[Biococoa-dev] read Fasta File with gap symbols
schristley at mac.com
Wed Apr 1 14:21:32 EDT 2009
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.
On Apr 1, 2009, at 3:05 AM, Stephan wrote:
> 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?
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