def select_consensus_files( consensus_file, output_file ):
selected_files = []
with open( consensus_file ) as handle:
for line in handle:
sequence_file, reference_file, consensus_file = line.strip().split()
if consensus_file.endswith('None'):
pass
elif fasta_count( consensus_file ) == 1:
selected_files.append( consensus_file )
else:
selected_files.append( reference_file )
output_selected_consensus( output_file, selected_files )
def select_consensus_files(consensus_file, output_file):
selected_files = []
with open(consensus_file) as handle:
for line in handle:
sequence_file, reference_file, consensus_file = line.strip().split(
)
if consensus_file.endswith('None'):
pass
elif fasta_count(consensus_file) == 1:
selected_files.append(consensus_file)
else:
selected_files.append(reference_file)
output_selected_consensus(output_file, selected_files)
def generate_consensus_files( cluster_list, consensus_tool, output_file ):
consensus_files = []
with open( cluster_list ) as handle:
for line in handle:
sequence_file, reference_file, count = line.strip().split()
print sequence_file, reference_file
if reference_file.endswith('None'):
consensus_files.append( (sequence_file, 'None', 'None') )
elif fasta_count( sequence_file ) == 1:
consensus_files.append( (sequence_file, reference_file, 'None') )
else:
consensus = consensus_tool( sequence_file, reference_file )
consensus_files.append( (sequence_file, reference_file, consensus) )
write_consensus_files( consensus_files, output_file )
def select_final_sequences( self, consensusFile ):
outputFile = self.process_setup( consensusFile,
'SequenceSelector',
suffix='consensus.selected' )
if self.output_files_exist( outputFile=outputFile ):
return outputFile
selectedFiles = []
with open( consensusFile ) as handle:
for line in handle:
referenceFile, consensusFile = line.strip().split()
if consensusFile.endswith('None'):
pass
elif fasta_count( consensusFile ) == 1:
selectedFiles.append( consensusFile )
else:
selectedFiles.append( referenceFile )
with open( outputFile, 'w' ) as handle:
for filename in selectedFiles:
handle.write(filename + '\n')
self.process_cleanup( outputFile=outputFile )
return outputFile
def select_final_sequences(self, consensusFile):
outputFile = self.process_setup(consensusFile,
'SequenceSelector',
suffix='consensus.selected')
if self.output_files_exist(output_file=outputFile):
return outputFile
selectedFiles = []
with open(consensusFile) as handle:
for line in handle:
referenceFile, consensusFile = line.strip().split()
if consensusFile.endswith('None'):
pass
elif fasta_count(consensusFile) == 1:
selectedFiles.append(consensusFile)
else:
selectedFiles.append(referenceFile)
with open(outputFile, 'w') as handle:
for filename in selectedFiles:
handle.write(filename + '\n')
self.process_cleanup(output_file=outputFile)
return outputFile
