diff srf2fastq/io_lib-1.12.2/progs/extract_fastq.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/extract_fastq.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,175 @@
+/*
+ * Copyright (c) Medical Research Council 1994-1999. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#include <stdio.h>
+#include <errno.h>
+#include <string.h>
+#include <strings.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <io_lib/Read.h>
+#include <io_lib/traceType.h>
+#include <io_lib/expFileIO.h>
+#include <io_lib/open_trace_file.h>
+
+static int do_trans(mFILE *infp, char *in_file, FILE *outfp, int format) {
+    Read *r;
+    char *p = strrchr(in_file, '/');
+    int i;
+
+    read_sections(READ_BASES);
+    if (NULL == (r = mfread_reading(infp, in_file, format))) {
+	fprintf(stderr, "Failed to read file '%s'\n", in_file);
+	return 1;
+    }
+
+    if (NULL == p)
+	p = in_file;
+    else
+	p++;
+
+    fprintf(outfp, "@%s\n", p);
+    fprintf(outfp, "%.*s\n", r->NBases, r->base);
+    fprintf(outfp, "+%s\n", p);
+    for (i = 0; i < r->NBases; i++) {
+	int qual;
+	switch (r->base[i]) {
+	case 'A':
+	case 'a':
+	    qual = r->prob_A[i];
+	    break;
+	case 'C':
+	case 'c':
+	    qual = r->prob_C[i];
+	    break;
+	case 'G':
+	case 'g':
+	    qual = r->prob_G[i];
+	    break;
+	case 'T':
+	case 't':
+	    qual = r->prob_T[i];
+	    break;
+	default:
+	    qual = 0;
+	}
+	fputc(qual + 33, outfp);
+    }
+    fputc('\n', outfp);
+
+    read_deallocate(r);
+    fflush(outfp);
+
+    return 0;
+}
+
+static void usage(void) {
+    fprintf(stderr, "Usage: extract_fastq [-(abi|alf|scf|exp|pln)]\n"
+	    "                   [-output output_name] [-fofn fofn] [input_name] ...\n");
+    exit(1);
+}
+
+int main(int argc, char **argv) {
+    int from_stdin = 1;
+    mFILE *infp = mstdin();
+    FILE *outfp = stdout;
+    int format = TT_ANY;
+    int ret = 0;
+    char *fofn = NULL;
+
+    for (argc--, argv++; argc > 0; argc--, argv++) {
+	if (strcasecmp(*argv, "-abi") == 0) {
+            format = TT_ABI;
+        } else if (strcasecmp(*argv, "-alf") == 0) {
+            format = TT_ALF;
+        } else if (strcasecmp(*argv, "-scf") == 0) {
+            format = TT_SCF;
+        } else if (strcasecmp(*argv, "-exp") == 0) {
+            format = TT_EXP;
+        } else if (strcasecmp(*argv, "-pln") == 0) {
+            format = TT_PLN;
+        } else if (strcasecmp(*argv, "-ztr") == 0) {
+            format = TT_ZTR;
+        } else if (strcasecmp(*argv, "-ctf") == 0) {
+            format = TT_CTF;
+	} else if (strcmp(*argv, "-fofn") == 0) {
+	    fofn = *++argv;
+	    argc--;
+	    from_stdin = 0;
+        } else if (strcasecmp(*argv, "-output") == 0) {
+	    if (NULL == (outfp = fopen(*++argv, "wb"))) {
+		perror(*argv);
+		return 1;
+	    }
+            argc--;
+	} else if (**argv != '-') {
+	    from_stdin = 0;
+	    break;
+        } else {
+            usage();
+        }
+    }
+
+    if (!from_stdin) {
+	if (fofn) {
+	    FILE *fofn_fp;
+	    char line[8192];
+
+	    if (strcmp(fofn, "stdin") == 0)
+		fofn_fp = stdin;
+	    else
+		fofn_fp = fopen(fofn, "r");
+
+	    if (fofn_fp) {
+		while (fgets(line, 8192, fofn_fp) != NULL) {
+		    char *cp;
+		    if (cp = strchr(line, '\n'))
+			*cp = 0;
+		    if (format == TT_EXP) {
+			infp = open_exp_mfile(line, NULL);
+		    } else {
+			infp = open_trace_mfile(line, NULL);
+		    }
+		    if (NULL == infp) {
+			perror(line);
+			ret = 1;
+		    } else {
+			ret |= do_trans(infp, line, outfp, format);
+			mfclose(infp);
+		    }
+		}
+		fclose(fofn_fp);
+	    }
+	}
+	for (;argc > 0; argc--, argv++) {
+	    if (format == TT_EXP) {
+		infp = open_exp_mfile(*argv, NULL);
+	    } else {
+		infp = open_trace_mfile(*argv, NULL);
+	    }
+	    if (NULL == infp) {
+		perror(*argv);
+		ret = 1;
+	    } else {
+		ret |= do_trans(infp, *argv, outfp, format);
+		mfclose(infp);
+	    }
+	}
+    } else {
+	ret = do_trans(infp, "<stdin>", outfp, format);
+    }
+
+    return ret;
+}
+