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hoffmangroup / segway

Application for semi-automated genomic annotation.
http://segway.hoffmanlab.org/
GNU General Public License v2.0
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Warn when a track contains no zero values #59

Open EricR86 opened 8 years ago

EricR86 commented 8 years ago

Original report (BitBucket issue) by Michael Hoffman (Bitbucket: hoffman, GitHub: michaelmhoffman).

People sometimes load tracks for use in Segway that only have positive values and no zero values. The generator of the track did not distinguish between locations of no signal (which should be zero) and location where no signal can be generated (for example, uninterrogated regions or repeat regions).

  1. Segway should generate a warning for any track in use where the minimum (as determined from genomedata mins attribute) is >0. This should be a new class called something like NeverZeroDataWarning, a child of a new DataWarning class, which is a warnings.UserWarning.
  2. When discussing data preparation, we should mention this issue, and include this warning and its meaning, and also how to turn it off using the PYTHONWARNINGS environment variable.
  3. If possible, this warning should include a link to the page on readthedocs.io that describes what to do.
  4. There should be a very simple test that tests this and disabling it with PYTHONWARNINGS.
EricR86 commented 8 years ago

Original comment by Michael Hoffman (Bitbucket: hoffman, GitHub: michaelmhoffman).

EricR86 commented 8 years ago

Original comment by Michael Hoffman (Bitbucket: hoffman, GitHub: michaelmhoffman).