Import error

[Phlya]

Hi, I upgraded PGT to the master branch and now can't import it in python:

ImportError                               Traceback (most recent call last)
<ipython-input-6-b7529b25397d> in <module>()
     29 import _mysql
     30 import re
---> 31 from pygenometracks import tracksClass# import BigWigTrack, BedGraphTrack, BedTrack
     32 import decimal

/usr/local/lib/python3.5/dist-packages/pygenometracks/tracksClass.py in <module>()
     29 from collections import OrderedDict
     30 
---> 31 from pygenometracks.tracks import *
     32 
     33 FORMAT = "[%(levelname)s:%(filename)s:%(lineno)s - %(funcName)20s()] %(message)s"

ImportError: No module named 'pygenometracks.tracks'

[fidelram]

how did you upgrade?

is PGT in your PYTHONPATH?

[fidelram]

ahh wait ... now I change the code a bit and all tracks are now in the tracks folder.

i think that you should do from pygenometracks.tracks import BigwigTrack

[fidelram]

@Phlya Did you solve the problem ?

[Phlya]

Hi, sorry, I forgot to try it out... Nope, this doesn't work either, I am afraid:

ImportError                               Traceback (most recent call last)
<ipython-input-1-d0e40cc69b2e> in <module>()
     29 import _mysql
     30 import re
---> 31 from pygenometracks.tracks import BigwigTrack, BedTrack# import BigWigTrack, BedGraphTrack, BedTrack
     32 import decimal

ImportError: No module named 'pygenometracks.tracks'

[fidelram]

for me this works:

from pygenometracks.tracks import BigWigTrack

I think that you may have two versions of pyGenomeTracks and that your PYTHONPATH is pointing towards the wrong one.

try to delete any previous version and install the latest.

[Phlya]

Mh. So, I rm -rf'd everything mentioning pygenometracks from dist-packages, checked that I can't import pygenometracks, then installed it from github. Now I can import just pygenometracks, but I still get this:

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-2-99a16a47b36d> in <module>()
     30 import re
     31 # from pygenometracks import tracksClass
---> 32 from pygenometracks.tracks import BigWigTrack, BedGraphTrack, BedTrack
     33 import decimal

ImportError: No module named 'pygenometracks.tracks'

[fidelram]

how did you install it?

if you just clone it from github you need to set up a PYTHONPATH variable that points to the pygenometracks folder.

[Phlya]

sudo pip3 install --upgrade https://github.com/deeptools/pyGenomeTracks/archive/master.zip

[Phlya]

The same error occurs when I try to use pygenometracks in the command line

s1529682:~/Documents/PhD/Hi-C/pygenometracks$ make_tracks_file --trackFiles ~/eddie/ilia/coolers/IMR90/Rao2014-IMR90-MboI-allreps-filtered.10kb.cool ~/Documents/PhD/refGene.txt ~/Documents/PhD/Nefeli_CCT.bed -o Nefeli.config 
Traceback (most recent call last):
  File "/usr/local/bin/make_tracks_file", line 4, in <module>
    from pygenometracks.makeTracksFile import main
  File "/usr/local/lib/python3.5/dist-packages/pygenometracks/makeTracksFile.py", line 4, in <module>
    from pygenometracks.tracksClass import PlotTracks
  File "/usr/local/lib/python3.5/dist-packages/pygenometracks/tracksClass.py", line 31, in <module>
    from pygenometracks.tracks import *
ImportError: No module named 'pygenometracks.tracks'

[vivekbhr]

@Phlya you can update the pygenometracks from master branch to solve this issue

[alexmascension]

I would like to add a small comment in here... I suffered from the issues https://github.com/deeptools/pyGenomeTracks/issues/22 and https://github.com/deeptools/pyGenomeTracks/issues/23, by installing deepTools and pyGenomeTracks with anaconda (python 3.6).

The way I found to solve all of the problems was simply by creating a new environment conda create -n PyGenomeTracks and then installing pyGenomeTracks within that environment conda install -n PyGenomeTracks -c bioconda pygenometracks

In this way, there are no known conflict between hicexplorer with cairosvg and other modules that seemed to be incompatible.