[Bioperl-l] contig disassembly

Andrew Stewart stewarta at nmrc.navy.mil
Thu Jan 18 12:56:16 EST 2007


Oh, I forgot to mention that I was referring to Bio::SeqUtils within  
my updated checkout of bioperl-live.  Anyhow, I removed it and got  
another checkout and I found the new method just fine.

Thanks for the help guys :)


On Jan 17, 2007, at 5:56 PM, Chris Fields wrote:

> 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
>
>



--
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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