Python file taken from Zaka Wing-Sze Yuen et al to transform wig output of Tombo to bed file

wig2bed.py

+import sys
+import pandas as pd
+import wiggelen
+import argparse
+
+
+parser = argparse.ArgumentParser(description=" Script to generate tsv ")
+plus = parser.add_argument('-plus', type=str, help="Path to plus file" )
+minus = parser.add_argument('-minus', type=str, help='Path to the minus file ')
+output = parser.add_argument('-output', type=str, help='Path to the output directory ')
+args = parser.parse_args()
+
+plus = args.plus
+minus = args.minus
+output = args.output
+# Positive strand
+r=[]
+p=[]
+v=[]
+
+with open(plus,'r') as fh:
+    for region, position, value in wiggelen.walk(fh):
+        r.append(region)
+        p.append(position)
+        v.append(value)
+    d_plus = pd.DataFrame(list(zip(r,p,v)), columns =['names', 'start','values'])
+    d_plus["strand"]="+"
+
+# Negative strand
+r_m=[]
+p_m=[]
+v_m=[]
+
+with open(minus,'r') as fh:
+    for region, position, value in wiggelen.walk(fh):
+        r_m.append(region)
+        p_m.append(position)
+        v_m.append(value)
+    d_minus = pd.DataFrame(list(zip(r_m,p_m,v_m)), columns =['names', 'start','values'])
+    d_minus["strand"]="-"
+d=pd.concat([d_plus, d_minus])
+d.sort_values(["names","start"], inplace=True)
+
+d.to_csv(output,sep="\t", header=True, index=False)
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