Open josephwb opened 3 years ago
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.
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).
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...
Other formats work, but not phylip for some raisin:
And yet is works on a phylip file: