--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cfsan_snp_pipeline_quast_select.py	Tue Oct 17 14:13:45 2023 +0000
@@ -0,0 +1,31 @@
+#!/usr/bin/env python
+
+import csv
+import sys
+
+
+def pick(rows, key, reverse=False):
+    sorted_rows = sorted(rows, key=lambda r: r[key], reverse=reverse)
+    return sorted_rows[0]['Assembly']
+
+
+def int_or_str(token):
+    try:
+        return int(token)
+    except ValueError:
+        return str(token)
+
+
+if __name__ == '__main__':
+    path, criterion = sys.argv[1:]
+    # QUAST tables have sample info as columns, so we need to transpose the table.
+    rows = list(zip(*csv.reader(open(path, "r"), delimiter='\t', dialect='excel')))
+    hed = rows.pop(0)
+    dict_rows = [{h: int_or_str(r[i]) for i, h in enumerate(hed)} for r in rows]
+    if "fewest" in criterion:
+        # If it's a count, we want the fewest.
+        reverse = False
+    else:
+        # Otherwise it's a length and we want the longest.
+        reverse = True
+    print(pick(dict_rows, criterion, reverse))