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

[James Thompson]

Alison (and Allen),

I was the aforementioned bug fixer. :)

Sorry if there's any confusion on this, but AFAIK Bioperl uses an one-based
inclusive coordinate system. While maf may have its own opinions on the best
way to do coordinates, maf is only one of the formats that are supported by
Bio::AlignIO.  The consensus in Bioperl appears to be that it makes more sense
to use one consistent coordinate system within all of the modules rather than
catering to the opinions and idiosyncrasies of all of the possible file
formats. If we did not fix the off-by-one bug in maf.pm, then would be
consistency issues with Bio::Align::AlignI objects created from different file
formats.

Here's a link to a message from the mailing list that seems relevant to the
topic at hand:

http://bioperl.org/pipermail/bioperl-l/2002-June/008309.html

Cheers,

James Thompson

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

> 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)
> 
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