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