[Bioperl-l] Next Gen Formats

Peter biopython at maubp.freeserve.co.uk
Thu Mar 11 12:35:32 EST 2010


On Mon, Mar 8, 2010 at 9:06 PM, Ryan Golhar <golharam at umdnj.edu> wrote:
> Does Bioperl support color-space sequences, or FASTA formatted quality value
> files?
>
> ABI's Solid platform generates a number of files, two of which are fairly
> important (at the moment):
>
> 1)  .csfasta
>
> Color-space sequences in FASTA format
>
> 2) .qual
>
> Quality values of each color call, also in FASTA format.

You mean the QUAL format which was originally introduced by PHRED.
Try "qual" as the format name in SeqIO,
http://bioperl.org/wiki/HOWTO:SeqIO#Formats

> I didn't see (at quick glance) support for this in Bioperl, but maybe
> someone can point me in the right direction?

I expect that (like in Biopython) you can treat color space FASTA + QUAL
just like sequence space files, provided you are happy to interpret the
color space strings yourself.

Are you hoping to get BioPerl to convert the color space data into
sequence space data for you?

Peter



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