Commit 0a73bd21 authored by nlecouvr's avatar nlecouvr
Browse files

Update GATC_finder.py

parent 2a820420
......@@ -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)
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