[Bioperl-l] extending the PHYLIP format

[Jason Stajich]

Should also ask Weigang what the status is, I think he implemented a  
lot of it.

-jason
On May 28, 2008, at 6:51 AM, Chris Fields wrote:

> Could you post a few example phylip sequences with long names to  
> svn and add a ticket to bugzilla?  I would consider this a somewhat  
> high-priority enhancement.
>
> I think keeping this in a single phylip module would be best, but  
> we'll to see how feasible it is.  I think it is possible to do so,  
> however, and still retain some backwards compatibility (I may even  
> have an idea how, just need to test it out).
>
> chris
>
> On May 28, 2008, at 3:23 AM, Heikki Lehvaslaiho wrote:
>
>> I just learned that a number of phylogenetics packages (PAUP,  
>> PHYML, Mr Bayes
>> at least ) now allow longer than 10 character IDs in PHYLIP  
>> format. The
>> documentation is scarce but the rules seem to be:
>>
>> 1. There can be spaces before the ID.
>> 2. The ID can be up to 50 characters long.
>> 3. ID can contain any characters. If you are using spaces within  
>> the ID, you
>> have to put the whole ID in single quotes ('). Single quotes can  
>> be used for
>> all IDs and are removed when parsing in.
>> 4. It is customary to have two spaces between the ID and the  
>> sequence.
>>
>> This custom seems to have come into PHYLIP format from Nexus.
>> Note that this allows sequences in a file to start at different  
>> columns.
>>
>> Can anyone shed more light into matter?
>>
>>
>> I need to get this into bioperl as the names in HIV sequences that  
>> I work with
>> are very long and can not be sensibly truncated.
>>
>> What would be the best way to do this?
>> 1. Add more options to the already heavily
>>   hacked Bio::AlignIO::phylip.pm
>> 2. Create a Bio::AlignIO::phyliplong.pm
>>
>> Do those ugly hacks for supporting fixed length long IDs really  
>> really belong
>> in the vanilla phylip.pm file?
>>
>> Opinions?
>>
>> 	-Heikki
>>
>> -- 
>> ______ _/      _/ 
>> _____________________________________________________
>>      _/      _/
>>     _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>>    _/_/_/_/_/  Senior Scientist    skype: heikki_lehvaslaiho
>>   _/  _/  _/  SANBI, South African National Bioinformatics Institute
>>  _/  _/  _/  University of Western Cape, South Africa
>>     _/      Phone: +27 21 959 2096   FAX: +27 21 959 2512
>> ___ _/_/_/_/_/ 
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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Marie-Claude Hofmann
> College of Veterinary Medicine
> University of Illinois Urbana-Champaign
>
>
>
>
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