[Bioperl-l] Next Gen Formats

Chris Fields cjfields at illinois.edu
Thu Mar 11 22:35:50 EST 2010


Ryan,

We would have to see example files to get an idea of how feasible it is.  You could possibly use a Bio::SeqIO::fasta and a Bio::SeqIO::qual stream, and interleave the two somehow.  However, BioPerl qual scores are PHRED-based by default, and I'm not sure how color-space data would work within that schematic.

chris

On Mar 11, 2010, at 8:19 PM, Ryan Golhar wrote:

> Not convert the sequences, just read the sequence file and allow me to
> process each one individually, sort of like:
> 
> $seqio = new Bio::Seq(...)
> while ($seq = $seqio->next_seq) {
> 	...
> }
> 
> Peter wrote:
>> 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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