rbbt-util 5.44.0 → 5.44.1
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- checksums.yaml +4 -4
- data/etc/app.d/base.rb +1 -1
- data/lib/rbbt/persist/tsv/sharder.rb +1 -1
- data/lib/rbbt/util/misc/omics.rb +2 -1
- data/lib/rbbt/util/misc/ssw.rb +298 -0
- data/lib/rbbt/workflow/step/info.rb +2 -2
- data/share/rbbt_commands/workflow/server +6 -1
- metadata +4 -3
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
---
|
|
2
2
|
SHA256:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: a9269fd6f3ed8e0b03f575c59f50d42c45a11bc07e138f4377e5069f3050fb29
|
|
4
|
+
data.tar.gz: 488a57247f23d41f8c94aa64cb38cf666c99ee43c4fa14399ed77b8bb1854519
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: 3a288fcd2e11209621bc61f911097c104e75c22c759ca7ac6ca0a1f908bf1ea1711587bf776b262f082a60c0296a9004cfc8fad85de738dabd6bad0bc45f6fed
|
|
7
|
+
data.tar.gz: 91e775b843358c29df1d87e1d9d5db8a92c37d842fd05757cc810a5f4c77a38cfe154a0a368429abb921cf43014333361426546a43aac09eabe81f07ca4315a5
|
data/etc/app.d/base.rb
CHANGED
data/lib/rbbt/util/misc/omics.rb
CHANGED
|
@@ -256,8 +256,9 @@ module Misc
|
|
|
256
256
|
ref = m[1]
|
|
257
257
|
num = m[2]
|
|
258
258
|
alt = m[3]
|
|
259
|
+
alt = "*" if alt == "Ter"
|
|
259
260
|
ref = THREE_TO_ONE_AA_CODE[ref.downcase]
|
|
260
|
-
alt = THREE_TO_ONE_AA_CODE[alt.downcase]
|
|
261
|
+
alt = THREE_TO_ONE_AA_CODE[alt.downcase] unless alt == "*"
|
|
261
262
|
mutation = [ref, num, alt] * ""
|
|
262
263
|
end
|
|
263
264
|
one_aa_code = THREE_TO_ONE_AA_CODE.values
|
|
@@ -0,0 +1,298 @@
|
|
|
1
|
+
require 'rbbt'
|
|
2
|
+
|
|
3
|
+
require 'inline'
|
|
4
|
+
|
|
5
|
+
# From: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
|
|
6
|
+
# Citation: SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications
|
|
7
|
+
# Mengyao Zhao, Wan-Ping Lee, Gabor T. Marth
|
|
8
|
+
# http://arxiv.org/abs/1208.6350
|
|
9
|
+
module SmithWaterman
|
|
10
|
+
|
|
11
|
+
inline(:C) do |builder|
|
|
12
|
+
prefix =<<-EOF
|
|
13
|
+
#include <stdlib.h>
|
|
14
|
+
#include <stdio.h>
|
|
15
|
+
#include <stdint.h>
|
|
16
|
+
#include #{'"' + Rbbt.share.software.opt.ssw["ssw.h"].find + '"'}
|
|
17
|
+
#include #{'"' + Rbbt.share.software.opt.ssw["ssw.c"].find + '"'}
|
|
18
|
+
EOF
|
|
19
|
+
|
|
20
|
+
prefix +=<<-'EOF'
|
|
21
|
+
void ssw_write (s_align* a,
|
|
22
|
+
char* ref_seq,
|
|
23
|
+
char* read_seq,
|
|
24
|
+
int8_t* table,
|
|
25
|
+
int fd) {
|
|
26
|
+
|
|
27
|
+
int max_length = 1000000;
|
|
28
|
+
dprintf(fd, "optimal_alignment_score: %d\tsub-optimal_alignment_score: %d\t", a->score1, a->score2);
|
|
29
|
+
if (a->ref_begin1 + 1) dprintf(fd, "target_begin: %d\t", a->ref_begin1 + 1);
|
|
30
|
+
dprintf(fd, "target_end: %d\t", a->ref_end1 + 1);
|
|
31
|
+
if (a->read_begin1 + 1) dprintf(fd, "query_begin: %d\t", a->read_begin1 + 1);
|
|
32
|
+
dprintf(fd, "query_end: %d\n\n", a->read_end1 + 1);
|
|
33
|
+
if (a->cigar) {
|
|
34
|
+
int32_t i, c = 0, left = 0, e = 0, qb = a->ref_begin1, pb = a->read_begin1;
|
|
35
|
+
while (e < a->cigarLen || left > 0) {
|
|
36
|
+
int32_t count = 0;
|
|
37
|
+
int32_t q = qb;
|
|
38
|
+
int32_t p = pb;
|
|
39
|
+
dprintf(fd, "Target: %8d ", q + 1);
|
|
40
|
+
for (c = e; c < a->cigarLen; ++c) {
|
|
41
|
+
int32_t letter = 0xf&*(a->cigar + c);
|
|
42
|
+
int32_t length = (0xfffffff0&*(a->cigar + c))>>4;
|
|
43
|
+
int32_t l = (count == 0 && left > 0) ? left: length;
|
|
44
|
+
for (i = 0; i < l; ++i) {
|
|
45
|
+
if (letter == 1) dprintf(fd, "-");
|
|
46
|
+
else {
|
|
47
|
+
dprintf(fd, "%c", *(ref_seq + q));
|
|
48
|
+
++ q;
|
|
49
|
+
}
|
|
50
|
+
++ count;
|
|
51
|
+
if (count == max_length) goto step2;
|
|
52
|
+
}
|
|
53
|
+
}
|
|
54
|
+
step2:
|
|
55
|
+
dprintf(fd, " %d\n ", q);
|
|
56
|
+
q = qb;
|
|
57
|
+
count = 0;
|
|
58
|
+
for (c = e; c < a->cigarLen; ++c) {
|
|
59
|
+
int32_t letter = 0xf&*(a->cigar + c);
|
|
60
|
+
int32_t length = (0xfffffff0&*(a->cigar + c))>>4;
|
|
61
|
+
int32_t l = (count == 0 && left > 0) ? left: length;
|
|
62
|
+
for (i = 0; i < l; ++i){
|
|
63
|
+
if (letter == 0) {
|
|
64
|
+
if (table[(int)*(ref_seq + q)] == table[(int)*(read_seq + p)])dprintf(fd, "|");
|
|
65
|
+
else dprintf(fd, "*");
|
|
66
|
+
++q;
|
|
67
|
+
++p;
|
|
68
|
+
} else {
|
|
69
|
+
dprintf(fd, "*");
|
|
70
|
+
if (letter == 1) ++p;
|
|
71
|
+
else ++q;
|
|
72
|
+
}
|
|
73
|
+
++ count;
|
|
74
|
+
if (count == max_length) {
|
|
75
|
+
qb = q;
|
|
76
|
+
goto step3;
|
|
77
|
+
}
|
|
78
|
+
}
|
|
79
|
+
}
|
|
80
|
+
step3:
|
|
81
|
+
p = pb;
|
|
82
|
+
dprintf(fd, "\nQuery: %8d ", p + 1);
|
|
83
|
+
count = 0;
|
|
84
|
+
for (c = e; c < a->cigarLen; ++c) {
|
|
85
|
+
int32_t letter = 0xf&*(a->cigar + c);
|
|
86
|
+
int32_t length = (0xfffffff0&*(a->cigar + c))>>4;
|
|
87
|
+
int32_t l = (count == 0 && left > 0) ? left: length;
|
|
88
|
+
for (i = 0; i < l; ++i) {
|
|
89
|
+
if (letter == 2) dprintf(fd, "-");
|
|
90
|
+
else {
|
|
91
|
+
dprintf(fd, "%c", *(read_seq + p));
|
|
92
|
+
++p;
|
|
93
|
+
}
|
|
94
|
+
++ count;
|
|
95
|
+
if (count == max_length) {
|
|
96
|
+
pb = p;
|
|
97
|
+
left = l - i - 1;
|
|
98
|
+
e = (left == 0) ? (c + 1) : c;
|
|
99
|
+
goto end;
|
|
100
|
+
}
|
|
101
|
+
}
|
|
102
|
+
}
|
|
103
|
+
e = c;
|
|
104
|
+
left = 0;
|
|
105
|
+
end:
|
|
106
|
+
dprintf(fd, " %d\n\n", p);
|
|
107
|
+
}
|
|
108
|
+
}
|
|
109
|
+
}
|
|
110
|
+
|
|
111
|
+
EOF
|
|
112
|
+
|
|
113
|
+
builder.prefix prefix
|
|
114
|
+
|
|
115
|
+
|
|
116
|
+
script = <<-EOF
|
|
117
|
+
int ssw_nt(char * read_seq, char * ref_seq){
|
|
118
|
+
int32_t l, m, k, match = 2, mismatch = 2, gap_open = 3, gap_extension = 1; // default parameters for genome sequence alignment
|
|
119
|
+
// reference sequence
|
|
120
|
+
//char ref_seq[40] = {'C', 'A', 'G', 'C', 'C', 'T', 'T', 'T', 'C', 'T', 'G', 'A', 'C', 'C', 'C', 'G', 'G', 'A', 'A', 'A', 'T',
|
|
121
|
+
// 'C', 'A', 'A', 'A', 'A', 'T', 'A', 'G', 'G', 'C', 'A', 'C', 'A', 'A', 'C', 'A', 'A', 'A', '\0'};
|
|
122
|
+
//char read_seq[16] = {'C', 'T', 'G', 'A', 'G', 'C', 'C', 'G', 'G', 'T', 'A', 'A', 'A', 'T', 'C', '\0'}; // read sequence
|
|
123
|
+
|
|
124
|
+
s_profile* profile;
|
|
125
|
+
int8_t* num = (int8_t*)malloc(16); // the read sequence represented in numbers
|
|
126
|
+
int8_t* ref_num = (int8_t*)malloc(64); // the read sequence represented in numbers
|
|
127
|
+
s_align* result;
|
|
128
|
+
|
|
129
|
+
/* This table is used to transform nucleotide letters into numbers. */
|
|
130
|
+
int8_t nt_table[128] = {
|
|
131
|
+
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
|
|
132
|
+
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
|
|
133
|
+
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
|
|
134
|
+
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
|
|
135
|
+
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
|
|
136
|
+
4, 4, 4, 4, 3, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
|
|
137
|
+
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
|
|
138
|
+
4, 4, 4, 4, 3, 0, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
|
|
139
|
+
};
|
|
140
|
+
|
|
141
|
+
// initialize scoring matrix for genome sequences
|
|
142
|
+
// A C G T N (or other ambiguous code)
|
|
143
|
+
// 2 -2 -2 -2 0 A
|
|
144
|
+
// -2 2 -2 -2 0 C
|
|
145
|
+
// -2 -2 2 -2 0 G
|
|
146
|
+
// -2 -2 -2 2 0 T
|
|
147
|
+
// 0 0 0 0 0 N (or other ambiguous code)
|
|
148
|
+
int8_t* mat = (int8_t*)calloc(25, sizeof(int8_t));
|
|
149
|
+
for (l = k = 0; l < 4; ++l) {
|
|
150
|
+
for (m = 0; m < 4; ++m) mat[k++] = l == m ? match : - mismatch; /* weight_match : -weight_mismatch */
|
|
151
|
+
mat[k++] = 0; // ambiguous base: no penalty
|
|
152
|
+
}
|
|
153
|
+
for (m = 0; m < 5; ++m) mat[k++] = 0;
|
|
154
|
+
|
|
155
|
+
for (m = 0; m < 15; ++m) num[m] = nt_table[(int)read_seq[m]];
|
|
156
|
+
profile = ssw_init(num, 15, mat, 5, 2);
|
|
157
|
+
for (m = 0; m < 39; ++m) ref_num[m] = nt_table[(int)ref_seq[m]];
|
|
158
|
+
|
|
159
|
+
// Only the 8 bit of the flag is setted. ssw_align will always return the best alignment beginning position and cigar.
|
|
160
|
+
result = ssw_align (profile, ref_num, 39, gap_open, gap_extension, 1, 0, 0, 15);
|
|
161
|
+
//ssw_write(result, ref_seq, read_seq, nt_tablte);
|
|
162
|
+
|
|
163
|
+
free(mat);
|
|
164
|
+
free(ref_num);
|
|
165
|
+
free(num);
|
|
166
|
+
return(0);
|
|
167
|
+
}
|
|
168
|
+
|
|
169
|
+
EOF
|
|
170
|
+
builder.c_singleton script
|
|
171
|
+
|
|
172
|
+
script = <<-EOF
|
|
173
|
+
int ssw_aa(char * read_seq, char * ref_seq, int read_seq_len, int ref_seq_len, int fd){
|
|
174
|
+
|
|
175
|
+
int32_t l, m, k, match = 2, mismatch = 2, gap_open = 3, gap_extension = 1; // default parameters for genome sequence alignment
|
|
176
|
+
|
|
177
|
+
s_profile* profile;
|
|
178
|
+
int8_t* num = (int8_t*)malloc(read_seq_len); // the read sequence represented in numbers
|
|
179
|
+
int8_t* ref_num = (int8_t*)malloc(ref_seq_len); // the reference sequence represented in numbers
|
|
180
|
+
s_align* result;
|
|
181
|
+
|
|
182
|
+
/* This table is used to transform amino acid letters into numbers. */
|
|
183
|
+
int8_t aa_table[128] = {
|
|
184
|
+
23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
|
|
185
|
+
23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
|
|
186
|
+
23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
|
|
187
|
+
23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23,
|
|
188
|
+
23, 0, 20, 4, 3, 6, 13, 7, 8, 9, 23, 11, 10, 12, 2, 23,
|
|
189
|
+
14, 5, 1, 15, 16, 23, 19, 17, 22, 18, 21, 23, 23, 23, 23, 23,
|
|
190
|
+
23, 0, 20, 4, 3, 6, 13, 7, 8, 9, 23, 11, 10, 12, 2, 23,
|
|
191
|
+
14, 5, 1, 15, 16, 23, 19, 17, 22, 18, 21, 23, 23, 23, 23, 23
|
|
192
|
+
};
|
|
193
|
+
|
|
194
|
+
int8_t mat[] = {
|
|
195
|
+
// A R N D C Q E G H I L K M F P S T W Y V B Z X *
|
|
196
|
+
5, -2, -1, -2, -1, -1, -1, 0, -2, -1, -2, -1, -1, -3, -1, 1, 0, -3, -2, 0, -2, -1, -1, -5, // A
|
|
197
|
+
-2, 7, -1, -2, -4, 1, 0, -3, 0, -4, -3, 3, -2, -3, -3, -1, -1, -3, -1, -3, -1, 0, -1, -5, // R
|
|
198
|
+
-1, -1, 7, 2, -2, 0, 0, 0, 1, -3, -4, 0, -2, -4, -2, 1, 0, -4, -2, -3, 5, 0, -1, -5, // N
|
|
199
|
+
-2, -2, 2, 8, -4, 0, 2, -1, -1, -4, -4, -1, -4, -5, -1, 0, -1, -5, -3, -4, 6, 1, -1, -5, // D
|
|
200
|
+
-1, -4, -2, -4, 13, -3, -3, -3, -3, -2, -2, -3, -2, -2, -4, -1, -1, -5, -3, -1, -3, -3, -1, -5, // C
|
|
201
|
+
-1, 1, 0, 0, -3, 7, 2, -2, 1, -3, -2, 2, 0, -4, -1, 0, -1, -1, -1, -3, 0, 4, -1, -5, // Q
|
|
202
|
+
-1, 0, 0, 2, -3, 2, 6, -3, 0, -4, -3, 1, -2, -3, -1, -1, -1, -3, -2, -3, 1, 5, -1, -5, // E
|
|
203
|
+
0, -3, 0, -1, -3, -2, -3, 8, -2, -4, -4, -2, -3, -4, -2, 0, -2, -3, -3, -4, -1, -2, -1, -5, // G
|
|
204
|
+
-2, 0, 1, -1, -3, 1, 0, -2, 10, -4, -3, 0, -1, -1, -2, -1, -2, -3, 2, -4, 0, 0, -1, -5, // H
|
|
205
|
+
-1, -4, -3, -4, -2, -3, -4, -4, -4, 5, 2, -3, 2, 0, -3, -3, -1, -3, -1, 4, -4, -3, -1, -5, // I
|
|
206
|
+
-2, -3, -4, -4, -2, -2, -3, -4, -3, 2, 5, -3, 3, 1, -4, -3, -1, -2, -1, 1, -4, -3, -1, -5, // L
|
|
207
|
+
-1, 3, 0, -1, -3, 2, 1, -2, 0, -3, -3, 6, -2, -4, -1, 0, -1, -3, -2, -3, 0, 1, -1, -5, // K
|
|
208
|
+
-1, -2, -2, -4, -2, 0, -2, -3, -1, 2, 3, -2, 7, 0, -3, -2, -1, -1, 0, 1, -3, -1, -1, -5, // M
|
|
209
|
+
-3, -3, -4, -5, -2, -4, -3, -4, -1, 0, 1, -4, 0, 8, -4, -3, -2, 1, 4, -1, -4, -4, -1, -5, // F
|
|
210
|
+
-1, -3, -2, -1, -4, -1, -1, -2, -2, -3, -4, -1, -3, -4, 10, -1, -1, -4, -3, -3, -2, -1, -1, -5, // P
|
|
211
|
+
1, -1, 1, 0, -1, 0, -1, 0, -1, -3, -3, 0, -2, -3, -1, 5, 2, -4, -2, -2, 0, 0, -1, -5, // S
|
|
212
|
+
0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 2, 5, -3, -2, 0, 0, -1, -1, -5, // T
|
|
213
|
+
-3, -3, -4, -5, -5, -1, -3, -3, -3, -3, -2, -3, -1, 1, -4, -4, -3, 15, 2, -3, -5, -2, -1, -5, // W
|
|
214
|
+
-2, -1, -2, -3, -3, -1, -2, -3, 2, -1, -1, -2, 0, 4, -3, -2, -2, 2, 8, -1, -3, -2, -1, -5, // Y
|
|
215
|
+
0, -3, -3, -4, -1, -3, -3, -4, -4, 4, 1, -3, 1, -1, -3, -2, 0, -3, -1, 5, -3, -3, -1, -5, // V
|
|
216
|
+
-2, -1, 5, 6, -3, 0, 1, -1, 0, -4, -4, 0, -3, -4, -2, 0, 0, -5, -3, -3, 6, 1, -1, -5, // B
|
|
217
|
+
-1, 0, 0, 1, -3, 4, 5, -2, 0, -3, -3, 1, -1, -4, -1, 0, -1, -2, -2, -3, 1, 5, -1, -5, // Z
|
|
218
|
+
-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -5, // X
|
|
219
|
+
-5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, -5, 1 // *
|
|
220
|
+
};
|
|
221
|
+
|
|
222
|
+
|
|
223
|
+
for (m = 0; m < read_seq_len; ++m) num[m] = aa_table[(int)read_seq[m]];
|
|
224
|
+
profile = ssw_init(num, read_seq_len, mat, 24, 2);
|
|
225
|
+
for (m = 0; m < ref_seq_len; ++m) ref_num[m] = aa_table[(int)ref_seq[m]];
|
|
226
|
+
|
|
227
|
+
// Only the 8 bit of the flag is setted. ssw_align will always return the best alignment beginning position and cigar.
|
|
228
|
+
result = ssw_align(profile, ref_num, ref_seq_len, gap_open, gap_extension, 1, 0, 0, read_seq_len );
|
|
229
|
+
ssw_write(result, ref_seq, read_seq, aa_table, fd);
|
|
230
|
+
|
|
231
|
+
free(num);
|
|
232
|
+
free(ref_num);
|
|
233
|
+
return(0);
|
|
234
|
+
}
|
|
235
|
+
|
|
236
|
+
EOF
|
|
237
|
+
builder.c_singleton script
|
|
238
|
+
|
|
239
|
+
end
|
|
240
|
+
|
|
241
|
+
def self.align(query_sequence, target_sequence)
|
|
242
|
+
Log.low { "Aligning #{ Misc.fingerprint query_sequence } to #{ Misc.fingerprint target_sequence }" }
|
|
243
|
+
|
|
244
|
+
begin
|
|
245
|
+
raise "No query sequence" if query_sequence.nil?
|
|
246
|
+
raise "No target sequence" if target_sequence.nil?
|
|
247
|
+
|
|
248
|
+
s_out = Misc.open_pipe do |s_in|
|
|
249
|
+
SmithWaterman.ssw_aa(query_sequence, target_sequence, query_sequence.length, target_sequence.length, s_in.fileno)
|
|
250
|
+
end
|
|
251
|
+
|
|
252
|
+
txt = s_out.read
|
|
253
|
+
s_out.close
|
|
254
|
+
s_out.join
|
|
255
|
+
txt
|
|
256
|
+
|
|
257
|
+
target_start, target, target_end = txt.match(/Target:\s+(\d+)\s+([A-Z\-?*]+)\s+(\d+)/).values_at 1, 2, 3
|
|
258
|
+
|
|
259
|
+
query_start, query, query_end = txt.match(/Query:\s+(\d+)\s+([A-Z\-?*]+)\s+(\d+)/).values_at 1, 2, 3
|
|
260
|
+
|
|
261
|
+
txt.replace ""
|
|
262
|
+
[("_" * (query_start.to_i - 1)) + query, ("_" * (target_start.to_i - 1)) + target]
|
|
263
|
+
rescue
|
|
264
|
+
Log.warn("Error in aligmnent: #{$!.message}")
|
|
265
|
+
return ["-", "-"]
|
|
266
|
+
end
|
|
267
|
+
end
|
|
268
|
+
|
|
269
|
+
def self.alignment_map(source, target)
|
|
270
|
+
alignment_source, alignment_target = SmithWaterman.align(source, target)
|
|
271
|
+
map = {}
|
|
272
|
+
|
|
273
|
+
offset_source, alignment_source = alignment_source.match(/^(_*)(.*)/).values_at( 1, 2)
|
|
274
|
+
offset_target, alignment_target = alignment_target.match(/^(_*)(.*)/).values_at( 1, 2)
|
|
275
|
+
|
|
276
|
+
gaps_source = 0
|
|
277
|
+
gaps_target = 0
|
|
278
|
+
miss_match = 0
|
|
279
|
+
alignment_source.chars.zip(alignment_target.chars).each_with_index do |p,i|
|
|
280
|
+
char_source, char_target = p
|
|
281
|
+
gaps_source += 1 if char_source == '-'
|
|
282
|
+
gaps_target += 1 if char_target == '-'
|
|
283
|
+
source_pos = i + 1 + offset_source.length - gaps_source
|
|
284
|
+
target_pos = i + 1 + offset_target.length - gaps_target
|
|
285
|
+
if char_source != char_target or char_source == "-"
|
|
286
|
+
miss_match += 1
|
|
287
|
+
else
|
|
288
|
+
map[source_pos] = target_pos
|
|
289
|
+
end
|
|
290
|
+
end
|
|
291
|
+
|
|
292
|
+
if miss_match + gaps_source > alignment_source.length.to_f / 2
|
|
293
|
+
{}
|
|
294
|
+
else
|
|
295
|
+
map
|
|
296
|
+
end
|
|
297
|
+
end
|
|
298
|
+
end
|
|
@@ -35,8 +35,8 @@ class Step
|
|
|
35
35
|
rescue Exception
|
|
36
36
|
Log.debug{"Error loading info file: " + info_file}
|
|
37
37
|
Log.exception $!
|
|
38
|
-
Open.rm info_file
|
|
39
|
-
Misc.sensiblewrite(info_file, Step.serialize_info({:status => :error, :messages => ["Info file lost"]}))
|
|
38
|
+
#Open.rm info_file
|
|
39
|
+
#Misc.sensiblewrite(info_file, Step.serialize_info({:status => :error, :messages => ["Info file lost"]}))
|
|
40
40
|
raise $!
|
|
41
41
|
end
|
|
42
42
|
end
|
|
@@ -134,7 +134,12 @@ TmpFile.with_file do |app_dir|
|
|
|
134
134
|
options.each do |k,v| fixed_options[k.to_sym] = v end
|
|
135
135
|
options = fixed_options
|
|
136
136
|
|
|
137
|
-
|
|
137
|
+
begin
|
|
138
|
+
Rack::Server.start(options)
|
|
139
|
+
rescue LoadError
|
|
140
|
+
require 'rackup'
|
|
141
|
+
Rackup::Server.start(options)
|
|
142
|
+
end
|
|
138
143
|
end
|
|
139
144
|
end
|
|
140
145
|
end
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: rbbt-util
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 5.44.
|
|
4
|
+
version: 5.44.1
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Miguel Vazquez
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2024-
|
|
11
|
+
date: 2024-12-10 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: rake
|
|
@@ -283,6 +283,7 @@ files:
|
|
|
283
283
|
- lib/rbbt/util/misc/options.rb
|
|
284
284
|
- lib/rbbt/util/misc/pipes.rb
|
|
285
285
|
- lib/rbbt/util/misc/serialize.rb
|
|
286
|
+
- lib/rbbt/util/misc/ssw.rb
|
|
286
287
|
- lib/rbbt/util/misc/system.rb
|
|
287
288
|
- lib/rbbt/util/named_array.rb
|
|
288
289
|
- lib/rbbt/util/open.rb
|
|
@@ -476,7 +477,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
476
477
|
- !ruby/object:Gem::Version
|
|
477
478
|
version: '0'
|
|
478
479
|
requirements: []
|
|
479
|
-
rubygems_version: 3.5.
|
|
480
|
+
rubygems_version: 3.5.23
|
|
480
481
|
signing_key:
|
|
481
482
|
specification_version: 4
|
|
482
483
|
summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
|