[Bioperl-l] Bio::SearchIO::axt - getting summary field info

[Jonathan Lim]

Yeah I don't know what happened to that first sentence. Some of the words must 
have gotten cut out. Anyway, I tried what you suggested and it worked.

Thanks a bunch

On Saturday 31 January 2004 01:14 am, Jason Stajich wrote:
> Sorry your 1st sentance didn't make sense - you want the
> 'values two chromosome name fields'?  The Query sequence name is in
> $result->query_name and the hit sequence name is in $hit->name.
>
> Alternatively $hsp->hit->seq_id and $hsp->query->seq_id should also get
> you what you want?
>
> So you want to write it like a fasta alignment with gaps?
>
> If you have an HSP you just call
>  my $msawriter = Bio::AlignIO->new(-format => 'fasta');
>
> for my $hsp ( $hit->hsps ) {
>  # get_aln gives you a Bio::SimpleAlign object
>  $msawriter->write_aln($hsp->get_aln);
> }
>
> This *should* work, but haven't tested it out.
>
> -jason
>
> On Fri, 30 Jan 2004, Jonathan Lim wrote:
> > I'm using Bio::SearchIO::axt to read an axt file and I want to get the
> > values two chromosome name fields from the summary lines for each HSP in
> > the axt file. I've figured out how to get all the other fields except
> > this one. Which method do I call?
> >
> > Also, is there a simply way, using bioperl, to convert this axt file to
> > another format like fasta?
> >
> > Thanks.

-- 
Jonathan Lim
Bioinformatics Software Developer
Wasserman Lab, Centre for Molecular Medicine and Therapeutics
University of British Columbia
Phone: (604) 875-2345 ext 7948
Email: jlim at cmmt.ubc.ca