1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
|
/** Save a segment of reads of a FASTQ file to another file
*/
/*****************************************************************************
*****************************************************************************
* *
* Copyright (C) 2010-2014 Genome Research Ltd. *
* *
* Author: Hannes Ponstingl (hp3@sanger.ac.uk) *
* *
* This file is part of SMALT. *
* *
* SMALT is free software: you can redistribute it and/or modify it under *
* the terms of the GNU General Public License as published by the Free *
* Software Foundation, either version 3 of the License, or (at your *
* option) any later version. *
* *
* This program is distributed in the hope that it will be useful, but *
* WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU *
* General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License along *
* with this program. If not, see <http://www.gnu.org/licenses/>. *
* *
*****************************************************************************
*****************************************************************************/
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <ctype.h>
#include "elib.h"
#include "sequence.h"
enum {
LINWIDTH = 0,
SEGMENTSIZ_REPORT = 1000000,
NCHAR_FILEXT = 6,
};
int main(int argc, char *argv[])
{
int errcode = ERRCODE_SUCCESS;
int ctr = 0, filctr = 0;
int readno_start, readno_end, readnum;
unsigned char is_partition = 0, is_verbose = 1, isFastaOutput;
char oufilnam[FILENAME_MAX];
char *infilnam, *oufilnamroot;
SeqIO *sfp_in, *sfp_out;
SeqFastq *seqp;
ErrMsg *errmsg = 0;
ERRMSG_CREATE(errmsg);
if (argc < 6) {
printf("usage: %s <fasta/fastq file [in]> <start read no (<0: partition)> "\
"<no of reads (0: all)> <convert to fasta [y/n]> <fasta/fastq file [out]>\n", argv[0]);
exit(0);
}
infilnam = argv[1];
readno_start = atoi(argv[2]);
if (readno_start < 0) {
is_partition = 1;
readno_start = 0;
}
readnum = atoi(argv[3]);
readno_end = readno_start + readnum - 1;
isFastaOutput = (unsigned char) (toupper(argv[4][0]) == 'Y');
oufilnamroot = argv[5];
if (strlen(oufilnamroot) + NCHAR_FILEXT > FILENAME_MAX)
ERRMSGNO(errmsg, ERRCODE_ARGRANGE);
if (!(seqp = seqFastqCreate(0, (char) ((isFastaOutput)? SEQTYP_FASTA: SEQTYP_UNKNOWN))))
ERRMSGNO(errmsg, ERRCODE_NOMEM);
sfp_in = seqIOopen(&errcode, infilnam, SEQIO_READ, 0);
if (!sfp_in) ERRMSGNO(errmsg, errcode);
while(!(seqIOstatus(sfp_in))) {
if (is_partition) {
sprintf(oufilnam, "%s_%3.3i", oufilnamroot, filctr);
} else {
strcpy(oufilnam, oufilnamroot);
}
sfp_out = seqIOopen(&errcode, oufilnam, SEQIO_WRITE_FASTQ, 0);
if (!sfp_out) ERRMSGNO(errmsg, errcode);
if (is_verbose)
printf("writing file %s ...\n", oufilnam);
while(!(seqIOstatus(sfp_in) || seqIOstatus(sfp_out))) {
if ((errcode = seqFastqRead(seqp, sfp_in)))
ERRMSGNO(errmsg, errcode);
if ((isFastaOutput) &&
(errcode = seqFastqSetType(seqp, SEQTYP_FASTA)))
ERRMSGNO(errmsg, errcode);
if ((errcode = seqFastqWrite(sfp_out, seqp, LINWIDTH)))
ERRMSGNO(errmsg, errcode);
ctr++;
if (ctr % SEGMENTSIZ_REPORT == 0)
printf("%i reads ... \n", ctr);
if (ctr < readno_start)
continue;
if (ctr > readno_end && readnum > 0)
break;
}
if (seqIOstatus(sfp_out))
ERRMSGNO(errmsg, seqIOstatus(sfp_out));
seqIOclose(sfp_out);
if (!is_partition)
break;
readno_end += readnum;
filctr++;
}
if ((seqIOstatus(sfp_in)) && seqIOstatus(sfp_in) != ERRCODE_EOF)
ERRMSGNO(errmsg, seqIOstatus(sfp_in));
seqIOclose(sfp_in);
seqFastqDelete(seqp);
ERRMSG_END(errmsg);
return ERRCODE_SUCCESS;
}
|
