[Bioperl-l] writing scf files

Chad Matsalla chad@sausage.usask.ca
Fri, 24 Aug 2001 10:59:26 -0600 (CST)


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