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

[Lee Ping Alison]

Hi,

Mr Day, thanks a lot for helping me with my queries.

I've just obtained the most recent bioperl-live code via cvs with the bug fixes you've mentioned. I'm wondering why the off-by-one bug fix (end = start+size-1) was necessary. I'm thinking that "end = start+size" is correct. Because the MAF file format by UCSC states that coordinates are half-open, zero-based. And I have understood it as the coordinates in "maf" module should be (start, end] (start exclusive, end inclusive). I've also tried several coordinates that agree with UCSC Genome Browser which uses [start, end]. Hence, in my opinion the bug fix was not necessary.

Will someone please enlighten me on this?

Thank you very much!

Alison.

  ----- Original Message ----- 
  From: Allen Day 
  To: Lee Ping Alison 
  Cc: Bioperl 
  Sent: 29 December, 2004 3:34 PM
  Subject: Re: Questions about Bio::AlignIO::maf


  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)