[Bioperl-l] clustalw to maf format

Chris Fields cjfields at illinois.edu
Mon Aug 2 17:31:20 EDT 2010


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
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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