[Bioperl-l] Re: Bio::SearchIO::amps and Bio::SearchIO::mrbayes_nexus

[Jason Stajich]

I added two init parameters to Bio::AlignIO::nexus

-show_symbols
-show_endblock

which should be set to '0' when initializing a nexus file for  
MrBayes.   This should be in 1.5.0.

This seemed to work okay for me. I'd rather not see a new module if  
we can just provide some parameters to tweak this.

AlignIO::nexus was never meant to be a full fledged nexus parser -  
the Bio::SimpleAlign object is not complex enough to store all the  
commands and blocks.  It would be nice if we could do a better job  
here - maybe by making an object which stores the blocks differently  
- AlignIO/SimpleAlign are only really applicable for the DATA block.

Definitely welcome your input/support on designing some new stuff  
Matthew.  If it makes more sense to you to write a new module that is  
fine too - but let's see how different it has to be from the current  
one and whether or not we can combine them in the end.

-jason

On May 11, 2005, at 8:31 AM, Matthew Betts wrote:

>
> Sorry, meant Bio::AlignIO::*
>
> (oops)
>
> On Wed, 11 May 2005, Matthew Betts wrote:
>
>
>>
>> Hi,
>>
>> I was thinking of writing a Bio::SearchIO module for AMPS block  
>> format. This is the format used by alscript and stamp. Both of  
>> these come with format converters, but would be useful for me to  
>> do it within bioperl. OK for me to write Bio::SearchIO::amps, or  
>> is there something else already? Is that name OK?
>>
>> Secondly, MrBayes doesn't like some things in the Nexus format  
>> output by Bio::SearchIO::nexus (the 'symbols' parameter, and it  
>> expects 'end;' rather than 'endblock;') even though they're valid  
>> nexus... OK to copy Bio::SearchIO::nexus to  
>> Bio::SearchIO::mrbayes_nexus and make the necessary changes, or is  
>> there a better way? (Though a full nexus parser and flexible  
>> outputter looks like a nightmare...)
>>
>> Thanks,
>>
>> Matthew
>>
>>
>>
>
> -- 
> Matthew Betts, Post Doc, Computational Biology Unit,
> BCCS, HiB, UiB, Thormøhlensgt. 55, 5008 Bergen, Norway
> tlf: (+47) 55 58 40 22, fax: (+47) 55 58 42 95
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