[Bioperl-l] Nexus symbols

[Jason Stajich]

-show_symbols => 0

If you use bp_sreformat.pl script specify --special="mrbayes" it will  
set both of the endblock and show_symbols values to 0.


perldoc Bio::AlignIO::nexus

        new

         Title   : new
         Usage   : $alignio = Bio::AlignIO->new(-format => ’nexus’, - 
file => ’filename’);
         Function: returns a new Bio::AlignIO object to handle  
clustalw files
         Returns : Bio::AlignIO::clustalw object
         Args    : -verbose => verbosity setting (-1,0,1,2)
                   -file    => name of file to read in or with ">" -  
writeout
                   -fh      => alternative to -file param - provide a  
filehandle
                               to read from/write to
                   -format  => type of Alignment Format to process or  
produce

                   Customization of nexus flavor output

                   -show_symbols => print the symbols="ATGC" in the  
data definition
                                    (MrBayes does not like this)
                                    boolean [default is 1]
                   -show_endblock => print an ’endblock;’ at the end  
of the data
                                    (MyBayes does not like this)
                                    boolean [default is 1]

On Sep 30, 2009, at 3:16 PM, Luis M Rodriguez-R wrote:

> Dear all,
>
> Is there a way to remove the "symbols" (i.e. the 'symbols="ATCG"')  
> from the "format" line in the Nexus output of Bio::AlignIO?
>
> My code (snippet) is:
>
> my $fasta_i = Bio::AlignIO->new(-file=>"<$outfile.aln.fasta", '- 
> format'=>"fasta");
> my $nexus_o = Bio::AlignIO->new(-file=>">$outfile.aln.nex", '- 
> format'=>"nexus");
> while(my $fasta_aln=$fasta_i->next_aln){$nexus_o- 
> >write_aln($fasta_aln);}
>
> And I would like to remove the symbols (is not compatible with  
> MrBayes v3.1.2: "Could not find parameter "symbols"").
>
> Also, it would be nice to be able to change the TITLE comment.
>
> Thanks all!
> Regards,
>
> Luis M. Rodriguez-R
> [http://bioinf.uniandes.edu.co/~miguel/]
> ---------------------------------
> Unidad de Bioinformática del Laboratorio de Micología y Fitopatología
> Universidad de Los Andes, Colombia
> [http://bioinf.uniandes.edu.co]
>
> + 57 1 3394949 ext 2619
> luisrodr at uniandes.edu.co
> me at miguel.weapps.com
>
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--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org