def write_results_to_file(fastq_dict, error_dict, opts):
"""Writes the result of the cloning/error adding to a file in the cwd
:param defaultdict fastq_dict: original dictionary from file
:param defaultdict error_dict: cloned/error dictionary
:param args opts: the parsed arguments from the command line
:return None: Writes to file only
"""
outfile = open(opts.fastq.name[:-6] + '_FastqErrorResult.txt', 'w')
for key in fastq_dict.keys():
outfile.writelines("{} no errors: {}\n".format(key, fastq_dict[key]))
outfile.writelines("{} with errors: {}\n\n".format(key, error_dict[key]))
print blue(''\
'Results written to {}'.format((''\
'{}/{}_FastqErrorResult.txt'\
'').format(os.getcwd(), opts.fastq.name[:-6])))
def main(args):
"""Main method
:param args: arguments
:return: None
"""
print green('Running...')
opts = parse_cmdline_params(args[1:])
infile = opts.fastq
fastq_dict = create_fastq_dict(infile, opts)
error_dict = decide_if_error(fastq_dict)
print yellow("[STATUS] Error dict created.")
if raw_input(blue('Would you like results printed to the terminal? Answer y or n: ')) is 'y':
print_results(fastq_dict, error_dict)
if raw_input(blue('Would you like to write the results to a file? Answer y or n: ')) is 'y':
write_results_to_file(fastq_dict, error_dict, opts)
print green('Done')
def write_results_to_file(fastq_dict, error_dict, opts):
"""Writes the result of the cloning/error adding to a file in the cwd
:param defaultdict fastq_dict: original dictionary from file
:param defaultdict error_dict: cloned/error dictionary
:param args opts: the parsed arguments from the command line
:return None: Writes to file only
"""
outfile = open(opts.fastq.name[:-6] + '_FastqErrorResult.txt', 'w')
for key in fastq_dict.keys():
outfile.writelines("{} no errors: {}\n".format(
key, fastq_dict[key]))
outfile.writelines("{} with errors: {}\n\n".format(
key, error_dict[key]))
print blue(''\
'Results written to {}'.format((''\
'{}/{}_FastqErrorResult.txt'\
'').format(os.getcwd(), opts.fastq.name[:-6])))
def main(args):
"""Main method
:param args: arguments
:return: None
"""
print green('Running...')
opts = parse_cmdline_params(args[1:])
infile = opts.fastq
fastq_dict = create_fastq_dict(infile, opts)
error_dict = decide_if_error(fastq_dict)
print yellow("[STATUS] Error dict created.")
if raw_input(
blue(
'Would you like results printed to the terminal? Answer y or n: '
)) is 'y':
print_results(fastq_dict, error_dict)
if raw_input(
blue(
'Would you like to write the results to a file? Answer y or n: '
)) is 'y':
write_results_to_file(fastq_dict, error_dict, opts)
print green('Done')
