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Commit cd120023 authored by Samuel Mondal's avatar Samuel Mondal
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skeleton for cli.py

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import argparse
import logging
from pre_bedtools import exon_extraction_from_gtf
from exon_concatenation import exon_concatenation
from polyA import PolyA_generator
from list_to_file import list_to_file
parser = argparse.ArgumentParser(
prog = 'transcript_sequence_extractor',
description = 'extracts transcript sequences from genome sequence and ouputs transcripts with PolyA tail added to them')
parser.add_argument('--input_fasta_file',
help='genome fasta file')
parser.add_argument('--input_gtf',
help='gtf file')
parser.add_argument('--output_file_name',
help='output fasta file')
args = parser.parse_args()
def main():
LOG.info("sequence_extractor begins")
exon_extraction_from_gtf()
exon_concatenation()
PolyA_generator()
list_to_file()
LOG.info("sequence_extractor ends")
if ___name__ == 'main':
logging.basicConfig(
format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
level=logging.INFO,
)
LOG = logging.getLogger(__name__)
main()
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