[Bioperl-l] writing scf files

Joel Martin j_martin@mhgc.lbl.gov
Fri, 24 Aug 2001 10:21:32 -0700 (PDT)

	Converting from/to scf files would be nice.  Another
sequencing center I work with has started to use scf files
for everything now so I at least would find it useful.


On Fri, 24 Aug 2001, Chad Matsalla wrote:

> Hi,
> Does anybody have use for a module that _writes_ scf files?
> I have a module that I put into SeqIO:: although I don't think it really
> belongs there. This module takes a Bio::Seq::SeqWithQuality object and
> writes an scf file with the traces matching the basecalls and qualities
> and the confidences matching the qualities.
> It is similar to the mktrace program in the Consed package except:
> 1. The traces that it synthesizes reflect the quality values in the
> SeqWithQuality object.
> 2. The confidences that are put into the scf file reflect the quality
> values in the SeqWithQuality object.
> 3. It is pure perl.
> I use this to synthesize artificial chromatograph files so that I can take
> consensus sequences out of Consed alignments and treat these consensus
> sequences like normal sequences (ie with chromats) and align them with
> other things.
> I started out by using Aaron's SeqIO::scf.pm as a model but I
> significantly altered from it once I got the hang of the header of the
> binary file. I think the existing SeqIO::scf.pm could be significantly
> altered so it provides sequence quality information (ie returns a
> SeqWithQuality object) when it reads an scf and so that it has the ability
> to write scf's.
> Anybody interested?
> Chad Matsalla
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