Mercurial > repos > portiahollyoak > pindel
diff create_config_file.py @ 0:dd513c72ea56 draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit 1f1c277219ca756c9baa453592b455597fd593d8-dirty
author | portiahollyoak |
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date | Tue, 17 May 2016 04:47:23 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/create_config_file.py Tue May 17 04:47:23 2016 -0400 @@ -0,0 +1,20 @@ +import argparse + + +description = ("This script will create a configuration file for samples to be run in Pindel") + + +parser = argparse.ArgumentParser() +parser.add_argument("--input_file", nargs="*", help="One or more alignment files") +parser.add_argument("--insert_size", nargs="+", help="Expected Insert size") +parser.add_argument("--sample_label", nargs="+", help="Sample label") +parser.add_argument("--output_config_file", help="Output config file") +args = parser.parse_args() + +template = "{input_file}\t{insert_size}\t{sample_label}\n" +with open(args.output_config_file, "w") as output: + for input_file, insert_size, sample_label in zip(args.input_file, args.insert_size, args.sample_label): + config_line = template.format(input_file=input_file, insert_size=insert_size, sample_label=sample_label) + output.write(config_line) + +