Update GATC_finder.py

src/.docker_modules/GATC_finder/script/GATC_finder.py

@@ -2,15 +2,14 @@ import sys
 import re
 from Bio import SeqIO
 
-if len(sys.argv) < 3:
-    raise IndexError("Please enter 2 arguments")
+print("test")
 
 # Gets the arguments in the command line
-out_file_path = str(sys.argv[2])
+out_file_path = "/GATC_finder"
 genome_file = str(sys.argv[1])
 
 # Opening the file to write the positions in
-f = open(out_file_path, "w")
+f = open("sites.bed", "w")
 
 # Motif we are looking for
 motif = "GATC"
@@ -29,4 +28,4 @@ for seq_record in SeqIO.parse(genome_file, "fasta"):
         
         # Writes the position in the .bed file (chro/start/end)
         line = f"{chrom}\t{start_pos}\t{end_pos}\n"
-        f.write(line)
\ No newline at end of file
+        f.write(line)