Mercurial > repos > portiahollyoak > breakdancer_max
view create_config_file.py @ 5:c2bb6aa52c74 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 65ddf081d2f1a76bc4d6d91f01ab72667b9e1549-dirty
author | portiahollyoak |
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date | Mon, 23 May 2016 06:06:09 -0400 |
parents | f65530d07350 |
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import argparse description = ("This script will create a configuration file for samples to be run in Breakdancer." "If pooled analysis desired, only one config file needed for all samples." "Otherwise, individual analysis requires individual config files for each sample.") parser = argparse.ArgumentParser() parser.add_argument("--input_file", nargs="*", help="One or more alignment files") parser.add_argument("--mean", nargs="+", help="Mean insert size") parser.add_argument("--std_dev", nargs="+", help="The standard deviation of insert size") parser.add_argument("--read_length", nargs="+", help="Average read length") parser.add_argument("--sample_name", nargs="+", help="Sample name") parser.add_argument("--output_config_file", help="Name of the output config file") args = parser.parse_args() template = "map:{input_file}\tmean:{mean}\tstd:{std_dev}\treadlen:{read_length}\tsample:{sample_name}\texe:samtools view\n" with open(args.output_config_file, "w") as output: for input_file, mean, std_dev, read_length, sample_name in zip(args.input_file, args.mean, args.std_dev, args.read_length, args.sample_name): config_line = template.format(input_file=input_file, mean=mean, std_dev=std_dev, read_length=read_length, sample_name=sample_name) output.write(config_line)