[Biococoa-dev] read Fasta File with gap symbols

Craig Bateman craig.bateman at gmail.com
Wed Apr 1 20:19:14 EDT 2009

I was going to recommend (or at least ask permission) to omit that very code
while I'm working on the file-based vs memory-based sequence classes.
Unfortunately, things have been very crazy at work for the last 2 months, so
I haven't had the time I'd like to work on this.  I only have skeletons of
the new BCSequence class cluster together, but I was not finding an easy way
to filter the file-based sequences like the memory-based ones are at init
time.  Omitting that code from the library is a breaking change...  So it's
probably not going to be well-received by any end-users.

I have not heard back from Peter Schols regarding repository access.  I
would really like to branch the source and check-in on a regular basis. Is
there anyone else that can grant this access?  If not to the trunk, at least
to a branched folder?

On Wed, Apr 1, 2009 at 11:21 AM, Scott Christley <schristley at mac.com> wrote:

> 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
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