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invalid characters crashes HyPhy (Read 1496 times)
Horacio Montenegro

invalid characters crashes HyPhy
Nov 8th, 2004 at 12:14pm
Some characters (I can just remember dot (.) now) in the name of a species (like "D.mel", no spaces) in tree files and sequence files (phylip format) generates an error message (could not ready data file, or something) in Hyphy, when using ModelTest.bf or phylogenetic analyses, respectively. After first trial, sucessive tentatives gives error message "Could not ready batch file foo/ModelTest.bf, etc" and sometimes results in crashes. Restarting program solves the issue. Note: these characters are accepted by phylip. Using HyPhy-p3.exe, Windows98.

cheers, Horacio
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Re: invalid characters crashes HyPhy
Reply #1 - Nov 8th, 2004 at 9:20pm
Dear Horacio,

The crashes are definitely a bug - I'll look into that.
Sequence names in HyPhy are more restrictive than usual - in essense they must be valid identifiers (alphanumeric with underscores). '.' is has a special meaning - not unlike the C/C++ syntax. In HyPhy tree_id.branch_id.parameter_id is the way to refer to a model paramater attcahed to a branch in a tree - if '.' is found in the middle of a sequence name, odd behaviour results. I'll put more informative error messages into the code. In the meantime, I'd recommend replacing '.' with underscore in sequence and tree branch names.

Sorry about the inconvenience.

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