plot_distance_vs_interactions issue

3DGenomes / TADbit

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

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plot_distance_vs_interactions issue #279

Open dawe opened 5 years ago

dawe commented 5 years ago

Hi again, During the tests I'm running, I've slipped into this error from plot_distance_vs_interactions function

 ddi = plot_distance_vs_interactions(reads, savefig='DDI.png', axe = ax,  max_diff=10000, resolution=1000000)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/dcittaro/.local/lib/python2.7/site-packages/pytadbit/mapping/analyze.py", line 430, in plot_distance_vs_interactions
    for k in xrange(max(dist_intr[diff]) - diff)]
ValueError: max() arg is an empty sequence

Any hint on how to tackle this is appreciated.

fransua commented 5 years ago

Hi @dawe sorry for the late repply. I guess that the problem here is that there is not data point in a given range. Perhaps you can play with the min_diff and max_diff parameters to focus on the range of distances where you do have data.

We will try to make TADbit robust to this case in the future.

thanks for reporting