Cannot import csamtools

[jokelley]

Hi, We are trying to run jitterbug and we are getting the error "ImportError: cannot import name csamtools". We would like to use this tool but are unable to get it working. We have pip installed all of the required dependencies (pysam, psutil, pybedtools, numpy)

[mbosio85]

Hi,
did you check the version of pysam you have installed as advised by @sidratools ?

Hi Felix,
To resolve this "ImportError: cannot import name csamtools" issue, you need to build the pysam. Note that, your selected pysam version should have csamtools.pyx (Example: pysam-0.7.5 or pysam-0.8.1 may be used).

or try to check this link
https://www.biostars.org/p/151219/

I answered on the other issue as well
Cheers

Mattia

[EricDeveaud]

check http://pysam.readthedocs.io/en/latest/faq.html#importerror-cannot-import-name-csamtools

just hack Run_TE_ID_* to import libcsamtools instead of just import csamtools

furthermore after a short reading, (lib)csamtools seems to be unused in the code ;-)