def read_names(sequence_file):
# Open the sequence file with the appropriate reader
if is_fasta(sequence_file):
reader = FastaReader(sequence_file)
elif is_fastq(sequence_file):
reader = FastqReader(sequence_file)
else:
raise ValueError
# Extract and return the sequence names
return [r.name.strip().split()[0] for r in reader]
def read_names( sequence_file ):
# Open the sequence file with the appropriate reader
if is_fasta( sequence_file ):
reader = FastaReader( sequence_file )
elif is_fastq( sequence_file ):
reader = FastqReader( sequence_file )
else:
raise ValueError
# Extract and return the sequence names
return [r.name.strip().split()[0] for r in reader]
def read_sequences( sequence_file ):
"""
Parse a list of records from either a Fasta or Fastq file
"""
if is_fasta( sequence_file ):
return list( FastaReader( sequence_file ))
elif is_fastq( sequence_file ):
return list( FastqReader( sequence_file ))
else:
msg = 'Sequence file must be either Fasta or Fastq'
log.error( msg )
raise TypeError( msg )
def read_sequences(sequence_file):
"""
Parse a list of records from either a Fasta or Fastq file
"""
if is_fasta(sequence_file):
return list(FastaReader(sequence_file))
elif is_fastq(sequence_file):
return list(FastqReader(sequence_file))
else:
msg = 'Sequence file must be either Fasta or Fastq'
log.error(msg)
raise TypeError(msg)
def combine_sequences( sequence_files, output_file ):
"""
Combine a series of sequence files into one Fasta or Fastq
"""
if all([is_fasta(f) for f in sequence_files]):
combine_fasta( sequence_files, output_file )
elif all([is_fastq(f) for f in sequence_files]):
combine_fastq( sequence_files, output_file )
else:
msg = "Input files must be all Fasta or Fastq"
log.error( msg )
raise TypeError( msg )
check_output_file( output_file )
return output_file
def combine_sequences(sequence_files, output_file):
"""
Combine a series of sequence files into one Fasta or Fastq
"""
if all([is_fasta(f) for f in sequence_files]):
combine_fasta(sequence_files, output_file)
elif all([is_fastq(f) for f in sequence_files]):
combine_fastq(sequence_files, output_file)
else:
msg = "Input files must be all Fasta or Fastq"
log.error(msg)
raise TypeError(msg)
check_output_file(output_file)
return output_file
def get_input_file( input ):
if os.path.isdir( input ):
log.info("Input appears to be a directory, looking for sequence files")
return get_amplicon_analysis_output( input )
elif valid_file( input ):
if is_fasta( input ):
log.info("Input appears to be a valid Fasta file")
return input
elif is_fastq( input ):
log.info("Input appears to be a valid Fastq file")
return input
else:
msg = "Input is not a valid Fasta or Fastq file!"
log.error( msg )
raise IOError( msg )
else:
msg = "Supplied input does not appear to be a valid AmpliconAnalysis file or directory"
log.error( msg )
raise IOError( msg )
def get_input_file(input):
if os.path.isdir(input):
log.info("Input appears to be a directory, looking for sequence files")
return get_amplicon_analysis_output(input)
elif valid_file(input):
if is_fasta(input):
log.info("Input appears to be a valid Fasta file")
return input
elif is_fastq(input):
log.info("Input appears to be a valid Fastq file")
return input
else:
msg = "Input is not a valid Fasta or Fastq file!"
log.error(msg)
raise IOError(msg)
else:
msg = "Supplied input does not appear to be a valid AmpliconAnalysis file or directory"
log.error(msg)
raise IOError(msg)