From 5ab127180bd2701ffd50e64d76536b01e93bcd05 Mon Sep 17 00:00:00 2001
From: Samuel Mondal <samuel.mondal@unibas.ch>
Date: Sat, 26 Nov 2022 21:18:20 +0100
Subject: [PATCH] Update cli (still not complete)
---
sequence_extractor/cli.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/sequence_extractor/cli.py b/sequence_extractor/cli.py
index 538ed72..c0e2e62 100644
--- a/sequence_extractor/cli.py
+++ b/sequence_extractor/cli.py
@@ -2,7 +2,7 @@ import argparse
import logging
from pre_bedtools import exon_extraction_from_gtf
from exon_concatenation import exon_concatenation
-from polyA import PolyA_generator
+from polyA import polyA_addition_to_fasta_list
from list_to_file import list_to_file
parser = argparse.ArgumentParser(
@@ -20,9 +20,9 @@ args = parser.parse_args()
def main():
LOG.info("sequence_extractor begins")
exon_extraction_from_gtf()
- exon_concatenation()
- PolyA_generator()
- list_to_file()
+ fasta_list = exon_concatenation(args.)
+ final_list = polyA_addition_to_fasta_list(fasta_list)
+ list_to_file(final_list,args.output_file_name)
LOG.info("sequence_extractor ends")
if ___name__ == 'main':
--
GitLab