C++ (Cpp) DBAdaptor_new Beispiele

Beispiel #1

int main(int argc, char *argv[]) {
  DBAdaptor *dba;
  Slice *slice;
  SliceAdaptor *sliceA;
  SequenceAdaptor *seqA;

  initEnsC(argc, argv);

  dba = DBAdaptor_new("ensembldb.ensembl.org","anonymous",NULL,"homo_sapiens_core_70_37",5306,NULL);
  //dba = DBAdaptor_new("ens-livemirror.internal.sanger.ac.uk","ensro",NULL,"homo_sapiens_core_70_37",3306,NULL);
  //dba = DBAdaptor_new("genebuild2.internal.sanger.ac.uk","ensadmin","ensembl","steve_hs_testdb",3306,NULL);

  sliceA = DBAdaptor_getSliceAdaptor(dba);
  seqA = DBAdaptor_getSequenceAdaptor(dba);

//
// Test fetch_by_Slice_start_end_strand
//
  slice = SliceAdaptor_fetchByRegion(sliceA,"chromosome",CHR,START,END,STRAND,NULL,0);
  compareComplements(slice, seqA);

  slice = SliceAdaptor_fetchByRegion(sliceA, "clone","AL031658.11", POS_UNDEF, POS_UNDEF, STRAND_UNDEF, NULL, 0);
  compareComplements(slice, seqA);

  slice = SliceAdaptor_fetchByRegion(sliceA, "supercontig","NT_028392", POS_UNDEF, POS_UNDEF, STRAND_UNDEF, NULL, 0);
  compareComplements(slice, seqA);

  slice = SliceAdaptor_fetchByRegion(sliceA, "contig", "AL031658.11.1.162976", POS_UNDEF, POS_UNDEF, STRAND_UNDEF, NULL, 0);
  compareComplements(slice, seqA);

  return 0;
}

Beispiel #2

int main(int argc, char *argv[]) {
  DBAdaptor *      dba;
  StatementHandle *sth;
  ResultRow *      row;
  Vector *         slices;
  int              nSlices;
  htsFile *      out;

  int   argNum = 1;

  char *inFName  = NULL;
  char *outFName = NULL;

  char *dbUser = "******";
  char *dbPass = NULL;
  int   dbPort = 3306;

  char *dbHost = "ens-staging.internal.sanger.ac.uk";
  char *dbName = "homo_sapiens_core_71_37";

  char *assName = "GRCh37";

  char *chrName = "1";


  int flags = 0;
  int   threads  = 1;

  initEnsC(argc, argv);

  while (argNum < argc) {
    char *arg = argv[argNum];
    char *val;

// Ones without a val go here
    if (!strcmp(arg, "-U") || !strcmp(arg,"--ucsc_naming")) {
      flags |= M_UCSC_NAMING;
    } else {
// Ones with a val go in this block
      if (argNum == argc-1) {
        Bamcov_usage();
      }

      val = argv[++argNum];
  
      if (!strcmp(arg, "-i") || !strcmp(arg,"--in_file")) {
        StrUtil_copyString(&inFName,val,0);
      } else if (!strcmp(arg, "-o") || !strcmp(arg,"--out_file")) {
        StrUtil_copyString(&outFName,val,0);
      } else if (!strcmp(arg, "-h") || !strcmp(arg,"--host")) {
        StrUtil_copyString(&dbHost,val,0);
      } else if (!strcmp(arg, "-p") || !strcmp(arg,"--password")) {
        StrUtil_copyString(&dbPass,val,0);
      } else if (!strcmp(arg, "-P") || !strcmp(arg,"--port")) {
        dbPort = atoi(val);
      } else if (!strcmp(arg, "-n") || !strcmp(arg,"--name")) {
        StrUtil_copyString(&dbName,val,0);
      } else if (!strcmp(arg, "-u") || !strcmp(arg,"--user")) {
        StrUtil_copyString(&dbUser,val,0);
      } else if (!strcmp(arg, "-t") || !strcmp(arg,"--threads")) {
        threads = atoi(val);
      } else if (!strcmp(arg, "-a") || !strcmp(arg,"--assembly")) {
        StrUtil_copyString(&assName,val,0);
      } else if (!strcmp(arg, "-v") || !strcmp(arg,"--verbosity")) {
        verbosity = atoi(val);
// Temporary
      } else if (!strcmp(arg, "-c") || !strcmp(arg,"--chromosome")) {
        StrUtil_copyString(&chrName,val,0);
      } else {
        fprintf(stderr,"Error in command line at %s\n\n",arg);
        Bamcov_usage();
      }
    }
    argNum++;
  }

  if (verbosity > 0) {
    printf("Program for calculating read coverage in a BAM file \n"
           "Steve M.J. Searle.  [email protected]  Last update April 2013.\n");
  }

  if (!inFName || !outFName) {
    Bamcov_usage();
  }

  dba = DBAdaptor_new(dbHost,dbUser,dbPass,dbName,dbPort,NULL);

  //nSlices = getSlices(dba, destName);
  nSlices = 1;

  slices = Vector_new();

  SliceAdaptor *sa = DBAdaptor_getSliceAdaptor(dba);

  Slice *slice = SliceAdaptor_fetchByRegion(sa,NULL,chrName,POS_UNDEF,POS_UNDEF,1,NULL, 0);

  Vector_addElement(slices,slice);

  if (Vector_getNumElement(slices) == 0) {
    fprintf(stderr, "Error: No slices.\n");
    exit(1);
  }

  htsFile *in = hts_open(inFName, "rb");
  if (in == 0) {
    fprintf(stderr, "Fail to open BAM file %s\n", inFName);
    return 1;
  }

  hts_set_threads(in, threads);
  hts_idx_t *idx;
  idx = bam_index_load(inFName); // load BAM index
  if (idx == 0) {
    fprintf(stderr, "BAM index file is not available.\n");
    return 1;
  }

  int i;
  for (i=0; i<Vector_getNumElement(slices); i++) {
    Slice *slice = Vector_getElementAt(slices,i);

    if (verbosity > 0) printf("Working on '%s'\n",Slice_getName(slice));

//    if (verbosity > 0) printf("Stage 1 - retrieving annotation from database\n");
//    Vector *genes = getGenes(slice, flags);

    if (verbosity > 0) printf("Stage 1 - calculating coverage\n");
    calcCoverage(inFName, slice, in, idx, flags);
  }


  hts_idx_destroy(idx);
  hts_close(in);

  if (verbosity > 0) printf("Done\n");
  return 0;
}