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Commit e9f8e37f authored by Laura Urbanska's avatar Laura Urbanska
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removed argparse_example

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import argparse
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description="transcript sampler",
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser.add_argument("--annotation", required=True, help="gtf file with genome annotation")
parser.add_argument("--expression_level", required=True, help="csv file with expression level")
parser.add_argument("--output_csv", required=True, help="output csv file")
parser.add_argument("--output_gtf", required=True, help="output gtf file")
parser.add_argument("--transcript_number", required=True, help="total number of transcripts to sample")
args = parser.parse_args()
# script name being whatever we call our workflow class/function that takes the inputs
script_name(args.annotation, args.expression_level, args.output_csv, args.output_gtf, args.transcript_number)
"""note:
so to run our entire workflow, it will suffice to type the following into the command line:
python filename.py \
--annotation filename1.gtf \
--expression_level filename2.gtf \
--output_csv output1.csv \
--output_gtf output2.gtf \
--transcript_number 100 (some number)
"""
\ No newline at end of file
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