[Bioperl-l] contig disassembly

Chris Fields cjfields at uiuc.edu
Wed Jan 17 17:56:00 EST 2007


It was added post-rel. 1.5.1, I believe, so it won't be there unless  
you're using the latest bioperl release (1.5.2) or bioperl-live.

chris

On Jan 17, 2007, at 4:21 PM, Andrew Stewart wrote:

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

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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