[Bioperl-l] SeqIO::abi use

[Roy Chaudhuri]

Hi Tom,

It looks from the docs/source like you can, with something like this:

use Bio::SeqIO;
my $seq=Bio::SeqIO->new(-file=>$ARGV[0], -format=>'abi', 
-get_trace_data=>1)->next_seq;
my @atrace=$seq->get_trace_graph(-trace=>'a'); # or c,g,t

Sorry, but I don't have Staden installed so I can't test if this works.
You might also look at the non-BioPerl ABI module on CPAN - again, I 
haven't tested this, but it looks like it could be useful for your purposes:
http://search.cpan.org/~MALAY/ABI/ABI.pm

Roy.


On 08/04/2010 23:30, Tom Keller wrote:
> Greetings, Can the Bio::SeqIO::abi module be used to access the raw
> fluorescence data? Are there any examples available? I'm wondering
> how to calculate ratios of mixed bases prior to the smoothing and
> scaling done by the base caller.
>
> thank you Tom kellert at ohsu.edu<mailto:kellert at ohsu.edu> 503-494-2442
>
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