Author Name: Carnë Draug (Carnë Draug)
Original Redmine Issue: 3406, https://redmine.open-bio.org/issues/3406
Original Date: 2013-02-03
Original Assignee: Bioperl Guts
The documentation of @ Bio::Tools::Run::Alignment::TCoffee@ is wrong, at least on the description of the quiet and outfile parameters.
quiet states that “no value” silences it and that STDOUT, STDERR are valid parameters. It’s the opposite. Any value silences the program and it’s not possible to use STDOUt or STDERR. TCoffee actually allows to configure quiet that way but any syntax for it would break the supposed compatibility with the Clustalw API (they are supposed to work the same way correct?). I can prepare a fix and even change the default to be quiet (like Clustalw) but that would imply either an exception for quiet on the new method, or change the way defaults are set. It would also be possible to actually implement what’s documented. What’s preferred?
the values mentioned for the parameter outfile are invalid. The code can actually only use the ones from Bio::AlignIO.
It seems to me that the documentation of the module was generated automatically from TCoffe’s manual hence why is just plain wrong. My guess is that there’s other instances where this happens.
Author Name: Carnë Draug (Carnë Draug) Original Redmine Issue: 3406, https://redmine.open-bio.org/issues/3406 Original Date: 2013-02-03 Original Assignee: Bioperl Guts
The documentation of @ Bio::Tools::Run::Alignment::TCoffee@ is wrong, at least on the description of the
quietandoutfileparameters.quietstates that “no value” silences it and that STDOUT, STDERR are valid parameters. It’s the opposite. Any value silences the program and it’s not possible to use STDOUt or STDERR. TCoffee actually allows to configure quiet that way but any syntax for it would break the supposed compatibility with the Clustalw API (they are supposed to work the same way correct?). I can prepare a fix and even change the default to be quiet (like Clustalw) but that would imply either an exception for quiet on the new method, or change the way defaults are set. It would also be possible to actually implement what’s documented. What’s preferred?outfileare invalid. The code can actually only use the ones from Bio::AlignIO.It seems to me that the documentation of the module was generated automatically from TCoffe’s manual hence why is just plain wrong. My guess is that there’s other instances where this happens.