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

[Lee Ping Alison]

Hi Mr Thompson,

Thanks for the reply. I understand the need for the one-based inclusive
coordinate system now; also partly because the major genome browsers use
that. However, since you're using inclusive coords, then shouldn't you add 1
to $start first before calculating $end, since $start is zero-based?

Alison.

----- Original Message -----
From: "James Thompson" <tex at biocompute.net>
To: "Lee Ping Alison" <g0404203 at nus.edu.sg>
Cc: "Allen Day" <allenday at ucla.edu>; "Bioperl" <bioperl-l at bioperl.org>
Sent: Wednesday, December 29, 2004 3:30 PM
Subject: Re: [Bioperl-l] Re: Questions about Bio::AlignIO::maf


> 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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> >
>
>