ORFs_scanning.py : check partial codon in truncated sequence

src/ORFs_scanning.py

@@ -16,15 +16,17 @@ def check_files(path):
 
 
 def read_arguments(argv):
-
+    __version__ = "0.1"
     parser = argparse.ArgumentParser()
     parser.add_argument('-i', '--input', required = True,
                         help='path to input file in fasta or multifasta format')
-    parser.add_argument('-o', '--output',
+    parser.add_argument('-o', '--output', required = True,
                         help='path to output file')
-    parser.add_argument('-s', '--startcodons', nargs='+',
+    parser.add_argument('-s', '--startcodon', nargs='+',
                         default = ['ATG', 'CTG'],
-                        help='list of start codons allowed')
+                        help='list of start codons allowed separate with space ex : -s ATG CTG GTG')
+    parser.add_argument('-v', '--version', action='version',
+                        version= '%(prog)s '+ __version__)
     args = parser.parse_args()
     return(args)
 
@@ -47,6 +49,8 @@ def calculateScoreKozak(seq, pos):
 
 def translate(record, start, stop):
     rec = record[start:stop]
+    if len(rec) % 3 != 0 : # if partial codon
+        rec = rec[:len(rec)-(len(rec) % 3)] # trim the sequence of partial codon
     translation = rec.translate()
     return(translation.seq)
 
@@ -81,22 +85,24 @@ def process_seq(record, args, output, writer):
     i=0
     while i <= len(seq)-1 :
         codon = seq[i:i+3]
-        if codon in args.startcodons :
+        if codon in args.startcodon :
             writer.writerow(determine_ORF(i, codon, seq, record))
         i+=1
 
 def main(argv):
+
     args=read_arguments(argv)
+
     print("input file : ", args.input,
             "\noutput file : ", args.output,
-            "\nstart codons : ", args.startcodons,
+            "\nstart codons : ", args.startcodon,
             "\n")
 
     check_files(args.input)
+    header = ['posStart','codonStart', 'posStop', 'codonStop', 'lengthInAA', 'seqKozak', 'scoreKozak', 'seqORF', 'seqAA']
 
     output = open(args.output, 'w')
     writer = csv.writer(output)
-    header = ['posStart','codonStart', 'posStop', 'codonStop', 'lengthInAA', 'seqKozak', 'scoreKozak', 'seqORF', 'seqAA']
     writer.writerow(header)
 
     input = open(args.input, 'r')
@@ -105,7 +111,5 @@ def main(argv):
         print('Done !')
 
 
-
-
 if __name__ == "__main__":
    main(sys.argv[1:])