[Bioperl-l] clustalw to maf format

shalabh sharma shalabh.sharma7 at gmail.com
Mon Aug 2 15:44:35 EDT 2010


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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