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