ETE3 compare stop filename truncation
Does anyone know how to prevent the ete3 toolkit compare tool from truncating names in it's output?
e.g.
ete3 compare -r /path/to/my_reference_tree_with_a_really_long_name.nwk -t /path/to/my_subject_tree_with_a_really_long_name.nwk
Yeilds:
source | ref | E.size | nRF | RF | maxRF | src-br+ | ref-br+ | subtre+ | treekoD
==============+ | ==============+ | ======+ | ======+ | ======+ | ======+ | ======+ | ======+ | ======+ | ======+
(..)long_name.n+ | (..)long_name.n+ | 13 | 0.00 | 0.00 | 20.00 | 1.00 | 1.00 | 1 | NA
I can script this myself to just echo out the file names, but I'm just wondering if anyone knows whether or not there's a built in mechanism for this?
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not possible at the moment. It would require a very small change in the code increasing the max length from 15 to anything else: https://github.com/etetoolkit/ete/blob/da6a23ae7adbe98be26a232a29fd90af3a66b0b5/ete3/tools/ete_compare.py#L185
OK, brilliant, thanks for letting me know. I've worked around it by just
echo-ing a bunch of file names and parsing the ETE3 output (result=$(ete3 compare..... | grep ... | sed ...)) for now!