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Hi,
I am having issues with Conifer plotting the call images.
It manages for about half the chromosomes - chr 1, 2, 10 to 19 with this command
python conifer.py plotcalls --input analysis.hdf5 --calls calls.txt --outputdir call_imgs
then I get this error
/usr/local/lib/python2.7/dist-packages/matplotlib-1.4.3-py2.7-linux-x86_64.egg/matplotlib/pyplot.py:424: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
max_open_warning, RuntimeWarning)
Traceback (most recent call last):
File "/home/neuro/Documents/CoNIFER/conifer_v0.2.2/conifer.py", line 682, in <module>
args.func(args)
File "/home/neuro/Documents/CoNIFER/conifer_v0.2.2/conifer.py", line 501, in CF_plotcalls
window_start = max(exons[0]-args.window,0)
IndexError: index 0 is out of bounds for axis 0 with size 0
Closing remaining open files: analysis.hdf5... done
Any help would be great
alig
I am having issues with Conifer plotting the call images.
It manages for about half the chromosomes - chr 1, 2, 10 to 19 with this command
python conifer.py plotcalls --input analysis.hdf5 --calls calls.txt --outputdir call_imgs
then I get this error
/usr/local/lib/python2.7/dist-packages/matplotlib-1.4.3-py2.7-linux-x86_64.egg/matplotlib/pyplot.py:424: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
max_open_warning, RuntimeWarning)
Traceback (most recent call last):
File "/home/neuro/Documents/CoNIFER/conifer_v0.2.2/conifer.py", line 682, in <module>
args.func(args)
File "/home/neuro/Documents/CoNIFER/conifer_v0.2.2/conifer.py", line 501, in CF_plotcalls
window_start = max(exons[0]-args.window,0)
IndexError: index 0 is out of bounds for axis 0 with size 0
Closing remaining open files: analysis.hdf5... done
Any help would be great
alig