--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/parse_aln.py	Wed Aug 28 08:08:47 2019 -0400
@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+'''
+parse .aln file - output from cap3 program. Output is fasta file and
+profile file
+'''
+import argparse
+
+
+def parse_args():
+    '''Argument parsin'''
+    description = """
+    parsing cap3 assembly aln output
+    """
+    parser = argparse.ArgumentParser(description=description,
+                                     formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument(
+        '-a', '--aln_file',
+        default=None, required=True,
+        help="Aln file input",
+        type=str,
+        action='store')
+    parser.add_argument(
+        '-f', '--fasta',
+        default=None, required=True,
+        help="fasta output file name",
+        type=str,
+        action='store')
+    parser.add_argument(
+        '-p', '--profile',
+        default=None, required=True,
+        help="output file for coverage profile",
+        type=str,
+        action="store"
+    )
+    return parser.parse_args()
+
+
+if __name__ == "__main__":
+
+    args = parse_args()
+    print(args.profile)
+
+