[Bioperl-l] Re: Questions about Bio::AlignIO::maf

[Allen Day]

Hi Alison,

I did not add strand information as I didn't need it at the time of
writing.  However, I believe this has come up on list recently and someone
has already patched in strand support, as well as an off-by-one bug in my
code.  Can whoever did these patches recently pipe in?  Thanks.

Alison, please keep the bioperl list CCed in your reply.

-Allen

On Wed, 29 Dec 2004, Lee Ping Alison wrote:

> Dear Mr Day,
> 
> While reading the Bioperl 1.4 documentation for the "Bio::AlignIO::maf" module, I found your email address and I have some questions about how to use "maf."
> 
> Am I right to say that the strand information of each sequence in an "maf" file is not recorded, when the LocateableSeq object is created in the nextAln() method? I observed that $strand was not one of the arguments in the call to the constructor.
> 
> If yes, what is the reason for not using the strand information? And subsequently, if I need to retrieve the strand information, how should I go about it?
> 
> Thank you very much for answering my queries.
> 
> Best Regards,
> Alison
> (Institute of Molecular and Cell Biology, Singapore)