Hi Hannes, if this is a more frequently used file format, would be great to get a parser for this... Any patches are welcome ! ;-)
Andreas On Wed, Dec 21, 2011 at 1:21 AM, Peter Cock <[email protected]> wrote: > On Monday, December 19, 2011, Hannes Brandstätter-Müller < > [email protected]> wrote: >> Hi! >> >> I have 2 files as output of my sequencer: one is a standard fasta, >> which is no problem, the other is a fasta file with the same headers, >> but instead of simple letters, there are integer values from 0 to 40 >> denoting the quality of the sequencing at this position. Is it easy to >> adapt the biojava fasta parser to read such files (by feeding >> different classes to the parser), or should I write a specialized >> parser from scratch? >> >> Hannes > > You mean a QUAL file? Often named example.qual or > example.fasta.qual and used in conjunction with a matching > FASTA file as a clumsy alternative to FASTQ (taking more > space on disk too). > > For Biopython we have a separate parser, although the > Header line handling is the same, the quality sequence > is quite different (splitting on white space, ASCII strings > then converted to integers). > > Peter > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
