Mercurial > repos > portiahollyoak > fastuniq

annotate create_input_list.py @ 0:816cb55b5a2d draft default tip

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planemo upload for repository https://github.com/portiahollyoak/Tools commit c4769fd68ad9583d4b9dbdf212e4ecb5968cef1c-dirty
author portiahollyoak
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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816cb55b5a2d planemo upload for repository https://github.com/portiahollyoak/Tools commit c4769fd68ad9583d4b9dbdf212e4ecb5968cef1c-dirty
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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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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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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)