srcipt to find and locate all GATC sites

src/GATC_finder.py

+import re
+
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas
+from Bio import SeqIO, motifs
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+
+
+def main():
+    
+    f = open("/home/nathan/projects/vscode_nextflow/nextflow-nathan/results/GATC/sites.bed", "w")
+    motif = "GATC"
+    pos_list = list()
+
+    for seq_record in SeqIO.parse("/home/nathan/projects/vscode_nextflow/nextflow-nathan/data/genome/data_G.fasta", "fasta"):
+        chrom = seq_record.id
+        
+        for match in re.finditer(motif, str(seq_record.seq)):
+            start_pos = match.start() +1
+            end_pos = match.end() + 1
+            
+            line = f"{chrom}\t{start_pos}\t{end_pos}\n"
+            
+            f.write(line)
+
+
+if __name__ == "__main__":
+    main()
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