diff srf2fastq/io_lib-1.12.2/progs/srf2fasta.c @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/progs/srf2fasta.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,137 @@
+/*
+ * ======================================================================
+ * This software has been created by Genome Research Limited (GRL).
+ *
+ * GRL hereby grants permission to use, copy, modify and distribute
+ * this software and its documentation for non-commercial purposes
+ * without fee at the user's own risk on the basis set out below.
+ *
+ * GRL neither undertakes nor accepts any duty whether contractual or
+ * otherwise in connection with the software, its use or the use of
+ * any derivative, and makes no representations or warranties, express
+ * or implied, concerning the software, its suitability, fitness for
+ * a particular purpose or non-infringement.
+ *
+ * In no event shall the authors of the software or GRL be responsible
+ * or liable for any loss or damage whatsoever arising in any way
+ * directly or indirectly out of the use of this software or its
+ * derivatives, even if advised of the possibility of such damage.
+ *
+ * Our software can be freely distributed under the conditions set out
+ * above, and must contain this copyright notice.
+ * ======================================================================
+ */
+
+/*
+ * This performs a linear (non-indexed) search for a trace in an SRF archive.
+ *
+ * It's not intended as a suitable production program or as a library of code
+ * to use, but as a test and benchmark statistic.
+ */
+
+#include <stdio.h>
+#include <math.h>
+#include <string.h>
+#include <fcntl.h>
+
+#include <io_lib/Read.h>
+#include <io_lib/misc.h>
+#include <io_lib/ztr.h>
+#include <io_lib/srf.h>
+
+/* ------------------------------------------------------------------------ */
+
+#define MAX_READ_LEN 10000
+void ztr2fasta(ztr_t *z, char *name) {
+    int i, nc;
+    char buf[MAX_READ_LEN*2 + 512 + 6];
+    char *seq = buf;
+    ztr_chunk_t **chunks;
+
+    /* Extract the sequence only */
+    chunks = ztr_find_chunks(z, ZTR_TYPE_BASE, &nc);
+    if (nc != 1) {
+	fprintf(stderr, "Zero or greater than one BASE chunks found.\n");
+	if (chunks)
+	    free(chunks);
+	return;
+    }
+
+    uncompress_chunk(z, chunks[0]);
+
+    /* Construct fasta entry */
+    *seq++ = '>';
+    while (*name)
+	*seq++ = *name++;
+    *seq++ = '\n';
+
+    for (i = 1; i < chunks[0]->dlength; i++) {
+	char base = chunks[0]->data[i];
+	switch (base) {
+	case 'A': case 'a':
+	case 'C': case 'c':
+	case 'G': case 'g':
+	case 'T': case 't':
+	    *seq++ = base;
+	    break;
+	default:
+	    *seq++ = 'N';
+	}
+    }
+    *seq++ = '\n';
+
+    fwrite(buf, 1, seq - buf, stdout);
+    free(chunks);
+
+    return;
+}
+
+/* ------------------------------------------------------------------------ */
+void usage(void) {
+    fprintf(stderr, "Usage: srf2fasta [-C] archive_name\n");
+    exit(1);
+}
+
+int main(int argc, char **argv) {
+    char *ar_name;
+    srf_t *srf;
+    char name[512];
+    ztr_t *ztr;
+    int mask = 0, i;
+
+    /* Parse args */
+    for (i = 1; i < argc && argv[i][0] == '-'; i++) {
+	if (!strcmp(argv[i], "-")) {
+	    break;
+	} else if (!strcmp(argv[i], "-C")) {
+	    mask = SRF_READ_FLAG_BAD_MASK;
+	} else {
+	    usage();
+	}
+    }    
+
+    if (i == argc) {
+	usage();
+    }
+    ar_name = argv[i];
+
+    if (NULL == (srf = srf_open(ar_name, "r"))) {
+	perror(ar_name);
+	return 4;
+    }
+
+    read_sections(READ_BASES);
+
+#ifdef _WIN32
+    _setmode(_fileno(stdout), _O_BINARY);
+#endif
+
+    while (NULL != (ztr = srf_next_ztr(srf, name, mask))) {
+	ztr2fasta(ztr, name);
+	delete_ztr(ztr);
+    }
+
+    srf_destroy(srf, 1);
+
+    return 0;
+}