[Bioperl-l] Bio::SeqIO::scf header/comments handling

Nancy Hansen nhansen at nhgri.nih.gov
Tue Oct 31 19:51:23 UTC 2006


	As sequencing centers begin to deposit trace data from "Medical
Sequencing" projects into the public archives, there is now the need to
"anonymize" sequence trace files by removing embedded information which
might be used to identify the individual who was the original source of
the DNA being sequenced.

	I was hoping I might be able to use Bio::SeqIO to manipulate the
comments contained in an SCF-formatted trace file, but I'm finding that
Bio::SeqIO/Bio::Seq::SequenceTrace doesn't seem to store this information.
Since SCF is a widely-accepted standard for trace files, would it be
reasonable to include fields like "scf_comments" and "scf_header" in a
Bio::Seq::SequenceTrace object and have Bio::SeqIO::scf populate them?
Likewise, it would be great if write_seq could pull these values right
from a SequenceTrace object rather than requiring them as arguments.

	I'd be happy to help in this effort if necessary.


Nancy F. Hansen, PhD	nhansen at nhgri.nih.gov
Bioinformatics Group
NIH Intramural Sequencing Center (NISC)
5625 Fishers Lane
Rockville, MD 20852
Phone: (301) 435-1560	Fax: (301) 435-6170

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