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/** Separate mates of paired-end reads into two different files
* based on '/1' and '/2' extension of the read names.
*/
/*****************************************************************************
*****************************************************************************
* *
* Copyright (C) 2010 -2014Genome 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 "elib.h"
#include "sequence.h"
enum {
LINWIDTH = 0,
MATE_LABEL_SEPARATOR = '/',
MATE_LABEL_1st = '1',
MATE_LABEL_2nd = '2',
SEGMENTSIZ_REPORT = 1000000,
};
int main(int argc, char *argv[])
{
int errcode = ERRCODE_SUCCESS;
int ctr = 0;
char *infilnam, *oufilnamA, *oufilnamB, *filnamprefix;
const char *namstrp;
size_t namlen;
SeqIO *sfp_in, *sfpA_out, *sfpB_out;
SeqFastq *seqp;
ErrMsg *errmsg = 0;
ERRMSG_CREATE(errmsg);
if (argc < 3) {
printf("usage: %s <fasta/fastq file [in]> <prefix (out)>\n", argv[0]);
exit(0);
}
infilnam = argv[1];
filnamprefix = argv[2];
ESTRCAT(oufilnamA, filnamprefix, "_1.fa");
ESTRCAT(oufilnamB, filnamprefix, "_2.fa");
if (!(seqp = seqFastqCreate(0,SEQTYP_UNKNOWN)))
ERRMSGNO(errmsg, ERRCODE_NOMEM);
sfp_in = seqIOopen(&errcode, infilnam, SEQIO_READ, 0);
if (!sfp_in) ERRMSGNO(errmsg, errcode);
sfpA_out = seqIOopen(&errcode, oufilnamA, SEQIO_WRITE_FASTQ, 0);
if (!sfpA_out) ERRMSGNO(errmsg, errcode);
sfpB_out = seqIOopen(&errcode, oufilnamB, SEQIO_WRITE_FASTQ, 0);
if (!sfpB_out) ERRMSGNO(errmsg, errcode);
while(!(seqIOstatus(sfp_in) || seqIOstatus(sfpA_out) || seqIOstatus(sfpB_out))) {
if ((errcode = seqFastqRead(seqp, sfp_in)))
ERRMSGNO(errmsg, errcode);
ctr++;
if (ctr % SEGMENTSIZ_REPORT == 0)
printf("%i reads ... \n", ctr);
namstrp = seqFastqGetSeqName(seqp);
namlen = strlen(namstrp);
if (namstrp[namlen-2] == MATE_LABEL_SEPARATOR) {
if (namstrp[namlen-1] == MATE_LABEL_1st) {
if ((errcode = seqFastqWrite(sfpA_out, seqp, LINWIDTH)))
ERRMSGNO(errmsg, errcode);
} else if (namstrp[namlen-1] == MATE_LABEL_2nd) {
if ((errcode = seqFastqWrite(sfpB_out, seqp, LINWIDTH)))
ERRMSGNO(errmsg, errcode);
} else {
printf("Unrecogised mate label: %s\n", namstrp);
}
} else {
printf("Missing mate label: %s\n", namstrp);
}
}
printf("Processed %i reads.\n", ctr);
if ((seqIOstatus(sfp_in)) && seqIOstatus(sfp_in) != ERRCODE_EOF)
ERRMSGNO(errmsg, seqIOstatus(sfp_in));
if (seqIOstatus(sfpA_out))
ERRMSGNO(errmsg, seqIOstatus(sfpA_out));
if (seqIOstatus(sfpB_out))
ERRMSGNO(errmsg, seqIOstatus(sfpB_out));
seqIOclose(sfpB_out);
seqIOclose(sfpA_out);
seqIOclose(sfp_in);
seqFastqDelete(seqp);
free(oufilnamA);
free(oufilnamB);
ERRMSG_END(errmsg);
return ERRCODE_SUCCESS;
}
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