Comments (3)
josephwb
commented on September 16, 2024
This is more general: phylip fails when piped to one of the alignments converts (pxs2*) as well. In this latter case, only 1 (the first) sequence is recognized and written to file.
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josephwb
commented on September 16, 2024
Gah I am stumped on this one... For the moment try to avoid piping phylip format (the only one that seems to behave different in a file vs. a stream). I suspect it has something to do with checking which of the Baskin-Robbins number of phylip sub-formats a file conforms to (i.e., there is some peeking ahead in the stream that may screw things up).
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josephwb
commented on September 16, 2024
Ok. The culprit indeed appears to be is_complicated_phylip (the function which tries to determine which (of a plethora of) format flavours is involved) i.e., when I comment this out (on a 'vanilla' phylip file, so no fancy-pants reading is necessary) things are processed properly. Geez, I was slightly proud of how it could handle everything thrown at it... But this seems to be a stream-specific issue. Anyway, baby steps...
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