heikki at sanbi.ac.za
Wed Nov 7 05:05:59 EST 2007
I started using your Mdust module in bioperl-run and run into problems
* Only Bio::Seq objects are accepted but not Bio::PrimarySeq objects,
although the docs say otherwise
* Sequences are modified in place. That is really bad, because that
means that the user has to know to create a copy before
running Mdust on it.
* The docs say that you have to set MDUSTDIR envvar to tell the program
where to find the binary. That is actually optional if the
binary is on your path.
* The tests do not cover any of the options to the program
As a quick fix, I suggest that we:
* leave the current way of working for Bio::SeqI objects:
sequence string is not masked but seqfeatures to that effect are added
* Modify run() to return the new masked sequence object when
the target is a Bio::PrimarySeqI.
* fix the documentation
After that it will be possible to simply write:
$mdust = Bio::Tools::Run::Mdust->new();
$seq_dusted = $m->run($seq); # $seq->isa(PrimarySeqI);
Are you happy for me to do this or do you want to do it yourself?
______ _/ _/_____________________________________________________
_/ _/ _/ Heikki Lehvaslaiho
_/_/_/_/_/ heikki at_sanbi _ac _za skype: heikki_lehvaslaiho
_/ _/ _/ SANBI, South African National Bioinformatics Institute
_/ _/ _/ University of Western Cape, South Africa
_/ Phone: +27 21 959 2096 FAX: +27 21 959 2512
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