Question: ETE3 compare stop filename truncation
0
gravatar for Joe
2.3 years ago by
Joe17k
United Kingdom
Joe17k wrote:

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?

ADD COMMENTlink written 2.3 years ago by Joe17k
1

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

ADD REPLYlink written 2.3 years ago by jhc2.8k

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!

ADD REPLYlink written 2.3 years ago by Joe17k
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