From 50a2153264329cdcfdc2c6af952071595881e3c9 Mon Sep 17 00:00:00 2001
From: Samuel Mondal <mondal0000@bz-rgab01-pdm02.bioz.unibas.ch>
Date: Tue, 13 Dec 2022 15:59:21 +0100
Subject: [PATCH] reducing the scope of cli.py to work only after bedtools
---
sequence_extractor/cli.py | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
diff --git a/sequence_extractor/cli.py b/sequence_extractor/cli.py
index 55c0393..5f01338 100644
--- a/sequence_extractor/cli.py
+++ b/sequence_extractor/cli.py
@@ -9,20 +9,18 @@ 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')
+ help='fasta file obtained from bedtools')
parser.add_argument('--output_file_name',
- help='output fasta file')
+ help='Name of the output fasta file')
args = parser.parse_args()
def main():
LOG.info("sequence_extractor begins")
- exon_extraction_from_gtf()
- fasta_list = exon_concatenation(args.)
+ fasta_list = exon_concatenation(args.input_fasta_file)
final_list = poly_a_addition_to_fasta_list(fasta_list)
- list_to_file(final_list,args.output_file_name)
+ with open(args.output_file_name, 'w') as fasta_out:
+ fasta_out.write('\n'.join('%s\n%s' % x for x in final_list))
LOG.info("sequence_extractor ends")
if ___name__ == 'main':
--
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