search

elzbth / jitterbug

Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.
17 stars 8 forks source link

Cannot import name csamtools #2

Closed fbemm closed 8 years ago

fbemm commented 8 years ago

I got the following error running jitterbug on a Ubuntu 14.04:

Traceback (most recent call last): File "./jitterbug.py", line 21, in from Run_TE_ID_reseq import * File "/ebio/abt6_projects9/abt6_software/bin/jitterbug/Run_TE_ID_reseq.py", line 12, in from pysam import csamtools ImportError: cannot import name csamtools

Dependencies are installed. I compiled pysam from source and installed it over pip. Both attempts show the same behavior. Any idea what is going on. pysam is version 0.9.0! Thx for help.

mbosio85 commented 8 years ago

Hi,

I don't personally know how to fix it but here there's some hints from someone with the same problem with pysam

https://www.biostars.org/p/151219/

Hope it's useful

sidratools commented 7 years ago

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).

jokelley commented 7 years ago

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 commented 7 years ago

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/