[Bioperl-l] contig disassembly

Andrew Stewart stewarta at nmrc.navy.mil
Wed Jan 17 17:21:43 EST 2007


I can't seem to find trunc_with_features anywhere in Bio::SeqUtils.   
Was this method or its functioning moved to another module / method  
within this module??

Thanks
-Andrew


On Jan 17, 2007, at 3:38 AM, Heikki Lehvaslaiho wrote:

> Andrew,
>
> The default interface to Bio::SeqI objects does not do it. The  
> methods leave
> you to deal with feature table changes after sequence changes.
>
> However, there are some attempts to provide this kind functionality  
> in the
> Bio::SeqUtils class.
>
> Bio::SeqUtils::cat
> Bio::SeqUtils::revcom_with_features
> Bio::SeqUtils::trunc_with_features
>
> These could be expanded and made more complete, maybe even a class  
> of its own
> if there is enough interest?
>
> 	-Heikki
>
>
> On Tuesday 16 January 2007 23:11, Andrew Stewart wrote:
>> If I want to take a Bio::Seq object representing a contig and
>> disassemble it into the constituent sequences which originally lead
>> to its formation, all the while preserving the feature annotation
>> associated with each sub-sequence, and with the coordinates of these
>> feature sets updated to reflect their position relative to these sub-
>> sequences, what is the best way to go about this?  If I take a
>> subsequence of a Seq object, will it carry over the relevant features
>> as well?
>>
>>
>> --
>> Andrew Stewart
>> Research Assistant, Genomics Team
>> Navy Medical Research Center (NMRC)
>> Biological Defense Research Directorate (BDRD)
>> BDRD Annex
>> 12300 Washington Avenue, 2nd Floor
>> Rockville, MD 20852
>>
>> email: stewarta at nmrc.navy.mil
>> phone: 301-231-6700 Ext 270
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/
>      _/  _/  _/  Heikki Lehvaslaiho    heikki at_sanbi _ac _za
>     _/_/_/_/_/  Associate Professor    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
> ___ _/_/_/_/_/________________________________________________________



--
Andrew Stewart
Research Assistant, Genomics Team
Navy Medical Research Center (NMRC)
Biological Defense Research Directorate (BDRD)
BDRD Annex
12300 Washington Avenue, 2nd Floor
Rockville, MD 20852

email: stewarta at nmrc.navy.mil
phone: 301-231-6700 Ext 270




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