BED file

[amitpande74]

Hi,
I ran this command
python safe_harbor.py -i "test.bed"

My BED file is formatted like this :
id position
chr10 662214 662257
chr10 2125062 2125105
chr10 2513114 2513157
chr10 3618171 3618214
chr10 4458513 4458556

the error I am getting
AttributeError: 'numpy.int64' object has no attribute 'replace'
Traceback (most recent call last):
File "safe_harbor.py", line 151, in
input_data['chr'], input_data['start'], input_data['stop'] = zip(*input_data.apply(get_bed_file, axis=1))
TypeError: zip argument #1 must support iteration

Do I calculate the safe harbors using the instructions listed here
https://github.com/erikaznauryan/GSH-1#prerequisites and then run the intersect tool using the genomic regions of interest ?
Kindly advice.

[dewshr]

hi, your input file is not in correct format, please check this link for format
input format