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

[Brandon Invergo]

Hi everyone,
This was a stupid mistake and I'm not sure how it got past me. I've
already addressed it and I'm about to do a pull request.

Sorry about that,
-brandon

On Wed, Jun 29, 2011 at 4:52 PM,  <redmine at redmine.open-bio.org> wrote:
>
> Issue #3259 has been reported by Brandon Invergo.
>
> ----------------------------------------
> 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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