commit

scripts/CheckProtein/src/check_prots.py

+import argparse
+import os, sys
+import re
+from Bio import SeqIO
+
+# Construct the argument parser
+ap = argparse.ArgumentParser()
+
+# Add the arguments to the parser
+ap.add_argument("-f", "--file", required=False, help="name of the file")
+args = vars(ap.parse_args())
+
+for record in SeqIO.parse(args['file'], "fasta"):
+    record.description=''
+    if ((record.seq[-1]=='.') or (record.seq[-1] == '*')):
+        record.seq=record.seq[:-1]
+    if ('.' in record.seq):
+        print(record.id + "Invalid seq : " + record.seq,  file=sys.stderr)
+
+    else : 
+        SeqIO.write(record,  sys.stdout, "fasta")
+
+    
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