[Bioperl-l] GMAP IO?

[Jason Stajich]

There hasn't been one yet that I know of. PSL can be parsed with
Bio::SearchIO parser.
The "non-standard" gff flavors is one of the annoyances but I just end
up writing very simple gff converters in simple scripts rather than a
master bioperl module that can handle all the different nuances that
are not part of a standard.  If you post the problematic alignment gff
can give you a better sense of what would be the code, but I suspect
it is just simple perl like this can standardize some things.  This is
my basic skeleton for that:
while(<>) {
 chomp;
 my @row = split(/\t/,$_);
 # assuming a gff3 file, map 9th column to hash, assume single
key=value pairs not key=value1,value2
 my %last = map { split(/=/,$_) } split(/;/,pop @row);
 # some more code to fix the 9th column fields...
 #
 # now print out the line
 print join("\t", @row, map { sprintf("%s=%s",$_,$last{$_}) } grep {
exists $last{$_} } qw(ID Parent Note)),"\n";
}
-jason
Jason Stajich
jason at bioperl.org
jason.stajich at gmail.com
http://bioperl.org/wiki/User:Jason


On Tue, Jul 21, 2009 at 4:14 PM, Smithies, Russell
<Russell.Smithies at agresearch.co.nz> wrote:
>
> Is there an IO module for GMAP output?
> I looked in the obvious places (Bio::AlignIO, Google etc..)
> I know GMAP will do gff or psl output and there are parsers for those (they're SeqIO, not AlignIO?), but I was hoping there might be a better way as I've found GMAP's gff needs a bit of post-processing to make it usable.
>
> It's a fairly large job (mammalian refseqs vs. a mammalian genome) so I want to do it as efficiently as possible.
>
> Thanx,
>
> Russell Smithies
>
> Bioinformatics Applications Developer
> T +64 3 489 9085
> E  russell.smithies at agresearch.co.nz
>
> Invermay  Research Centre
> Puddle Alley,
> Mosgiel,
> New Zealand
> T  +64 3 489 3809
> F  +64 3 489 9174
> www.agresearch.co.nz
>
>
>
> =======================================================================
> Attention: The information contained in this message and/or attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or privileged
> material. Any review, retransmission, dissemination or other use of, or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> =======================================================================
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l