-
-/*
- * fastq-grep: regular expression searches of the sequences within a fastq file
+/*
+ * This file is part of fastq-tools.
+ *
+ * Copyright (c) 2011 by Daniel C. Jones <dcjones@cs.washington.edu>
*
- * Febuary 2011 / Daniel Jones <dcjones@cs.washington.edu>
+ * fastq-grep :
+ * Regular expression searches of the sequences within a FASTQ file.
*
*/
+#include "common.h"
+#include "parse.h"
#include <stdio.h>
#include <string.h>
#include <getopt.h>
#include <zlib.h>
#include <pcre.h>
-#include "kseq.h"
-KSEQ_INIT(gzFile, gzread)
+
+#if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)
+# include <fcntl.h>
+# include <io.h>
+# define SET_BINARY_MODE(file) setmode(fileno(file), O_BINARY)
+#else
+# define SET_BINARY_MODE(file)
+#endif
+
+
+static const char* prog_name = "fastq-grep";
void print_help()
{
- fprintf( stderr,
+ fprintf(stdout,
"fastq-grep [OPTION]... PATTERN [FILE]...\n"
-"Search for PATTERN in the read sequence in each FILE or standard input.\n"
-"PATTERN, by default, is a perl compatible regular expression."
+"Search for PATTERN in the read sequences in each FILE or standard input.\n"
+"PATTERN, by default, is a perl compatible regular expression.\n\n"
+"Options:\n"
+" -i, --id match the read id (by default, sequence is matched)\n"
+" -v, --invert-match select nonmatching entries\n"
+" -m, --mismatches=FILE output mismatching entries to the given file\n"
+" -c, --count output only the number of matching sequences\n"
+" -h, --help print this message\n"
+" -V, --version output version information and exit\n"
);
-
}
static int invert_flag;
-static int help_flag;
+static int count_flag;
+static int id_flag;
+
+
+
+void fastq_grep(FILE* fin, FILE* fout, FILE* mismatch_file, pcre* re)
+{
+ int rc;
+ int ovector[3];
+ size_t count = 0;
+
+ fastq_t* fqf = fastq_create(fin);
+ seq_t* seq = seq_create();
+
+ while (fastq_read(fqf, seq)) {
+
+ rc = pcre_exec(re, /* pattern */
+ NULL, /* extra data */
+ id_flag ? seq->id1.s : seq->seq.s,
+ id_flag ? seq->id1.n : seq->seq.n,
+ 0, /* subject offset */
+ 0, /* options */
+ ovector, /* output vector */
+ 3 ); /* output vector length */
+
+ if ((invert_flag && rc == PCRE_ERROR_NOMATCH) || (!invert_flag && rc >= 0)) {
+ if (count_flag) count++;
+ else fastq_print(fout, seq);
+ }
+ else if (mismatch_file) {
+ fastq_print(mismatch_file, seq);
+ }
+ }
+
+ seq_free(seq);
+ fastq_free(fqf);
+
+ if (count_flag) fprintf(fout, "%zu\n", count);
+}
+
+
int main(int argc, char* argv[])
{
+ SET_BINARY_MODE(stdin);
+ SET_BINARY_MODE(stdout);
+
+ const char* pat;
+ pcre* re;
+ const char* pat_error;
+ int pat_error_offset;
+
+ FILE* fin;
+
+
+ invert_flag = 0;
+ count_flag = 0;
+ id_flag = 0;
int opt;
int opt_idx;
+ FILE* mismatch_file = NULL;
+
static struct option long_options[] =
{
- {"help", no_argument, &help_flag, 1},
+ {"id", no_argument, &id_flag, 1},
{"invert-match", no_argument, &invert_flag, 1},
+ {"mismatches", required_argument, NULL, 'm'},
+ {"count", no_argument, &count_flag, 1},
+ {"help", no_argument, NULL, 'h'},
+ {"version", no_argument, NULL, 'V'},
{0, 0, 0, 0}
};
while (1) {
- opt = getopt_long(argc, argv, "hv", long_options, &opt_idx);
+ opt = getopt_long(argc, argv, "ivmchV", long_options, &opt_idx);
- if( opt == -1 ) break;
+ if (opt == -1) break;
switch (opt) {
case 0:
if (long_options[opt_idx].flag != 0) break;
if (optarg) {
- /* TODO */
}
break;
- case 'h':
- help_flag = 1;
+ case 'i':
+ id_flag = 1;
break;
case 'v':
invert_flag = 1;
break;
+ case 'm':
+ mismatch_file = fopen(optarg, "w");
+ if (mismatch_file == NULL) {
+ fprintf(stderr, "No such file '%s'.\n", optarg);
+ return 1;
+ }
+ break;
+
+ case 'c':
+ count_flag = 1;
+ break;
+
+ case 'h':
+ print_help();
+ return 0;
+
+ case 'V':
+ print_version(stdout, prog_name);
+ return 0;
+
+ case '?':
+ return 1;
+
default:
abort();
}
}
- if (help_flag) {
- print_help();
- return 0;
+ if (optind >= argc) {
+ fprintf(stderr, "A pattern must be specified.\n");
+ return 1;
+ }
+
+ pat = argv[optind++];
+ re = pcre_compile( pat, PCRE_CASELESS, &pat_error, &pat_error_offset, NULL );
+
+
+ if (re == NULL) {
+ fprintf(stderr, "Syntax error in PCRE pattern at offset: %d: %s\n",
+ pat_error_offset, pat_error );
+ return 1;
+ }
+
+
+ if (optind >= argc || (argc - optind == 1 && strcmp(argv[optind],"-") == 0)) {
+ fastq_grep(stdin, stdout, mismatch_file, re);
+ }
+ else {
+ for (; optind < argc; optind++) {
+ fin = fopen(argv[optind], "rb");
+ if (fin == NULL) {
+ fprintf(stderr, "No such file '%s'.\n", argv[optind]);
+ continue;
+ }
+
+ fastq_grep(fin, stdout, mismatch_file, re);
+
+ fclose(fin);
+ }
}
- /* TODO */
+ pcre_free(re);
+ if (mismatch_file) fclose(mismatch_file);
return 0;
}
projects / fastq-tools.git / blobdiff