[Bioperl-l] clustalw to maf format

shalabh sharma shalabh.sharma7 at gmail.com
Mon Aug 2 16:53:31 EDT 2010


Hi Russell,
            Thanks for the reply, but i  have around 400 alignments and some
huge ones :(

Thanks
Shalabh


On Mon, Aug 2, 2010 at 4:25 PM, Smithies, Russell <
Russell.Smithies at agresearch.co.nz> wrote:

> This might work if you only have a few:
> http://www.ibi.vu.nl/programs/convertalignwww/
>
> --Russell
>
>
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of shalabh sharma
> > Sent: Tuesday, 3 August 2010 7:45 a.m.
> > To: bioperl-l
> > Subject: [Bioperl-l] clustalw to maf format
> >
> > Hi,
> >     I am trying to convert clustalw to maf format.
> > I am trying to use AlignIO for that but its not working.
> >
> > Its giving me the following error:
> >
> > EXCEPTION Bio::Root::NotImplemented -------------
> > MSG: Abstract method "Bio::AlignIO::maf::write_aln" is not implemented by
> > package Bio::AlignIO::maf.
> > This is not your fault - author of Bio::AlignIO::maf should be blamed!
> >
> > STACK Bio::Root::RootI::throw_not_implemented
> > /Library/Perl/5.8.8/Bio/Root/RootI.pm:707
> > STACK Bio::AlignIO::maf::write_aln /Library/Perl/5.8.8/Bio/AlignIO/
> > maf.pm:176
> > STACK Bio::AlignIO::PRINT /Library/Perl/5.8.8/Bio/AlignIO.pm:492
> > STACK toplevel msf2mafy.pl:11
> >
> >
> > Is there any other way i can convert clustalw to maf?
> >
> > I would really appreciate if anyone can help me out.
> >
> > Thanks
> > Shalabh
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
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