skeleton for cli.py

sequence_extractor/cli.py

+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()