260 lines
4.9 KiB
C
260 lines
4.9 KiB
C
/*
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Title: getMCH
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File: getMCH.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 "seqRead.h"
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#include "mystdlib.h" /* IMPORT: exit */
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#include "traceType.h"
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/*
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* EMBL_STYLE
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* Produce output in EMBL_STYLE output
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*/
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#define EMBL_STYLE
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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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int bottom;
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char * raw;
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int header;
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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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/*
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** Hacked from sqeOutput.c
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*/
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#ifdef EMBL_STYLE
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#define BasesPerLine 60
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#else /*EMBL_STYLE*/
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#define BasesPerLine 50
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#endif /*EMBL_STYLE*/
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Boolean writeSeq(Seq seq, char *fn)
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/*
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Write the clipped, edited part of the ABI format sequence `seq'
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into file `fn'. The result indicates success.
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Currently, this just writes the bases out as text.
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*/
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{
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FILE *fp;
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int baseNum, lineLen;
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/* Open for writing, text */
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if ((fp=fopen(fn, "w")) == NULL) return(False);
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lineLen = 0;
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/* write experiment file header */
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fprintf(fp,"SQ\n");
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/* write sequence */
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#ifdef EMBL_STYLE
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for (baseNum=0; baseNum<seq->NedBases; baseNum++) {
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if (lineLen==0) fputs(" ",fp);
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fputc(getBase(seq, EdBases, baseNum), fp);
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if (++lineLen == BasesPerLine) {
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fputc('\n', fp);
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lineLen = 0;
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} else if ((lineLen % 10)==0) fputc(' ', fp);
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}
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#else /*EMBL_STYLE*/
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for (baseNum=0; baseNum<seq->NedBases; baseNum++) {
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fputc(getBase(seq, EdBases, baseNum), fp);
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if (++lineLen == BasesPerLine) {
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fputc('\n', fp);
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lineLen = 0;
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}
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}
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#endif /*EMBL_STYLE*/
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if (lineLen != 0) fputc('\n', fp);
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/* write experiment file header */
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fprintf(fp,"//\n");
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/* write cutoffs */
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#ifdef EMBL_STYLE
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fprintf(fp,"CC Quality clipping by newted May-1992\n");
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fprintf(fp,"QL %d\n",seq->leftCutoff);
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fprintf(fp,"QR %d\n",seq->NedBases-seq->rightCutoff+1);
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#else /*EMBL_STYLE*/
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fprintf(fp,"CC Quality clipping by newted May-1992\n");
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fprintf(fp,"QL %d\n",seq->leftCutoff);
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fprintf(fp,"QR %d\n",seq->NedBases-seq->rightCutoff+1);
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#endif /*EMBL_STYLE*/
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(void) fclose(fp);
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return(True);
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}
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/* ---- Exported functions ---- */
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void setScaleFactor(float f)
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/* a dummy routine */
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{ }
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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 = "TAGAGGCTCCCC";
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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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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 {
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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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if (args.plain != NULL)
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currSeq = readSeq(fn,0,"",trace_types[TT_PLN]);
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else if (args.ABI != NULL)
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currSeq = readSeq(fn,0,"",trace_types[TT_ABI]);
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else if (args.ALF != NULL)
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currSeq = readSeq(fn,0,"",trace_types[TT_ALF]);
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else if (args.SCF != NULL)
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currSeq = readSeq(fn,0,"",trace_types[TT_SCF]);
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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);
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if (!rc) {
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fprintf(stderr,"Error writing file %s\n",o_fn);
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exit(1);
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}
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exit(0);
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}
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