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asntech / intervene

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
http://intervene.rtfd.io/
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Support for zero interval files #10

Open jma1991 opened 5 years ago

jma1991 commented 5 years ago

I use Intervene in a computational pipeline to check overlaps from multiple BED files. The command I use is:

intervene pairwise --input <INPUT> --compute jaccard --output <OUTPUT>

Sometimes one of the BED files contains zero intervals. When this occurs Intervene throws the following error:

Performing a pairwise intersection analysis. Please wait...

Traceback (most recent call last):
  File "/home/s1437643/conda/bin/intervene", line 606, in <module>
    main()
  File "/home/s1437643/conda/bin/intervene", line 426, in main
    pairwise.pairwise_intersection(label_names, options)
  File "/home/s1437643/conda/lib/python3.6/site-packages/intervene/modules/pairwise/pairwise.py", line 480, in pairwise_intersection
    barplot(series, matrix, outfile, options, max_size=max(bed_sizes))
  File "/home/s1437643/conda/lib/python3.6/site-packages/intervene/modules/pairwise/pairwise.py", line 135, in barplot
    cax, order = heatmap_triangle(matrix, ax, options)
  File "/home/s1437643/conda/lib/python3.6/site-packages/intervene/modules/pairwise/pairwise.py", line 211, in heatmap_triangle
    Z = sch.linkage(D, method='average')
  File "/home/s1437643/conda/lib/python3.6/site-packages/scipy/cluster/hierarchy.py", line 713, in linkage
    raise ValueError("The condensed distance matrix must contain only "
ValueError: The condensed distance matrix must contain only finite values.

Would you be able to provide support for zero interval files? Preferably, the file is still included in all the analysis results rather than just not using the file.