Python vcf2wt_main Examples

Example #1

File: script02_convert_to_wt.py Project: BSGOxford/BrowseVCF

def create_one_wormtable(schema_path, inp_file, out_file):
  """
  Create a single wormtable database from the input file and an .xml schema.
  """

  cachesize = '16G '
  if WIN_PLATFORM_NONFREE:
      cachesize = '4G ' # to deal with BDB error...

  runargs = '-q --schema ' + schema_path + ' --cache-size=' + cachesize + \
            inp_file + ' ' + out_file
  #run vcf2wt as a library function, no system calls
  try:
      wt.vcf2wt_main(runargs.split())
  except:
      raise #return quietly

  # add row index for this wormtable
  # supersedes add_all_rowid_indexes() and add_one_rowid_index()
  # doing it here means we avail of the thread/process that is already spawned
  # sys.stderr.write('Indexing %s\n' % (out_file,))
  runargs = 'add -q --cache-size=' + cachesize + out_file + ' row_id'
  wt.wtadmin_main(runargs.split())

  return

Example #2

File: script02_convert_to_wt.py Project: sandwu/BrowseVCF

def create_one_wormtable(schema_path, inp_file, out_file):
  """
  Create a single wormtable database from the input file and an .xml schema.
  """

  cachesize = '16G '
  if WIN_PLATFORM_NONFREE:
      cachesize = '4G ' # to deal with BDB error...

  runargs = '-q --schema ' + schema_path + ' --cache-size=' + cachesize + \
            inp_file + ' ' + out_file
  #run vcf2wt as a library function, no system calls
  try:
      wt.vcf2wt_main(runargs.split())
  except:
      raise #return quietly

  # add row index for this wormtable
  # supersedes add_all_rowid_indexes() and add_one_rowid_index()
  # doing it here means we avail of the thread/process that is already spawned
  # sys.stderr.write('Indexing %s\n' % (out_file,))
  runargs = 'add -q --cache-size=' + cachesize + out_file + ' row_id'
  wt.wtadmin_main(runargs.split())

  return

Example #3

File: script01_preprocess.py Project: sandwu/BrowseVCF

def create_general_schema(out_folder):
    """
  Create the general .xml schema which will be used as template for the creation
  of several other schemas (one for each field in the .vcf file).
  """

    schema_file = ""
    preproc_file = out_folder + '/pre_processed_inp_file.vcf.gz'
    if WIN_PLATFORM_NONFREE:
        schema_file = out_folder
        schema_file = schema_file.replace('\\', '\\\\')
        schema_file += '\\\\schema.xml'
        preproc_file = preproc_file.replace('\\', '\\\\')
        preproc_file = preproc_file.replace('/', '\\\\')
    else:
        schema_file = out_folder + '/schema.xml'
    runargs = '-q -g ' + preproc_file + ' ' + schema_file
    # call vcf2wt as a library function
    wt.vcf2wt_main(runargs.split())
    return schema_file

Example #4

File: script01_preprocess.py Project: BSGOxford/BrowseVCF

def create_general_schema(out_folder):
  """
  Create the general .xml schema which will be used as template for the creation
  of several other schemas (one for each field in the .vcf file).
  """

  schema_file = ""
  preproc_file = out_folder + '/pre_processed_inp_file.vcf.gz'
  if WIN_PLATFORM_NONFREE:
    schema_file = out_folder
    schema_file = schema_file.replace('\\', '\\\\')
    schema_file += '\\\\schema.xml'
    preproc_file = preproc_file.replace('\\', '\\\\')
    preproc_file = preproc_file.replace('/', '\\\\')
  else:
    schema_file = out_folder + '/schema.xml'
  runargs = '-q -g ' + preproc_file + ' ' + schema_file
  # call vcf2wt as a library function
  wt.vcf2wt_main(runargs.split())
  return schema_file

Example #5

File: vcf2wt_dev.py Project: basesLoaded/wormtable

import wormtable as wt

if __name__ == "__main__":
    wt.vcf2wt_main()

Example #6

 def setUp(self):
     super(WtadminTest, self).setUp()
     wt.vcf2wt_main([EXAMPLE_VCF, self._homedir, "-fq"])
     self._table = wt.open_table(self._homedir)

Example #7

File: utilities.py Project: varun-ramraj/wormtable

 def setUp(self):
     super(WtadminTest, self).setUp()
     wt.vcf2wt_main([EXAMPLE_VCF, self._homedir, "-fq"])
     self._table = wt.open_table(self._homedir)