added helper file to generate a quality summary for HISAT2 output

helper/hisat2_stats.py

@@ -0,0 +1,33 @@
+#!/usr/bin/env python3
+"""
+Script to iterate over HISAT2 output and grab quality statistics
+"""
+import os
+import re
+
+from sys import argv
+from collections import defaultdict
+
+hisat2_path = argv[1]
+
+values = defaultdict(list)
+
+# Prepare regex
+re_mapped = re.compile('\t(.*)% overall alignment rate')
+
+# Get all directories in this path
+for sf in os.listdir(path=hisat2_path):
+    # Only consider .stats files
+    if os.path.isfile(os.path.join(hisat2_path, sf)) and sf.endswith('.stats'):
+        summary = os.path.join(hisat2_path, sf)
+        # process summary file
+        with open(summary) as f:
+            lines = '\t'.join(f.readlines())
+            hits = re_mapped.search(lines)
+            if hits:
+                values['samples'].append(sf)
+                values['mapped_percentages'].append(float(hits.group(1)))
+
+print('sample', 'mapped_percentage', sep='\t')
+for s, p in zip(values['samples'], values['mapped_percentages']):
+    print(s, p, sep='\t')