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deeptools / pyGenomeTracks

python module to plot beautiful and highly customizable genome browser tracks
GNU General Public License v3.0
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Y axis is missing ? #44

Closed siddharthst closed 5 years ago

siddharthst commented 6 years ago

I'm not sure if I'm doing something terribly wrong or if this is a bug. But when I'm plotting the bigwig files the Y axis is simply missing. Bellow is my configuration file:

[smF]
file = smRNA.reverse.bw
height = 8
title = bigwig
min_value = 0
max_value = 160
show data range = yes
color = #0000FF80

[spacer]

[smR]
file = smRNA.forward.bw
height = 8
title = bigwig
min_value = 0
max_value = 150
show data range = yes
orientation = inverted
color = #FF000080

[spacer]

[t_f]
file = B1.forward.bw
height = 8
title = bigwig
min_value = 0
max_value = 10
show data range = yes
color = #0000FF80

[spacer]

[t_r]
file = B1.reverse.bw
height = 8
title = bigwig
min_value = 0
max_value = 10
orientation = inverted
show data range = yes
color = #FF000080

[x-axis]

I'm using the bioconda route to use the package in an isolated environment. Output: bigwig.pdf

fidelram commented 6 years ago

did you try removing the line show data range = yes? By default the y axis is shown. Let me know if this works and I will revise the code.

siddharthst commented 6 years ago

I did, but still same result.

fidelram commented 6 years ago

That's very strange. Which version of matplolib do you have?

pip freeze | grep matplotlib

siddharthst commented 6 years ago

I have tested it on matplotlib version 3.0.0 and 2.1.0 so far, and both are producing same result.

fidelram commented 6 years ago

The automatic tests indicate that there is no problem with the code and that the range is being shown. For example, the test can create this image:

https://github.com/deeptools/pyGenomeTracks/blob/master/pygenometracks/tests/test_data/master_bigwig.png

Can you try to run the tests in your set up? you will need to install py.test and then run

cd pyGenomeTracks
py.test pygenometracks --doctest-modules
siddharthst commented 6 years ago

Sorry for the late reply. I needed to send in the machine for repairs. So apparaently after getting it back and installing pyGenomeTracks using conda route results in completely unusable program. 

(py36) siddharth@ubuntu:~/Downloads/pyGenomeTracks$ py.test pygenometracks --doctest-modules
============================= test session starts ==============================
platform linux -- Python 3.6.6, pytest-3.8.2, py-1.6.0, pluggy-0.7.1
rootdir: /home/siddharth/Downloads/pyGenomeTracks, inifile:
plugins: remotedata-0.3.0, openfiles-0.3.0, doctestplus-0.1.3, arraydiff-0.2
collected 1 item / 23 errors                                                   

==================================== ERRORS ====================================
______________ ERROR collecting pygenometracks/makeTracksFile.py _______________
pygenometracks/makeTracksFile.py:4: in <module>
    from pygenometracks.tracksClass import PlotTracks
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
________________ ERROR collecting pygenometracks/plotTracks.py _________________
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
________________ ERROR collecting pygenometracks/tracksClass.py ________________
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
______ ERROR collecting pygenometracks/tests/test_bedGraphMatrixTrack.py _______
pygenometracks/tests/test_bedGraphMatrixTrack.py:7: in <module>
    import pygenometracks.plotTracks
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
______ ERROR collecting pygenometracks/tests/test_bedGraphMatrixTrack.py _______
ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_bedGraphMatrixTrack.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
pygenometracks/tests/test_bedGraphMatrixTrack.py:7: in <module>
    import pygenometracks.plotTracks
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
__________ ERROR collecting pygenometracks/tests/test_bigWigTrack.py ___________
pygenometracks/tests/test_bigWigTrack.py:7: in <module>
    import pygenometracks.plotTracks
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
__________ ERROR collecting pygenometracks/tests/test_bigWigTrack.py ___________
ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_bigWigTrack.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
pygenometracks/tests/test_bigWigTrack.py:7: in <module>
    import pygenometracks.plotTracks
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
_________ ERROR collecting pygenometracks/tests/test_epilogosTrack.py __________
pygenometracks/tests/test_epilogosTrack.py:6: in <module>
    import pygenometracks.plotTracks
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
_________ ERROR collecting pygenometracks/tests/test_epilogosTrack.py __________
ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_epilogosTrack.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
pygenometracks/tests/test_epilogosTrack.py:6: in <module>
    import pygenometracks.plotTracks
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
________ ERROR collecting pygenometracks/tests/test_hiCMatrixTracks.py _________
pygenometracks/tests/test_hiCMatrixTracks.py:6: in <module>
    import pygenometracks.plotTracks
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
________ ERROR collecting pygenometracks/tests/test_hiCMatrixTracks.py _________
ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_hiCMatrixTracks.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
pygenometracks/tests/test_hiCMatrixTracks.py:6: in <module>
    import pygenometracks.plotTracks
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
__________ ERROR collecting pygenometracks/tests/test_make_tracks.py ___________
pygenometracks/tests/test_make_tracks.py:4: in <module>
    import pygenometracks.makeTracksFile
pygenometracks/makeTracksFile.py:4: in <module>
    from pygenometracks.tracksClass import PlotTracks
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
__________ ERROR collecting pygenometracks/tests/test_make_tracks.py ___________
ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_make_tracks.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
pygenometracks/tests/test_make_tracks.py:4: in <module>
    import pygenometracks.makeTracksFile
pygenometracks/makeTracksFile.py:4: in <module>
    from pygenometracks.tracksClass import PlotTracks
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
________ ERROR collecting pygenometracks/tests/test_narrowPeakTrack.py _________
pygenometracks/tests/test_narrowPeakTrack.py:7: in <module>
    import pygenometracks.plotTracks
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
________ ERROR collecting pygenometracks/tests/test_narrowPeakTrack.py _________
ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_narrowPeakTrack.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
pygenometracks/tests/test_narrowPeakTrack.py:7: in <module>
    import pygenometracks.plotTracks
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
__________ ERROR collecting pygenometracks/tests/test_plot_tracks.py ___________
pygenometracks/tests/test_plot_tracks.py:7: in <module>
    import pygenometracks.plotTracks
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
__________ ERROR collecting pygenometracks/tests/test_plot_tracks.py ___________
ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_plot_tracks.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
pygenometracks/tests/test_plot_tracks.py:7: in <module>
    import pygenometracks.plotTracks
pygenometracks/plotTracks.py:152: in <module>
    import pygenometracks.tracksClass
pygenometracks/tracksClass.py:30: in <module>
    from pygenometracks.tracks import *
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
______________ ERROR collecting pygenometracks/tracks/__init__.py ______________
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
____________ ERROR collecting pygenometracks/tracks/BigWigTrack.py _____________
../../anaconda3/envs/py36/lib/python3.6/site-packages/py/_path/local.py:668: in pyimport
    __import__(modname)
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
___________ ERROR collecting pygenometracks/tracks/EpilogosTrack.py ____________
../../anaconda3/envs/py36/lib/python3.6/site-packages/py/_path/local.py:668: in pyimport
    __import__(modname)
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
___________ ERROR collecting pygenometracks/tracks/HiCMatrixTrack.py ___________
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
_____________ ERROR collecting pygenometracks/tracks/LinksTrack.py _____________
../../anaconda3/envs/py36/lib/python3.6/site-packages/py/_path/local.py:668: in pyimport
    __import__(modname)
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
__________ ERROR collecting pygenometracks/tracks/NarrowPeakTrack.py ___________
../../anaconda3/envs/py36/lib/python3.6/site-packages/py/_path/local.py:668: in pyimport
    __import__(modname)
pygenometracks/tracks/__init__.py:7: in <module>
    mod = __import__('.'.join([__name__, py]), fromlist=[py])
pygenometracks/tracks/HiCMatrixTrack.py:1: in <module>
    from hicmatrix import HiCMatrix
E   ModuleNotFoundError: No module named 'hicmatrix'
!!!!!!!!!!!!!!!!!!! Interrupted: 23 errors during collection !!!!!!!!!!!!!!!!!!!
=========================== 23 error in 0.74 seconds ===========================

Apparently this is an issue with HiCExplorer or associated libraries ? I'm not sure but now instead of worrying about Y-axis, I think there is another issue altogether. Attached is the list of packages.txt packages installed in the current conda environment. I'm using Ubuntu 18.04.1 LTS.

fidelram commented 6 years ago

you need to install the HiCMatrix package. Simply reinstall HiCExplorer with conda and it should work.

On Fri, Oct 12, 2018 at 11:05 AM Siddharth Tomar notifications@github.com wrote:

Sorry for the late reply. I needed to send in the machine for repairs. So apparaently after getting it back and installing pyGenomeTracks using conda route results in completely unusable program.

(py36) siddharth@ubuntu:~/Downloads/pyGenomeTracks$ py.test pygenometracks --doctest-modules ============================= test session starts ============================== platform linux -- Python 3.6.6, pytest-3.8.2, py-1.6.0, pluggy-0.7.1 rootdir: /home/siddharth/Downloads/pyGenomeTracks, inifile: plugins: remotedata-0.3.0, openfiles-0.3.0, doctestplus-0.1.3, arraydiff-0.2 collected 1 item / 23 errors

==================================== ERRORS ==================================== __ ERROR collecting pygenometracks/makeTracksFile.py _ pygenometracks/makeTracksFile.py:4: in from pygenometracks.tracksClass import PlotTracks pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import * pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' ____ ERROR collecting pygenometracks/plotTracks.py ___ pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' ____ ERROR collecting pygenometracks/tracksClass.py ____ pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' __ ERROR collecting pygenometracks/tests/test_bedGraphMatrixTrack.py _____ pygenometracks/tests/test_bedGraphMatrixTrack.py:7: in import pygenometracks.plotTracks pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import * pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' ____ ERROR collecting pygenometracks/tests/test_bedGraphMatrixTrack.py ___ ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_bedGraphMatrixTrack.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: pygenometracks/tests/test_bedGraphMatrixTrack.py:7: in import pygenometracks.plotTracks pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import * pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' ____ ERROR collecting pygenometracks/tests/test_bigWigTrack.py ___ pygenometracks/tests/test_bigWigTrack.py:7: in import pygenometracks.plotTracks pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import * pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' ____ ERROR collecting pygenometracks/tests/test_bigWigTrack.py _ ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_bigWigTrack.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: pygenometracks/tests/test_bigWigTrack.py:7: in import pygenometracks.plotTracks pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import * pygenometracks/tracks/init.py:7: in mod = import('.'.join([name_, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' ERROR collecting pygenometracks/tests/test_epilogosTrack.py __ pygenometracks/tests/testepilogosTrack.py:6: in import pygenometracks.plotTracks pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import * pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' ____ ERROR collecting pygenometracks/tests/test_epilogosTrack.py __ ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_epilogosTrack.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: pygenometracks/tests/test_epilogosTrack.py:6: in import pygenometracks.plotTracks pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' ____ ERROR collecting pygenometracks/tests/testhiCMatrixTracks.py ____ pygenometracks/tests/test_hiCMatrixTracks.py:6: in import pygenometracks.plotTracks pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' ____ ERROR collecting pygenometracks/tests/testhiCMatrixTracks.py ____ ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_hiCMatrixTracks.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: pygenometracks/tests/test_hiCMatrixTracks.py:6: in import pygenometracks.plotTracks pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' __ ERROR collecting pygenometracks/tests/test_make_tracks.py ___ pygenometracks/tests/test_make_tracks.py:4: in import pygenometracks.makeTracksFile pygenometracks/makeTracksFile.py:4: in from pygenometracks.tracksClass import PlotTracks pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' __ ERROR collecting pygenometracks/tests/test_make_tracks.py _____ ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_make_tracks.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: pygenometracks/tests/test_make_tracks.py:4: in import pygenometracks.makeTracksFile pygenometracks/makeTracksFile.py:4: in from pygenometracks.tracksClass import PlotTracks pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' ____ ERROR collecting pygenometracks/tests/testnarrowPeakTrack.py ____ pygenometracks/tests/test_narrowPeakTrack.py:7: in import pygenometracks.plotTracks pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' __ ERROR collecting pygenometracks/tests/testnarrowPeakTrack.py ____ ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_narrowPeakTrack.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: pygenometracks/tests/test_narrowPeakTrack.py:7: in import pygenometracks.plotTracks pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' __ ERROR collecting pygenometracks/tests/test_plot_tracks.py ___ pygenometracks/tests/test_plot_tracks.py:7: in import pygenometracks.plotTracks pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' __ ERROR collecting pygenometracks/tests/test_plot_tracks.py _ ImportError while importing test module '/home/siddharth/Downloads/pyGenomeTracks/pygenometracks/tests/test_plot_tracks.py'. Hint: make sure your test modules/packages have valid Python names. Traceback: pygenometracks/tests/test_plot_tracks.py:7: in import pygenometracks.plotTracks pygenometracks/plotTracks.py:152: in import pygenometracks.tracksClass pygenometracks/tracksClass.py:30: in from pygenometracks.tracks import * pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' __ ERROR collecting pygenometracks/tracks/init.py __ pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' ____ ERROR collecting pygenometracks/tracks/BigWigTrack.py ___ ../../anaconda3/envs/py36/lib/python3.6/site-packages/py/_path/local.py:668: in pyimport import(modname) pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' _____ ERROR collecting pygenometracks/tracks/EpilogosTrack.py ____ ../../anaconda3/envs/py36/lib/python3.6/site-packages/py/_path/local.py:668: in pyimport import(modname) pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' __ ERROR collecting pygenometracks/tracks/HiCMatrixTrack.py pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' ERROR collecting pygenometracks/tracks/LinksTrack.py ../../anaconda3/envs/py36/lib/python3.6/site-packages/py/path/local.py:668: in pyimport import(modname) pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' __ ERROR collecting pygenometracks/tracks/NarrowPeakTrack.py __ ../../anaconda3/envs/py36/lib/python3.6/site-packages/py/_path/local.py:668: in pyimport import(modname) pygenometracks/tracks/init.py:7: in mod = import('.'.join([name, py]), fromlist=[py]) pygenometracks/tracks/HiCMatrixTrack.py:1: in from hicmatrix import HiCMatrix E ModuleNotFoundError: No module named 'hicmatrix' !!!!!!!!!!!!!!!!!!! Interrupted: 23 errors during collection !!!!!!!!!!!!!!!!!!! =========================== 23 error in 0.74 seconds ===========================

Apparently this is an issue with HiCExplorer or associated libraries ? I'm not sure but now instead of worrying about Y-axis, I think there is another issue altogether. Attached is the list of packages.txt https://github.com/deeptools/pyGenomeTracks/files/2472378/packages.txt packages installed in the current conda environment. I'm using Ubuntu 18.04.1 LTS.

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siddharthst commented 6 years ago

I reinstalled HiCExplorer using conda install hicexplorer -c bioconda -c conda-forge and still the same exact error. Maybe opening another issue regarding installation would be more appropriate.

fidelram commented 6 years ago

Yes, I think that is better.

siddharthst commented 6 years ago

The installation issue solved with latest installation of Ubuntu 18.10 - probably because I installed a fresh copy of Anaconda. This is perplexing...there is definitely something going on with dependencies here. Anyways, now I'm back to the first issue - Y axis being missing. Using py.test throws a similar error that it cannot find module named hicmatrix - I installed hicexplorer before installing pygenometracks this time. The plots are being generated now, so that's good. Matplotlib version is 2.1.2. Also python version is 3.6 instead of the default 3.7.

LeilyR commented 5 years ago

You might need to try this conda install -c bioconda hicmatrix

siddharthst commented 5 years ago

I can say that everything is working with the current release now. I believe the problem was with the handling of hicmatrix by conda and the inability of pygenometracks to find it. The issue can be closed now but I might recommend better handling of hicmatrix dependency - or atleast in a way that absence of it doesn't breaks pygenometracks.

bgruening commented 5 years ago

@siddharthst please give the latest version a try. it should solve your issue. You can try the newest version here: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/