Mercurial > repos > portiahollyoak > breakdancer
comparison create_config_file.py @ 0:694cbef83948 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 9700cff725be112c4a813f914eca946e158fbebd-dirty
| author | portiahollyoak |
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| date | Fri, 13 May 2016 11:47:32 -0400 |
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| children |
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| -1:000000000000 | 0:694cbef83948 |
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| 1 import argparse | |
| 2 | |
| 3 | |
| 4 description = ("This script will create a configuration file for samples to be run in Breakdancer." | |
| 5 "If pooled analysis desired, only one config file needed for all samples." | |
| 6 "Otherwise, individual analysis requires individual config files for each sample.") | |
| 7 | |
| 8 parser = argparse.ArgumentParser() | |
| 9 parser.add_argument("--input_file", nargs="*", help="One or more alignment files") | |
| 10 parser.add_argument("--mean", nargs="+", help="Mean insert size") | |
| 11 parser.add_argument("--std_dev", nargs="+", help="The standard deviation of insert size") | |
| 12 parser.add_argument("--read_length", nargs="+", help="Average read length") | |
| 13 parser.add_argument("--sample_name", nargs="+", help="Sample name") | |
| 14 parser.add_argument("--output_config_file", help="Name of the output config file") | |
| 15 args = parser.parse_args() | |
| 16 | |
| 17 template = "map:{input_file}\tmean:{mean}\tstd:{std_dev}\treadlen:{read_length}\tsample:{sample_name}\texe:samtools view\n" | |
| 18 with open(args.output_config_file, "w") as output: | |
| 19 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): | |
| 20 config_line = template.format(input_file=input_file, mean=mean, std_dev=std_dev, read_length=read_length, sample_name=sample_name) | |
| 21 output.write(config_line) |