def get_matching_files(all_fastq, all_mapping, read_indicator, barcode_indicator, mapping_indicator):
 read_files = []
 barcode_files = []
 mapping_files = {}
 matching_files = {}
 for curr_file in all_mapping:
  try:
   curr_mapping = curr_file.split(mapping_indicator)
   mapping_files[(curr_mapping[0] + splitext(curr_mapping[1])[0])] = curr_file
  except IndexError:
   raise IndexError(('Found file with a mapping file extension that does not contain the mapping file indicators (see mapping_indicator): %s' % curr_file))
 for curr_file in all_fastq:
  curr_file_string_read = curr_file.split(read_indicator)
  curr_file_string_bc = curr_file.split(barcode_indicator)
  if (len(curr_file_string_read) == 2):
   read_files.append(curr_file_string_read)
  elif (len(curr_file_string_bc) == 2):
   barcode_files.append(curr_file_string_bc)
  else:
   raise ValueError(((('Invalid filename found for splitting on input ' + ('for file %s, ' % curr_file)) + 'check input read indicator ') + 'and barcode indicator parameters.'))
 for curr_read in read_files:
  for curr_bc in barcode_files:
   if (curr_read == curr_bc):
    curr_read_sans_ext = (curr_read[0] + curr_read[1].split('.f')[0])
    try:
     matching_files[read_indicator.join(curr_read)] = (barcode_indicator.join(curr_bc), mapping_files[curr_read_sans_ext])
    except KeyError:
     raise KeyError(('Found read file with no matching mapping file: %s' % read_indicator.join(curr_read)))
 return matching_files

def get_matching_files ( all_fastq , all_mapping , read_indicator , barcode_indicator , mapping_indicator ) : read_files = [ ] barcode_files = [ ] mapping_files = { } matching_files = { } for curr_file in all_mapping : try : curr_mapping = curr_file . split ( mapping_indicator ) mapping_files [ ( curr_mapping [ 0 ] + splitext ( curr_mapping [ 1 ] ) [ 0 ] ) ] = curr_file except IndexError : raise IndexError ( ( 'Found file with a mapping file extension that does not contain the mapping file indicators (see mapping_indicator): %s' % curr_file ) ) for curr_file in all_fastq : curr_file_string_read = curr_file . split ( read_indicator ) curr_file_string_bc = curr_file . split ( barcode_indicator ) if ( len ( curr_file_string_read ) == 2 ) : read_files . append ( curr_file_string_read ) elif ( len ( curr_file_string_bc ) == 2 ) : barcode_files . append ( curr_file_string_bc ) else : raise ValueError ( ( ( ( 'Invalid filename found for splitting on input ' + ( 'for file %s, ' % curr_file ) ) + 'check input read indicator ' ) + 'and barcode indicator parameters.' ) ) for curr_read in read_files : for curr_bc in barcode_files : if ( curr_read == curr_bc ) : curr_read_sans_ext = ( curr_read [ 0 ] + curr_read [ 1 ] . split ( '.f' ) [ 0 ] ) try : matching_files [ read_indicator . join ( curr_read ) ] = ( barcode_indicator . join ( curr_bc ) , mapping_files [ curr_read_sans_ext ] ) except KeyError : raise KeyError ( ( 'Found read file with no matching mapping file: %s' % read_indicator . join ( curr_read ) ) ) return matching_files
get all file names in a directory .