Re: [Seqan-dev] reading fasta with non-DNA5 characters

["Weese, David" <weese@campus.fu-berlin.de>]

Hi,

actually it should automatically convert every non-ACGT character to N (or A for Dna targets). Have you already tried reading your files into string over Dna5 alphabets?

Cheers,
David
--
David Weese				weese@inf.fu-berlin.de
Freie Universität Berlin		http://www.inf.fu-berlin.de/
Institut für Informatik			Phone: +49 30 838 75246
Takustraße 9					Algorithmic Bioinformatics
14195 Berlin					Room 021 

Am 25.04.2012 um 11:08 schrieb Bernd Jagla:

> Hi,
> 
> I have a couple of genome seqeunces that contain characters other than ACTGN (i.e. Y, M,...)...
> 
> Is there a way to read those sequences in as well and automatically convert those non conforming letters to N?
> 
> Thanks,
> 
> Bernd
> 
> PS:
> 
> I am using:
> 
>        RecordReader<String<char, MMap<> >, DoublePass<Mapped> > refReader(seqMMapString);
>        int read2out = read2(seqIds, faSeqs, refReader, Fasta());
> 
> for reading in the data and get an INVALID_FORMAT error...
> 
> 
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