diff annot2krona.py @ 17:d14b68e9fd1d draft

Uploaded - new tools added

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/annot2krona.py	Wed Apr 28 08:37:20 2021 +0000
@@ -0,0 +1,53 @@
+#!/usr/bin/env python3
+'''
+take various inputs and convert it to krona tabular format for visualization
+supported inputs:
+- DANTE gff3
+- TODO PROFREP gff3
+- TODO RE archive - normal run
+- TODO  RE archive - comparative
+-
+'''
+import argparse
+import re
+import collections
+
+
+def parse_dante_gff(f):
+    '''load gff3 file and return classification with counts'''
+    r = re.compile("Final_Classification=")
+    cls_count = collections.defaultdict(int)
+    for line in f:
+        if re.match("#", line.strip()):
+            continue
+        attributes = line.split("\t")[8].split(";")
+        cls_raw = list(filter(r.match, attributes))[0]
+        cls = re.sub(r, "",cls_raw)
+        cls_count[cls] += 1
+
+    return cls_count
+
+
+def export_classification(cls, f):
+    '''save classification to tab delimited file'''
+    for i in cls:
+        f.write('{}\t{}\n'.format(cls[i], i.replace("|","\t")))
+
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-f', '--format', choices=['dante', 'profrep', 're'])
+    parser.add_argument('-i', '--input', type=argparse.FileType('r'))
+    parser.add_argument('-o', '--output', type=argparse.FileType('w'))
+
+    args = parser.parse_args()
+
+    if args.format == "dante":
+        classification = parse_dante_gff(args.input)
+
+    if args.format in ["profrep" 're']:
+        print("Not implemented")
+        exit(0)
+
+    export_classification(classification, args.output)