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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.
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Cannot import csamtools #13

Open jokelley opened 7 years ago

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/

I answered on the other issue as well Cheers

Mattia

EricDeveaud commented 7 years ago

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

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

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