185 lines
3.4 KiB
C
185 lines
3.4 KiB
C
/*
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Title: autoted
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File: autoted.c
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Purpose: Main module
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Last update: Thursday 11 July 1991
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Change log:
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*/
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/*
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*/
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/* ---- Includes ---- */
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#include "seq.h" /* IMPORT: Seq, NULLBaseNum */
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#include <stdio.h> /* IMPORT: stderr, fprintf */
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#include "seqIOABI.h"
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#include "seqIOALF.h"
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#include "seqIOSCF.h"
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#include "seqIOPlain.h"
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#include "mystdlib.h" /* IMPORT: exit */
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/* ---- Static variables ---- */
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/*
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Where to put the command line arguments when we dig them
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out of the resources.
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*/
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typedef struct
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{ char * plain;
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char * ABI;
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char * ALF;
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char * SCF;
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char * output;
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char * enzyme;
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int bottom;
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char * raw;
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} Arguments;
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/* ---- Callbacks ---- */
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/* ---- Internal functions ---- */
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static void usage(int argc, char **argv)
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{ int i;
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if (argc != 1)
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{ fprintf(stderr, "%s: unknown option%s:", argv[0], (argc>2)?"s":"");
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for (i=1; i<argc; i++)
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fprintf(stderr, " %s", argv[i]);
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fprintf(stderr, "\n\n");
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}
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fprintf(stderr,
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"usage: %s\n", argv[0]);
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fprintf(stderr,
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" [(-PLN | -ABI | -ALF | -SCF ) {tracefilename} [-bottom {1(true) or 0(false)}]\n");
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fprintf(stderr,
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" -output {outputfilename}\n");
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}
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/* ---- Exported functions ---- */
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void main(unsigned int argc, char **argv)
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{
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Arguments args;
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char *fn;
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char *o_fn;
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Seq currSeq;
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int rc;
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int count;
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char *enzString = "CAGGTC";
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/* parse command line arguments here */
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count=1;
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fn = NULL;
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args.ABI = NULL;
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args.ALF = NULL;
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args.SCF = NULL;
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args.output = NULL;
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args.plain = NULL;
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args.bottom = 0;
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args.raw = 0;
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args.enzyme = NULL;
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while (count < argc) {
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char *a = argv[count];
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if ( *a != '-') {
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usage(argc, argv);
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fprintf(stderr,"not a - switch\n");
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exit(1);
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}
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if (strcmp(a,"-PLN") == 0) {
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args.plain = fn = argv[++count];
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} else if (strcmp(a,"-ABI") == 0) {
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args.ABI = fn = argv[++count];
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} else if (strcmp(a,"-ALF") == 0) {
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args.ALF = fn = argv[++count];
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} else if (strcmp(a,"-SCF") == 0) {
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args.SCF = fn = argv[++count];
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} else if (strcmp(a,"-output") == 0) {
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args.output = o_fn = argv[++count];
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} else if (strcmp(a,"-bottom") == 0) {
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args.bottom = atoi(argv[++count]);
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} else if (strcmp(a,"-raw") == 0) {
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args.raw = argv[++count];
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} else if (strcmp(a,"-enzyme") == 0) {
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args.enzyme = enzString = argv[++count];
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} else {
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usage(argc, argv);
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fprintf(stderr,"switch not recognised\n");
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exit(1);
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}
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count++;
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}
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/*
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Die if bad options given.
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*/
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if ((args.plain==NULL &&
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args.ABI==NULL &&
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args.ALF==NULL &&
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args.SCF==NULL))
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{
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usage(argc, argv);
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fprintf(stderr,"illegal argument combination\n");
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exit(1);
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}
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/* if ( args.output==NULL )
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{
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usage(argc, argv);
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fprintf(stderr,"no output specified\n");
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exit(1);
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}
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*/
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if (args.plain != NULL)
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currSeq = readSeqPlain(fn,args.bottom,enzString);
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else if (args.ABI != NULL)
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currSeq = readSeqABI(fn,args.bottom,enzString);
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else if (args.ALF != NULL)
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currSeq = readSeqALF(fn,args.bottom,enzString);
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else if (args.SCF != NULL)
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currSeq = readSeqSCF(fn,args.bottom,enzString);
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if (currSeq == NULLSeq) {
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fprintf(stderr,"Error reading file %s\n",fn);
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exit(1);
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}
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/* rc=writeSeq(currSeq, o_fn, (args.raw == NULL)?fn:args.raw,1);*/
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printf("%s: %d\n",fn,currSeq->info.primerPos);
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}
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