[Biococoa-dev] read Fasta File with gap symbols

Stephan stschiff80 at googlemail.com
Wed Apr 1 15:10:12 EDT 2009

Hi Scott,

Thank you for answering.
In fact I looked through the code and found a workaround in the  
BioCocoa Source Code.

One more question: The newest version of BioCocoa is not Mac OS X  
Tiger compatible... is that right?

Actually, I wanted to ask how active the community is right now... I  
might be able to contribute something to the project. I am working in  
the bioinformatics field and just digging into Cocoa (coming from C++  
and python). How easy/hard is it to get a developer account? Also I  
could help updating the webpage or writing some more tutorials...


Am 01.04.2009 um 20:21 schrieb Scott Christley:

> Hello Stephan,
> Yes this is an issue.  BioCocoa attempts to determine the sequence  
> type by looking at the symbols, once it makes a decision it strips  
> any unknown symbols, of course it can make a wrong decision or more  
> likely in your case, it considers the gap symbol as unknown.
> Unfortunately there isn't a direct workaround unless you are  
> willing to make a modification to the BioCocoa source code, there  
> are just a few lines you can comment out in BCSequence.m that will  
> skip.
> I think BioCocoa probably needs to be changed so that it doesn't  
> modify the sequence data at all, and the user is responsible for  
> initiating a sequence type check and/or filtering.
> cheers
> Scott
> On Apr 1, 2009, at 3:05 AM, Stephan wrote:
>> Hi,
>> I am new to BioCocoa and was wondering whether there is a way of  
>> parsing FASTA files that contain alignment-information, i.e. they  
>> include sequences with the gap-symbol "-".
>> Right now, if I parse the file, the gaps are filtered out.
>> Any sugguestions?
>> Best,
>> Stephan
>> _______________________________________________
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
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