[Bioperl-l] BioPerl for indexing quality score files

[Gregory Jordan]

Hi all,

I'm wondering if anyone has tried using BioPerl to index sequence quality
score files? The files I'm looking at tend to look like Fasta files, but
with numbers (between 0 and 99) and spaces instead of sequence strings.
Something like:
---
>chr1
 0 20 20 20 50 99 99 99 99 30 30 20 20 10 10 0 0 0 0
---
(An example for Chimpanzee can be found here, as the file
'panTro2.quals.fa.gz':
http://hgdownload.cse.ucsc.edu/goldenPath/panTro2/bigZips/ )

I'm currently using a home-brewed file indexing system to access subsets of
these quality scores, but it's kind of slow and (probably) buggy. I'd much
rather use something like Bio::DB::Fasta, but (without having actually tried
it) I expect it wouldn't be too happy with these not-quite-fasta format
quality files.

Has anyone run into a similar situation and found a solution using Bioperl
(or something else)?

I'd be happy to hack around a bit to get this to work, if necessary; if
anyone could provide pointers on where to start, I'd be much obliged.

Cheers,
 Greg

PS - it's great to see the GitHub migration moving along so swiftly! I'll be
*much* more likely to start bug-hunting and patch-submitting with the code
living there now. :)