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

[Andreas Prlic]

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 <p.j.a.cock at googlemail.com> wrote:
> 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
>
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