[Bioperl-l] clustalw to maf format

Smithies, Russell Russell.Smithies at agresearch.co.nz
Mon Aug 2 16:25:26 EDT 2010


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
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