Exemple #1
0
int main(int argc, char *argv[])
{
  struct lineFile *pf, *ef, *apf;
  FILE *of, *nf, *enf=NULL;
  char *efName=NULL, filename[256];
  int verb = 0;

verboseSetLevel(0);
optionInit(&argc, argv, optionSpecs);
if (argc < 3)
    {
      fprintf(stderr, "USAGE: pslAnal [-epcr=<file> -verbose=<level>] <isPCR psl file> <all.primers> <outfile>\n");
    return 1;
    }
verb = optionInt("verbose", 0);
verboseSetLevel(verb);

 efName = optionVal("epcr", NULL);
 pf = pslFileOpen(argv[1]);
 apf = lineFileOpen(argv[2], TRUE);

 of = mustOpen(argv[3], "w");
 sprintf(filename, "%s.notfound.primers", argv[3]);
 nf = mustOpen(filename, "w");

 verbose(1, "Reading all.primers file\n");
 readPrimerInfo(apf);

 if (efName)
   {
     ef = lineFileOpen(efName, TRUE);
     verbose(1, "Reading epcr file\n");
     readEpcr(ef);
   }

 verbose(1, "Reading and processing isPCR file\n");
 processPrimers(pf, of);

 if (efName)
   {
     verbose(1, "Writing epcr.not.found file\n");
     sprintf(filename, "epcr.not.found");
     enf = mustOpen(filename, "w");
     writeEpcrNotFound(enf);
   }

 verbose(1, "Writing out primers not found\n");
 writePrimersNotFound(nf);

 if (efName)
   {
     lineFileClose(&ef);
     fclose(enf);
   }
 lineFileClose(&pf);
 lineFileClose(&apf);
 fclose(of);
 fclose(nf);

 return(0);
}
int main(int argc, char *argv[])
{
  struct lineFile *pf, *ef, *apf;
  FILE *of, *nf, *enf=NULL;
  char *efName=NULL, filename[256], notFound[256];
  int verb = 0;

verboseSetLevel(0);
optionInit(&argc, argv, optionSpecs);
if (argc < 3)
    {
      verbose(0, "usage: pslFilterPrimers [-epcr=<file> -verbose=<level>] <isPCR psl file> <all.primers> <outfile>\n");
    return 1;
    }
verb = optionInt("verbose", 0);
verboseSetLevel(verb);

 efName = optionVal("epcr", NULL);
 pf = pslFileOpen(argv[1]);
 apf = lineFileOpen(argv[2], TRUE);

 of = mustOpen(argv[3], "w");
 safef(notFound, sizeof(filename), "%s.notfound.primers", argv[3]);
 nf = mustOpen(notFound, "w");

 verbose(1, "Reading all primers file: '%s'\n", argv[2]);
 readPrimerInfo(apf);

 if (efName)
   {
     ef = lineFileOpen(efName, TRUE);
     verbose(1, "Reading epcr file: '%s'\n", efName);
     readEpcr(ef);
   }

 verbose(1, "Reading isPCR file: '%s' processing output to: '%s'\n", argv[1], argv[3]);
 processPrimers(pf, of);

 if (efName)
   {
     safef(filename, sizeof(filename), "epcr.not.found");
     verbose(1, "Writing %s file\n", filename);
     enf = mustOpen(filename, "w");
     writeEpcrNotFound(enf);
   }

 verbose(1, "Writing primers not found to file: '%s'\n", notFound);
 writePrimersNotFound(nf);

 if (efName)
   {
     lineFileClose(&ef);
     fclose(enf);
   }
 lineFileClose(&pf);
 lineFileClose(&apf);
 fclose(of);
 fclose(nf);

 return(0);
}