[Bioperl-l] clustalw to maf format

shalabh sharma shalabh.sharma7 at gmail.com
Mon Aug 2 18:30:41 EDT 2010


Hi All,
      Thanks for the replies.
Actually i am working on a pipeline involving RNAz.
I had impression that there must be a converter available as their webserver
can take xmfa or maf format but standalone is only accepting maf format.

I think i will use a program that can output as xmfa and write to those
people if they can provide me with the converter.

Thanks
Shalabh


On Mon, Aug 2, 2010 at 5:31 PM, Chris Fields <cjfields at illinois.edu> wrote:

> No other format will work?  The main reason you see unimplemented methods
> like this is there is no active interest in working with this format beyond
> getting the information stored within them into objects and other
> commonly-used formats.
>
> chris
>
> On Aug 2, 2010, at 3:53 PM, shalabh sharma wrote:
>
> > 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
> >>> _______________________________________________
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> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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