Question: ETE3 compare stop filename truncation
0
gravatar for Joe
17 months ago by
Joe14k
United Kingdom
Joe14k 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 17 months ago by Joe14k
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 17 months 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 17 months ago by Joe14k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1966 users visited in the last hour