--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/coverage2gff.py	Tue Sep 03 05:20:02 2019 -0400
@@ -0,0 +1,65 @@
+#!/usr/bin/env python3
+import argparse
+import tempfile
+import shutil
+import sys
+
+def parse_args():
+    '''Argument parsin'''
+    description = """
+    parsing cap3 assembly aln output
+    """
+
+    parser = argparse.ArgumentParser(
+        description=description,
+        formatter_class=argparse.RawTextHelpFormatter)
+    parser.add_argument(
+        '-g',
+        '--gff_file',
+        default=None,
+        required=True,
+        help="input gff3 file for appending coverage information",
+        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()
+
+def read_coverage(profile):
+    with open(profile) as p:
+        d = {}
+        for name, prof in zip(p, p):
+            d[name[1:].strip()] = [int(i) for i in prof.split()]
+    print(d, file=sys.stderr)
+    return d
+
+
+def main():
+    args = parse_args()
+    coverage_hash = read_coverage(args.profile)
+    gff_tmp = tempfile.NamedTemporaryFile()
+    with open(args.gff_file) as f, open(gff_tmp.name, 'w') as out:
+        for line in f:
+            if line[0] == "#":
+                out.write(line)
+            else:
+                line_parts = line.split()
+                start = int(line_parts[3])
+                end = int(line_parts[4])
+                coverage = round( sum(coverage_hash[line_parts[0]][(
+                    start - 1):end]) / (end - start + 1), 3)
+                new_line = "{};Coverage={}\n".format(line.strip(), coverage)
+                out.write(new_line)
+
+    shutil.copyfile(gff_tmp.name, args.gff_file)
+
+
+if __name__ == "__main__":
+
+    main()