--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/call_amr_mutations.py	Tue Mar 21 19:26:55 2023 +0000
@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+
+# NOTE: This tool provides the functionality of the PIMA filter_varsacn()
+# function here https://github.com/appliedbinf/pima_md/blob/main/pima.py#L3012
+
+import argparse
+import re
+import subprocess
+import sys
+
+
+def run_command(self, command):
+    try:
+        return re.split('\\n', subprocess.check_output(command, shell=True).decode('utf-8'))
+    except Exception:
+        message = 'Command %s failed: exiting...' % command
+        sys.exit(message)
+
+
+def filter_varscan(varscan_raw, output):
+    cmd = ' '.join(['cat', varscan_raw,
+                    '| awk \'(NR > 1 && $9 == 2 && $5 + $6 >= 15)',
+                    '{OFS = "\\t";f = $6 / ($5 + $6); gsub(/.*\\//, "", $4);s = $4;gsub(/[+\\-]/, "", s);$7 = sprintf("%.2f%%", f * 100);'
+                    'min = 1 / log(length(s) + 2) / log(10) + 2/10;if(f > min){print}}\'',
+                    '1>' + output])
+    output = run_command(cmd)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument('--varscan_raw', action='store', dest='varscan_raw', help='Raw varscan mpileup VCF file')
+    parser.add_argument('--output', action='store', dest='output', help='Output filtered VCF file')
+
+    args = parser.parse_args()
+
+    filter_varscan(args.varscan_raw, args.output)