McTavishLab / physcraper

Welcome to Physcraper’s repository! Automatic gene tree updating using the Open Tree of Life.
https://physcraper.readthedocs.io/en/main/
GNU General Public License v3.0
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reviewer 1 - comment 8 - Error on treebase tree #147

Closed snacktavish closed 3 years ago

snacktavish commented 3 years ago

physcraper_run.py -s pg_328 -t tree322 -r -tb -o chenopodia

snacktavish commented 3 years ago

aha! The supertreebase mirror has a file for that study, but the data consists of the single character 'x', so the data set loading crashes. https://raw.githubusercontent.com/TreeBASE/supertreebase/master/data/treebase/S12369.xml

Updated function to look on treebase if supertreebase fails, even if it appears to have a file.

snacktavish commented 3 years ago

Fixed and tested in https://github.com/McTavishLab/physcraper/commit/d293dc741318b14118c52f3beca417a3afb985a5

snacktavish commented 3 years ago

Merged to main.