Question: scatter plots with single chromosome gives IndexError
0
gravatar for fenrir.sivar
5 months ago by
fenrir.sivar0 wrote:

I'm using cnvkit from the BCBIO 1.0.9 pipeline to find a rearrangement on chromosome 8 and 21 of a sample against hg19, wgrs, 35x

I'm using the following commands to create some plots:

cnvkit.py scatter -s Sample.cns -o Sample.png Sample.cnr results in the ususal overview plot with all chromosomes in one plot

specifying a single chromosome chr1 results in a single plot of chr1 as expected

cnvkit.py scatter -s Sample.cns -c chr1 -o Sample.chr1.png Sample.cnr

cnvkit.py scatter -s Sample.cns -c chr21 -o Sample.chr21.png Sample.cnr

results in

IndexError: positional indexers are out-of-bounds error, same for all remaining chromosomes:
How can I get an overview per chromosome?


Traceback (most recent call last):
  File "/data/tools/bin/cnvkit.py", line 13, in <module>
    args.func(args)
  File "/data/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/commands.py", line 899, in _cmd_scatter
    **scatter_opts)
  File "/data/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/scatter.py", line 49, in do_scatter
    y_min, y_max, title, segment_color)
  File "/data/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/scatter.py", line 216, in chromosome_scatter
    show_gene, window_width)
  File "/data/tools/bcbio/anaconda/lib/python2.7/site-packages/cnvlib/scatter.py", line 341, in select_range_genes
    if cnarr else CNA([]))
  File "/data/tools/bcbio/anaconda/lib/python2.7/site-packages/skgenome/gary.py", line 369, in in_range
    return self.as_dataframe(next(results))
  File "/data/tools/bcbio/anaconda/lib/python2.7/site-packages/future/builtins/newnext.py", line 59, in newnext
    return iterator.next()
  File "/data/tools/bcbio/anaconda/lib/python2.7/site-packages/skgenome/intersect.py", line 85, in iter_ranges
    subtable = table.iloc[region_idx]
  File "/data/tools/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/indexing.py", line 1478, in __getitem__
    return self._getitem_axis(maybe_callable, axis=axis)
  File "/data/tools/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/indexing.py", line 2091, in _getitem_axis
    return self._get_list_axis(key, axis=axis)
  File "/data/tools/bcbio/anaconda/lib/python2.7/site-packages/pandas/core/indexing.py", line 2073, in _get_list_axis
    raise IndexError("positional indexers are out-of-bounds")
IndexError: positional indexers are out-of-bounds
bcbio cnvkit • 315 views
ADD COMMENTlink modified 8 weeks ago by Vijay Lakhujani3.4k • written 5 months ago by fenrir.sivar0
0
gravatar for Brad Chapman
8 weeks ago by
Brad Chapman9.2k
Boston, MA
Brad Chapman9.2k wrote:

Thanks for this report and apologies for missing this when initially posted. I was able to reproduce this problem and sent in a pull request to CNVkit that should fix the problem: https://github.com/etal/cnvkit/pull/393 Hope this small fix will work for you and comes in a reasonable time to help with your work.

ADD COMMENTlink written 8 weeks ago by Brad Chapman9.2k
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