From cd120023a9c1470e7e4dee98d1a66ec52b3a539b Mon Sep 17 00:00:00 2001
From: Samuel Mondal <samuel.mondal@unibas.ch>
Date: Tue, 15 Nov 2022 18:58:36 +0100
Subject: [PATCH] skeleton for cli.py
---
sequence_extractor/cli.py | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
diff --git a/sequence_extractor/cli.py b/sequence_extractor/cli.py
index e69de29..538ed72 100644
--- a/sequence_extractor/cli.py
+++ b/sequence_extractor/cli.py
@@ -0,0 +1,34 @@
+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()
--
GitLab