def validate_settings(self):
# Validate the input file
root, ext = split_root_from_ext( self.input_file )
if ext in ['.bas.h5', '.fofn']:
self.data_type = 'bash5'
elif ext in ['.fq', '.fastq']:
self.data_type = 'fastq'
elif ext in ['.fa', '.fsa', '.fasta']:
self.data_type = 'fasta'
else:
raise TypeError('Sequence file must be a bas.h5 file, a ' + \
'fasta file, or a fofn of multiple such files')
self.consensusTool = DagConRunner('gcon.py', 'r')
# Searching for Mothur executable, and set the Mothur Process counter
self.mothur = validate_executable( self.mothur )
self.processCount = 0
def validate_settings(self):
# Validate the input file
root, ext = split_root_from_ext(self.input_file)
if ext in ['.bas.h5', '.fofn']:
self.data_type = 'bash5'
elif ext in ['.fq', '.fastq']:
self.data_type = 'fastq'
elif ext in ['.fa', '.fsa', '.fasta']:
self.data_type = 'fasta'
else:
raise TypeError('Sequence file must be a bas.h5 file, a ' + \
'fasta file, or a fofn of multiple such files')
self.consensusTool = DagConRunner('gcon.py', 'r')
# Searching for Mothur executable, and set the Mothur Process counter
self.mothur = validate_executable(self.mothur)
self.processCount = 0
def validate_settings(self):
# Validate the input file
root, ext = split_root_from_ext( self.input_file )
if ext in ['.bas.h5', '.fofn']:
self.data_type = 'bash5'
elif ext in ['.fq', '.fastq']:
self.data_type = 'fastq'
elif ext in ['.fa', '.fsa', '.fasta']:
self.data_type = 'fasta'
self.enable_masking = False
self.enable_consensus = False
else:
raise TypeError('Sequence file must be a bas.h5 file, a ' + \
'fasta file, or a fofn of multiple such files')
# If Clustering was disabled, also disable the consensus process
if not self.enable_clustering:
self.enable_consensus = False
# If Consensus is enabled, initialize the appropriate tool
if self.enable_consensus:
self.consensusTool = DagConRunner('gcon.py', 'r')
# Searching for Mothur executable, and set the Mothur Process counter
self.mothur = validate_executable( self.mothur )
self.processCount = 0
def validate_settings(self):
# Validate the input file
root, ext = split_root_from_ext(self.input_file)
if ext in ['.bas.h5', '.fofn']:
self.data_type = 'bash5'
elif ext in ['.fq', '.fastq']:
self.data_type = 'fastq'
elif ext in ['.fa', '.fsa', '.fasta']:
self.data_type = 'fasta'
self.enable_masking = False
self.enable_consensus = False
else:
raise TypeError('Sequence file must be a bas.h5 file, a ' + \
'fasta file, or a fofn of multiple such files')
# If Clustering was disabled, also disable the consensus process
if not self.enable_clustering:
self.enable_consensus = False
# If Consensus is enabled, initialize the appropriate tool
if self.enable_consensus:
self.consensusTool = DagConRunner('gcon.py', 'r')
# Searching for Mothur executable, and set the Mothur Process counter
self.mothur = validate_executable(self.mothur)
self.processCount = 0
