Mercurial > repos > portiahollyoak > fastuniq
view create_input_list.py @ 0:816cb55b5a2d draft default tip
planemo upload for repository https://github.com/portiahollyoak/Tools commit c4769fd68ad9583d4b9dbdf212e4ecb5968cef1c-dirty
author | portiahollyoak |
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date | Thu, 02 Jun 2016 11:34:51 -0400 |
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import argparse description = ("This script will create a input list file for input into FastUniq") parser = argparse.ArgumentParser() parser.add_argument("--fastq_R1", nargs="*", help="Path to Fastq file containing R1 reads") parser.add_argument("--fastq_R2", nargs="*", help="Path to Fastq file containing R2 reads") parser.add_argument("--output_list", help="List containing file paths") args = parser.parse_args() template = "{fastq_R1}\n{fastq_R2}\n" with open(args.output_list, "w") as output: for fastq_R1, fastq_R2 in zip(args.fastq_R1, args.fastq_R2): list_line = template.format(fastq_R1=fastq_R1, fastq_R2=fastq_R2) output.write(list_line)