[Bioperl-l] Next Gen Formats

Ryan Golhar golharam at umdnj.edu
Thu Mar 11 21:19:37 EST 2010


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
> 


More information about the Bioperl-l mailing list