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
