changeset 1:733edda2eb48 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/concat_cov_and_iupac_results.py	Thu Jun 13 14:50:57 2024 +0000
@@ -0,0 +1,53 @@
+#!/usr/python3
+# -*- coding: utf-8 -*-
+
+import os
+import argparse
+import sys
+
+
+# MAIN
+def __main__():
+  # Script options:
+  parser = argparse.ArgumentParser(description='''Add iupac value to coverage file.''',
+                                   epilog="""This script need few options, use -h to see it.""")
+  parser.add_argument('-c', '-covfile', dest='fc', help='Coverage file.')
+  parser.add_argument('-i', '-iupacfile', dest='fi', help='IUPAC file.')
+  parser.add_argument('-o', '-output_file', dest='output_file', help='Output File')
+
+  # Get script options:
+  options = parser.parse_args()
+  fc = options.fc
+  fi = options.fi
+  output_file = options.output_file
+
+  # Check options:
+  if len(sys.argv) < 7 or len(sys.argv) > 7:
+    parser.print_help()
+    sys.exit(1)
+
+  # Output file
+  outputfile = open(output_file, "w")
+
+  # Variables:
+  iup_list_ref = {}
+
+  # Storing iupac values
+  for i in open(fi, "r").readlines():
+    list_i = i.split("\t")
+    iup_list_ref[list_i[0]] = list_i[1]
+
+  print(iup_list_ref.keys())
+  # Add iupac value to coverage value:
+  for li in open(fc, "r").readlines():
+    print(li)
+    outputfile.write(li)
+    ref = li.rstrip()
+    if ref in iup_list_ref.keys():
+      print("line for iupac find")
+      outputfile.write(f"Percentage IUPAC: {iup_list_ref[ref]}")
+
+
+# MAIN END
+if __name__ == "__main__":
+  __main__()