pybedtools.BedTool.intersect not working, install problem

Question

[juncheng]

I just installed pybedtools on my mac (10.9) as follow:

sudo pip install pybedtools

pybedtools==0.6.7

Then I test the script as recommended for test installing:

import pybedtools
a = pybedtools.example_bedtool('a.bed')
b = pybedtools.example_bedtool('b.bed')
print a.intersect(b)

The last step do not work.

NotImplementedError: "intersectBed" does not appear to be installed or on the path, so this method is disabled.  Please install a more recent version of BEDTools and re-import to use this method.

I didn't find someone with the same problem on pybedtools. Does anyone knows the problem?

Thanks,
Jun

Answer 1

[Ryan Dale]

Since pybedtools wraps and extends BEDTools, it needs to have BEDTools installed and on the path. BEDTools can't be found on your system, so you're getting this error message.

The bedtools installation docs show multiple methods for installing, including Homebrew and MacPorts.

[rpb1001]

Since pybedtools wraps and extends BEDTools, it needs to have BEDTools installed and on the path

That is, even more simply put, copy paste the BEDTools binary file to the same directory as the pybedtools binary file.

[ATpoint]

There is no guarantee that this works. It will depend on how the tool calls bedtools. The PATH solution is more generic and reliable.