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Exception: columns m_score are missing in input file #16

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danielhyduke opened this issue Oct 28, 2015 · 0 comments
Open

Exception: columns m_score are missing in input file #16

danielhyduke opened this issue Oct 28, 2015 · 0 comments

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@danielhyduke
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I'm running pyprophet 0.18.3 on results generated from OpenSwathWorkflow from OpenMS and I'm getting an exception (this exception did not occur with pyprophet 0.13.3):

File "/usr/local/lib/python2.7/site-packages/pyprophet-0.18.3-py2.7-linux-x86_64.egg/pyprophet/data_handling.py", line 162, in check_header
raise Exception("columns %s are missing in input file" % ", ".join(missing))
Exception: columns m_score are missing in input file

This looks like it's an issue with this bit of code:
https://github.com/uweschmitt/pyprophet/blob/master/pyprophet/main.py#L121

if CONFIG.get("export.mayu"):
            self.check_cols += mayu_cols()

one of the elements in mayu_cols is 'm_score'; however, the m_score appears to be something that's calculated by pyprophet and not present in the openswath results.

OpenSwathWorkflow -- Complete workflow to run OpenSWATH
Version: 2.0.0 Sep 9 2015, 13:29:57, Revision: 66a7739
CENTOS 7 64-bit
python 2.7.9

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