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deeptools plotProfile error when parsing reference-point mode output #1011

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Adrien-Evo opened this issue Sep 11, 2019 · 1 comment
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bug: core Bug in the main MultiQC code
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@Adrien-Evo
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Adrien-Evo commented Sep 11, 2019

Description of bug:
Hi,
The deeptools module breaks when parsing the text output from deeptools plotProfile when in reference point. In this case, there is no --endLabel options so there is no key TES in the bin_labels dictionary

Also, there is was an error in the parsePlotProfileData function :

    bins.append(int(col))
ValueError: invalid literal for int() with base 10: '1.0'

because the plotProfile tools outputs the bin number as float (1.0) which causes this error. But that's easily solvable with sed 's/\.0\t/\t/g'

MultiQC Error log:

Module deeptools raised an exception: Traceback (most recent call last):
  File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/bin/multiqc", line 440, in multiqc
    output = mod()
  File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/lib/python3.6/site-packages/multiqc/modules/deeptools/deeptools.py", line 75, in __init__
    n['plotProfile'] = self.parse_plotProfile()
  File "/sandbox/users/foucal-a/miniconda3/envs/deeptools/lib/python3.6/site-packages/multiqc/modules/deeptools/plotProfile.py", line 36, in parse_plotProfile
    {'from': converted_bin_labels[bin_labels.index('TES')], 'to': converted_bin_labels[-1], 'color': '#f7cfcf'},
ValueError: 'TES' is not in list

File that triggers the error:
test.plotProfile.txt

MultiQC run details (please complete the following):

  • Command used to run MultiQC: [multiqc test.plotProfile]
  • MultiQC Version: [eg. MultiQC v1.7]
  • Operating System: [unix]
  • Python Version: [eg. Python 3.6]
@ewels ewels added the bug: core Bug in the main MultiQC code label Sep 13, 2019
@ewels ewels added this to the MultiQC v1.8 milestone Nov 13, 2019
ewels added a commit to MultiQC/test-data that referenced this issue Nov 15, 2019
ewels added a commit that referenced this issue Nov 15, 2019
@ewels ewels closed this as completed in 808fe08 Nov 15, 2019
@ewels
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ewels commented Nov 15, 2019

Hi @Adrien-Evo,

Sorry for the delay and thanks for reporting this. With the help of your example file I figured out what was going on and have just pushed a fix. With your data you sadly won't get the nice coloured background bands behind the plot, but you will still get a plot and it won't crash any more.

Let me know how you get on!

Phil

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