[Bioperl-l] GMAP IO?

Jason Stajich jason.stajich at gmail.com
Tue Jul 21 23:26:56 UTC 2009

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(<>) {
 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 Stajich
jason at bioperl.org
jason.stajich at gmail.com

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
>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
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