Mercurial > repos > portiahollyoak > fastuniq
comparison create_input_list.py @ 0:816cb55b5a2d draft default tip
planemo upload for repository https://github.com/portiahollyoak/Tools commit c4769fd68ad9583d4b9dbdf212e4ecb5968cef1c-dirty
| author | portiahollyoak |
|---|---|
| date | Thu, 02 Jun 2016 11:34:51 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:816cb55b5a2d |
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| 1 import argparse | |
| 2 | |
| 3 | |
| 4 description = ("This script will create a input list file for input into FastUniq") | |
| 5 | |
| 6 parser = argparse.ArgumentParser() | |
| 7 parser.add_argument("--fastq_R1", nargs="*", help="Path to Fastq file containing R1 reads") | |
| 8 parser.add_argument("--fastq_R2", nargs="*", help="Path to Fastq file containing R2 reads") | |
| 9 parser.add_argument("--output_list", help="List containing file paths") | |
| 10 args = parser.parse_args() | |
| 11 | |
| 12 template = "{fastq_R1}\n{fastq_R2}\n" | |
| 13 with open(args.output_list, "w") as output: | |
| 14 for fastq_R1, fastq_R2 in zip(args.fastq_R1, args.fastq_R2): | |
| 15 list_line = template.format(fastq_R1=fastq_R1, fastq_R2=fastq_R2) | |
| 16 output.write(list_line) |