Re: [Seqan-dev] reading fasta with non-DNA5 characters
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...
>
>
> _______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
> https://lists.fu-berlin.de/listinfo/seqan-dev
