hoffmangroup / segway

Application for semi-automated genomic annotation.
http://segway.hoffmanlab.org/
GNU General Public License v2.0
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Better handling when --ruler is set and no segment table is specified #47

Closed EricR86 closed 9 years ago

EricR86 commented 9 years ago

Original report (BitBucket issue) by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).


Currently when a --ruler option is set to non-default values and no seg-table/segment table is specified it assumes a 10bp ruler (from data/seg_table.tab) and errors.

If a --ruler is set to something other than the default there should be better handling in terms of error messages or assuming that the segment table has a ruler of the set value in the options for all labels.

The error looks like this:

  File "/gpfs/home/lua137/arch/Linux-x86_64/opt/python-2.7.10/lib/python2.7/site-packages/segway-1.2.0.dev_r0-py2.7.egg/segway/run.py", line 883, in seg_table
    assert len_slice.step == ruler_scale
AssertionError
EricR86 commented 9 years ago

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


This would be good. The reason this is specified in the seg table is I wanted to preserve the ability to maybe have a different ruler for different segment labels. We haven't needed that so far. This might be a backward- and forward-compatible solution:

EricR86 commented 9 years ago

Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).


Resolved in Pull Request #34