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FePhyFoFum / phyx

phylogenetics tools for linux (and other mostly posix compliant) computers
blackrim.org
GNU General Public License v3.0
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pxlssq gets Nexus labels wrong if contiain spaces #154

Closed josephwb closed 3 years ago

josephwb commented 3 years ago

Related to fbfef0d. When read in by pxlssq, the label is terminated at the first space (token). Can be seen with:

pxlssq -s seq_file -l

Example:

'GU931859.1 Dendroica adelaidae voucher STRI-SLDAD10 aconitase 1 (ACO1) gene, exon 8 and partial cds'

is reported as:

GU931859.1

It also obviously messes up character state counts, number of characters, whether it is aligned, etc. Oof.

TODO: if label begins with a quote, read label until closing quote. This can get more complicated when the label itself contains quotes (e.g., "Bewick's Wren"). Don't worry about that until it surfaces.

josephwb commented 3 years ago

Involves both read_next_seq_from_stream() and read_interleaved_nexus().

josephwb commented 3 years ago

First one fixed with 496bea7

josephwb commented 3 years ago

And the second bf78f55