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

Lee Ping Alison g0404203 at nus.edu.sg
Wed Dec 29 09:45:49 EST 2004


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!


  ----- 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.


  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)

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