--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trim_reference.py	Fri Jan 28 18:47:34 2022 +0000
@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import sys
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('input_file', type=argparse.FileType())
+    parser.add_argument('output_file', type=argparse.FileType('w'), nargs='?', default=sys.stdout)
+    args = parser.parse_args()
+    lines = args.input_file.readlines()
+    i = len(lines) - 1
+    trimmed = False
+    # step backwards through the lines, removing all As until we find a non-A nucleotide
+    while not trimmed:
+        line = lines[i].upper().rstrip()
+        for j in range(len(line) - 1, -1, -1):
+            # walk backwards through the line, checking for a non-A (and non-space) character
+            if line[j] not in ['A', ' ']:
+                lines[i] = line[:j + 1] + '\n'
+                trimmed = True
+                break
+        else:
+            # we processed the whole line - all As - so we don't include this line in the output
+            i -= 1
+    args.output_file.write(''.join(lines[:i + 1]))