diff srf2fastq/io_lib-1.12.2/io_lib/traceType.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/io_lib/traceType.c	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,240 @@
+/*
+ * Copyright (c) Medical Research Council 1994. 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.
+ */
+
+/*
+  Title:  traceType
+
+  File:   traceType.c
+  Purpose: determining trace format
+
+  Last update: 01/09/94
+
+  Change log : Update for use with the Read library.
+*/
+
+/* ---- Imports ---- */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+
+#include "io_lib/stdio_hack.h"
+
+#include "io_lib/traceType.h"
+#include "io_lib/Read.h"
+#include "io_lib/open_trace_file.h"
+
+#ifdef USE_BIOLIMS
+#include "spBiolims.h"
+#endif
+
+#ifndef isascii
+#define isascii(c) ((c) >= 0 && (c) <= 0x7f)
+#endif
+
+/* ---- Privates ---- */
+static struct {
+    int type;
+    int offset;
+    char *string;
+} magics[] = {
+	{ TT_SCF, 0,   ".scf" } ,
+	{ TT_CTF, 1,   "\007\375\343\000" } ,   /* mieg */
+	{ TT_ZTR, 0,   "\256ZTR\r\n\032\n" } ,
+	{ TT_ABI, 0,   "ABIF" } ,
+	{ TT_ABI, 128, "ABIF" } ,
+	{ TT_ALF, 518, "ALF " } ,
+	{ TT_SCF, 0,   "\234\330\300\000" }, /* Amersham variant */
+	{ TT_SFF, 0,   ".sff" } ,
+	{ TT_EXP, 0,	"ID   " } ,
+	{ TT_ALF, 0,   "ALF " } , /* Added by newer alfsplit programs */
+	{ TT_ALF, 0,   "\021G\021G" } , /* Pharmacia's alfsplit equiv */
+	{ TT_ALF, 1546,"X-axis" } /* Good guestimation if all else fails */
+};
+
+#define Number(A) ( sizeof(A) / sizeof((A)[0]) )
+
+/* ---- exported ---- */
+
+/* unix specific file deletion routine */
+int remove_file(char *fn) { return unlink(fn); }
+
+
+/*
+ * Determine the trace type for FILE * 'fp'.
+ *
+ * NB - This function should NOT be used when biolims support is required
+ * (as biolims doesn't use files !)
+ *
+ * Returns:
+ *     TT_SCF, TT_CTF, TT_ZTR, TT_ABI, TT_ALF, or TT_PLN for success.
+ *     TT_UNK for unknown type.
+ *     TT_ERR for error.
+ */
+int fdetermine_trace_type(FILE *fp)
+{
+    unsigned int i;
+    size_t len;
+    char buf[512];
+    int ps;
+    int acgt;
+    int c;
+
+    /* check magics */
+    for (i = 0 ; i < Number(magics) ; i++) {
+	if (fseek(fp,magics[i].offset,0) == 0) {
+	    len = strlen(magics[i].string);
+	    if (fread(buf,1,len,fp)==len) {
+		if (strncmp(buf,magics[i].string,len)==0) {
+		    return magics[i].type;
+		}
+	    }
+	}
+    }
+    fseek(fp, 0, 0);
+
+    /* determine if this is a text file */
+    len = 0; ps = 0; acgt = 0;
+    for (i = 0; i < 512; i++) {
+	if ( ( c = fgetc(fp) ) == EOF ) break;
+	switch(c) {
+	case 'a': case 'c': case 'g': case 't':
+	case 'A': case 'C': case 'G': case 'T':
+	/*YUK! need the next line?*/
+	case 'n': case 'N': case '-':
+	    acgt++;
+	default:
+	    len++;
+	    if ( (isprint(c) && isascii(c)) || isspace(c) ) ps++;
+	}
+    }
+    fseek(fp, 0, 0);
+    /*YUK! 75% of characters printable means text*/
+    if ( 100 * (size_t)ps > 75 * len ) {
+	/*YUK! 75% of printables ACGTN means plain*/
+	if (100 * acgt > 75 * ps) {
+	    return TT_PLN;
+	}
+    }
+
+    /* YUK! short files are not traces? */
+    if (len<512) {
+        return TT_UNK;
+    }
+
+    return TT_UNK;
+}
+
+/*
+ * Determine the trace type for file 'fn'.
+ *
+ * Returns:
+ *     TT_SCF, TT_CTF, TT_ZTR, TT_ABI, TT_ALF, TT_BIO, or TT_PLN for success.
+ *     TT_UNK for unknown type.
+ *     TT_ERR for error.
+ */
+int determine_trace_type(char *fn)
+{
+    FILE *fp;
+    int r;
+
+#ifdef USE_BIOLIMS
+    if(IS_BIOLIMS_PATH(fn))
+      return TT_BIO;
+#endif
+
+    if ( (fp = open_trace_file(fn, NULL)) == NULL ) return TT_ERR;
+
+    r = fdetermine_trace_type(fp);
+    fclose(fp);
+
+    return r;
+}
+
+/*
+ * Converts a trace type string to an integer.
+ */
+int trace_type_str2int(char *str) {
+    if (strcmp(str, "SCF") == 0 || strcmp(str, "scf") == 0)
+	return TT_SCF;
+    else if (strcmp(str, "SFF") == 0 || strcmp(str, "sff") == 0)
+        return TT_SFF;   /* 454 */
+    else if (strcmp(str, "CTF") == 0 || strcmp(str, "ctf") == 0)
+        return TT_CTF;   /* mieg */
+    else if (strcmp(str, "ZTR") == 0 || strcmp(str, "ztr") == 0)
+        return TT_ZTR;
+    else if (strcmp(str, "ZTR1") == 0 || strcmp(str, "ztr1") == 0)
+        return TT_ZTR1;
+    else if (strcmp(str, "ZTR2") == 0 || strcmp(str, "ztr2") == 0)
+        return TT_ZTR2;
+    else if (strcmp(str, "ZTR3") == 0 || strcmp(str, "ztr3") == 0)
+        return TT_ZTR3;
+    else if (strcmp(str, "ABI") == 0 || strcmp(str, "abi") == 0)
+	return TT_ABI;
+    else if (strcmp(str, "ALF") == 0 || strcmp(str, "alf") == 0)
+	return TT_ALF;
+    else if (strcmp(str, "PLN") == 0 || strcmp(str, "pln") == 0)
+	return TT_PLN;
+    else if (strcmp(str, "EXP") == 0 || strcmp(str, "exp") == 0)
+	return TT_EXP;
+    else if (strcmp(str, "BIO") == 0 || strcmp(str, "bio") == 0)
+        return TT_BIO;
+    else if (strcmp(str, "ANYTR") == 0 || strcmp(str, "anytr") == 0)
+        return TT_ANYTR;
+    else
+	return TT_UNK;
+}
+
+/*
+ * Converts a trace type integer to a string.
+ */
+char *trace_type_int2str(int type) {
+    char *t;
+
+    switch(type) {
+    case TT_SCF: t = "SCF"; break;
+    case TT_SFF: t = "SFF"; break;  /* 454 */
+    case TT_CTF: t = "CTF"; break;  /* mieg */
+    case TT_ZTR: t = "ZTR";break;
+    case TT_ZTR1: t = "ZTR1";break;
+    case TT_ZTR2: t = "ZTR2";break;
+    case TT_ZTR3: t = "ZTR3";break;
+    case TT_ABI: t = "ABI"; break;
+    case TT_ALF: t = "ALF"; break;
+    case TT_PLN: t = "PLN"; break;
+    case TT_EXP: t = "EXP"; break;
+    case TT_BIO: t = "BIO"; break;
+    case TT_ANYTR: t="ANYTR"; break;
+    default:
+    case TT_UNK: t = "UNK"; break;
+    }
+
+    return t;
+}
+
+/*
+ * Returns a statically declared string containing a 3 character
+ * identifier for the trace type of this file.
+ * "ERR" represents error, and "UNK" for unknown.
+ * Successful values are "SCF", "ABI", "ALF", "PLN", "CTF", "ZTR" and "BIO".
+ */
+char *trace_type_str(char *traceName)
+{
+    int t;
+
+    if ((t = determine_trace_type(traceName)) == TT_ERR)
+	return "ERR";
+    else
+	return trace_type_int2str(t);
+}