[Biopython-dev] [Biopython - Bug #3259] (New) PAML: run() methods can't find output file for parsing

[redmine at redmine.open-bio.org]

Issue #3259 has been reported by Brandon Invergo.

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Bug #3259: PAML: run() methods can't find output file for parsing
https://redmine.open-bio.org/issues/3259

Author: Brandon Invergo
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


All three PAML programs (baseml, codeml, and yn00) attempt to parse the output file given a path relative to the paml working directory. If this is different then the current (python) working directory, the output file won't be found.

The erroneous line is the same in all three files and thus the same fix is needed for all three:
baseml.py (line 177), codeml.py (line 187), yn00.py (line 104)

<pre>
        if parse:
---->       results = read(self._rel_out_file)
        else:
            results = None
</pre>

change to:
<pre>
        if parse:
---->       results = read(self.out_file)
        else:
            results = None
</pre>






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