[Biojava-l] Is a modification of the FASTA parser for my needs easy or should I implement something else?

[Peter Cock]

On Monday, December 19, 2011, Hannes Brandstätter-Müller <
biojava at hannes.oib.com> 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