I have a sample inputfile.txt:
chr1 34870071 34899867 pi-Fam168b.1 -
chr11 98724946 98764609 pi-Wipf2.1 +
chr11 105898192 105920636 pi-Dcaf7.1 +
chr11 120486441 120495268 pi-Mafg.1 -
chr12 3891106 3914443 pi-Dnmt3a.1 +
chr12 82815946 82882157 pi-Map3k9.1 -
Column1=chromosome_number
Column2=start
Column3=end
Column4=gene
Column5=strand (either + or -)
This is the code that I have:
import pandas as pd
df1=pd.read_csv('filename.txt',names= ['chr','start','stop','gene','strand'], delimiter=r'\s+')
count =0
c = 0
for i in df1.index:
for y in df1.index:
if abs(df1.loc[i,"start"]- df1.loc[y,"stop"]) < 201:
if i != y:
index
c +=1
print(c)
I keep on getting this error that the index is not defined:
File "./filename.py", line 25, in <module>
index
NameError: name 'index' is not defined
I have Python 2.7.10 Any feedback much appreciated. Thanks
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