.1
14
+ AGCTTT -16.1
15
+ AGGAAT -16.1
16
+ AGGGAT -16.1
17
+ AGGGGT -6.4
18
+ AGTAAT -16.1
19
+ AGTGAT -16.1
20
+ AGTTCT -16.1
21
+ ATTCGT -16.1
22
+ ATTTGT -16.1
23
+ ATTTTT -16.1
24
+ CAAAAG 12.9
25
+ CAAACG 0
26
+ CAACAG 0
27
+ CAACCG 0
28
+ CCTTGG -25.7
29
+ CGAAAG 0
30
+ CGAGAG 0
31
+ CGATAG 0
32
+ CGCAAG 0
33
+ CGCGAG 0
34
+ CGCTTG 0
35
+ CGGAAG 0
36
+ CGGGAG 0
37
+ CGGGGG 9.7
38
+ CGTAAG 0
39
+ CGTGAG 0
40
+ CGTTCG 0
41
+ CTTCGG 0
42
+ CTTTGG 0
43
+ CTTTTG 0
44
+ GAAAAC 32.3
45
+ GAAACC 0
46
+ GAACAC 0
47
+ GCTTGC -25.7
48
+ GGAAAC 0
49
+ GGAGAC 0
50
+ GGATAC 0
51
+ GGCAAC 0
52
+ GGCGAC 0
53
+ GGCTTC 0
54
+ GGGAAC 0
55
+ GGGGAC 0
56
+ GGGGGC 9.7
57
+ GGTAAC 0
58
+ GGTGAC 0
59
+ GGTTCC 0
60
+ GTTCGC 0
61
+ GTTTGC 0
62
+ GTTTTC 0
63
+ TAAAAA -3.2
64
+ TAAACA -16.1
65
+ TAACAA -16.1
66
+ TCTTGA -41.9
67
+ TGAAAA -16.1
68
+ TGAGAA -16.1
69
+ TGATAA -16.1
70
+ TGCAAA -16.1
71
+ TGCGAA -16.1
72
+ TGCTTA -16.1
73
+ TGGAAA -16.1
74
+ TGGGAA -16.1
75
+ TGGGGA -6.4
76
+ TGTAAA -16.1
77
+ TGTGAA -16.1
78
+ TGTTCA -16.1
79
+ TTTCGA -16.1
80
+ TTTTGA -16.1
81
+ TTTTTA -16.1
data/lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.dh ADDED
@@ -0,0 +1,21 @@
1
+
2
+ /* triloop bonus*/
3
+
4
+ /* Enthalpy Hairpin loop */
5
+
6
+ AGAAT 15
7
+ AGCAT 15
8
+ AGGAT 15
9
+ AGTAT 15
10
+ CGAAG 20
11
+ CGCAG 20
12
+ CGGAG 20
13
+ CGTAG 20
14
+ GGAAC 20
15
+ GGCAC 20
16
+ GGGAC 20
17
+ GGTAC 20
18
+ TGAAA 15
19
+ TGCAA 15
20
+ TGGAA 15
21
+ TGTAA 15
data/lib/qu/cmdwrapper/primer3_config/interpretations/triloop_i.ds ADDED
@@ -0,0 +1,18 @@
1
+ /* bonuses for GNA triloops */
2
+
3
+ AGAAT 0
4
+ AGCAT 0
5
+ AGGAT 0
6
+ AGTAT 0
7
+ CGAAG 0
8
+ CGCAG 0
9
+ CGGAG 0
10
+ CGTAG 0
11
+ GGAAC 0
12
+ GGCAC 0
13
+ GGGAC 0
14
+ GGTAC 0
15
+ TGAAA 0
16
+ TGCAA 0
17
+ TGGAA 0
18
+ TGTAA 0