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Fix error handling + cases where with bigwigAverage with more than 2 bigwigs #1257

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Merged
WardDeb merged 4 commits into from
Sep 27, 2023
Merged

Fix error handling + cases where with bigwigAverage with more than 2 bigwigs #1257

WardDeb merged 4 commits into from
Sep 27, 2023

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@lldelisle
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@lldelisle lldelisle commented Sep 25, 2023

I got an error when using bigwigAverage:

Traceback (most recent call last):
  File "/data/galaxy/galaxy/var/dependencies/_conda/envs/mulled-v1-9dd4e5433cf4f47ee04cca722ff3869495cfcd627aecb78c70b6dcb65b45e293/bin/bigwigAverage", line 12, in <module>
    main(args)
  File "/data/galaxy/galaxy/var/dependencies/_conda/envs/mulled-v1-9dd4e5433cf4f47ee04cca722ff3869495cfcd627aecb78c70b6dcb65b45e293/lib/python3.8/site-packages/deeptools/bigwigAverage.py", line 140, in main
    writeBedGraph_bam_and_bw.writeBedGraph(
  File "/data/galaxy/galaxy/var/dependencies/_conda/envs/mulled-v1-9dd4e5433cf4f47ee04cca722ff3869495cfcd627aecb78c70b6dcb65b45e293/lib/python3.8/site-packages/deeptools/writeBedGraph_bam_and_bw.py", line 209, in writeBedGraph
    res = mapReduce.mapReduce((tileSize, fragmentLength, bamOrBwFileList,
  File "/data/galaxy/galaxy/var/dependencies/_conda/envs/mulled-v1-9dd4e5433cf4f47ee04cca722ff3869495cfcd627aecb78c70b6dcb65b45e293/lib/python3.8/site-packages/deeptools/mapReduce.py", line 146, in mapReduce
    res = list(map(func, TASKS))
  File "/data/galaxy/galaxy/var/dependencies/_conda/envs/mulled-v1-9dd4e5433cf4f47ee04cca722ff3869495cfcd627aecb78c70b6dcb65b45e293/lib/python3.8/site-packages/deeptools/writeBedGraph_bam_and_bw.py", line 42, in writeBedGraph_wrapper
    return writeBedGraph_worker(*args)
  File "/data/galaxy/galaxy/var/dependencies/_conda/envs/mulled-v1-9dd4e5433cf4f47ee04cca722ff3869495cfcd627aecb78c70b6dcb65b45e293/lib/python3.8/site-packages/deeptools/writeBedGraph_bam_and_bw.py", line 74, in writeBedGraph_worker
    getCoverageFromBigwig(
  File "/data/galaxy/galaxy/var/dependencies/_conda/envs/mulled-v1-9dd4e5433cf4f47ee04cca722ff3869495cfcd627aecb78c70b6dcb65b45e293/lib/python3.8/site-packages/deeptools/writeBedGraph_bam_and_bw.py", line 25, in getCoverageFromBigwig
    coverage = np.asarray(bigwigHandle.values(chrom, start, end))
RuntimeError: Invalid interval bounds!

I think it is because in the code there is a except ValueError instead of RuntimeError. The switch in pyBigwig occured in deeptools/pyBigWig@17f8dab which has been merged in version 0.2.1...

  • Does the PR contain new feature?
  • Does the PR contain bugfix?
  • Does the PR contain documentation changes?
  • Does the PR contain changes to the galaxy wrapper?

@lldelisle lldelisle changed the title Fix error handling Fix error handling = = Sep 26, 2023
@lldelisle lldelisle changed the title Fix error handling = = Fix error handling + cases where with bigwigAverage with more than 2 bigwigs Sep 26, 2023
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lldelisle commented Sep 27, 2023

The test that fails has been solved by #1258 .
Do you want me to merge develop or (to save energy) you accept the PR like this?
Do you think it would be possible to do a release quickly with this bug fix?

@WardDeb
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WardDeb commented Sep 27, 2023

We'll merge like this,
I'll add the PR for mpl version as well and then tag a new release today still. Thanks @lldelisle !

@WardDeb WardDeb merged commit d56b016 into deeptools:develop Sep 27, 2023
@lldelisle lldelisle deleted the fix_error_handling branch September 27, 2023 07:40
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lldelisle commented Sep 27, 2023

Thanks.

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@lldelisle @WardDeb