Mercurial > repos > portiahollyoak > fastuniq
diff 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 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/create_input_list.py Thu Jun 02 11:34:51 2016 -0400 @@ -0,0 +1,16 @@ +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) \ No newline at end of file