a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
  Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/utils/faTrans/faTrans.c src/utils/faTrans/faTrans.c
index 07b0ccd..8f801b3 100644
--- src/utils/faTrans/faTrans.c
+++ src/utils/faTrans/faTrans.c
@@ -1,83 +1,82 @@
 /* faTrans - Translate DNA .fa file to peptide. */
 #include "common.h"
 #include "dnautil.h"
 #include "dnaseq.h"
 #include "fa.h"
 #include "options.h"
 
-static char const rcsid[] = "$Id: faTrans.c,v 1.6 2005/09/15 06:15:52 markd Exp $";
 
 /* command line options */
 static struct optionSpec optionSpecs[] =
 {
     {"stop", OPTION_BOOLEAN},
     {"offset", OPTION_INT},
     {"cdsUpper", OPTION_BOOLEAN},
     {NULL, 0}
 };
 
 boolean clStop = FALSE;
 int clOffset = 0;
 boolean clCdsUpper = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "faTrans - Translate DNA .fa file to peptide\n"
   "usage:\n"
   "   faTrans in.fa out.fa\n"
   "options:\n"
   "   -stop stop at first stop codon (otherwise puts in Z for stop codons)\n"
   "   -offset=N start at a particular offset.\n"
   "   -cdsUpper - cds is in upper case\n"
 );
 }
 
 struct dnaSeq *transOne(struct dnaSeq *dna)
 /* translate one mRNA sequence to a peptide */
 {
 int off = clOffset;
 if (clCdsUpper)
     {
     /* adjust offset to first upper */
     char *p = dna->dna + off;
     while ((*p != '\0') && islower(*p))
         p++;
     off = p - dna->dna;
     /* zero-terminate at first lower */
     while ((*p != '\0') && isupper(*p))
         p++;
     *p = '\0';
     }
 return translateSeq(dna, off, clStop);
 }
 
 void faTrans(char *inFile, char *outFile)
 /* faTrans - Translate DNA .fa file to peptide. */
 {
 struct lineFile *lf = lineFileOpen(inFile, TRUE);
 FILE *f = mustOpen(outFile, "w");
 struct dnaSeq dna, *pep;
 ZeroVar(&dna);
 
 while (faMixedSpeedReadNext(lf, &dna.dna, &dna.size, &dna.name))
     {
     pep = transOne(&dna);
     faWriteNext(f, pep->name, pep->dna, pep->size);
     freeDnaSeq(&pep);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, optionSpecs);
 if (argc != 3)
     usage();
 clStop = optionExists("stop");
 clOffset = optionInt("offset", clOffset);
 clCdsUpper = optionExists("cdsUpper");
 faTrans(argv[1], argv[2]);
 return 0;
 }