[Biojava-l] jRe: using phred calls with ChromatogramGraphic produced from ab1 files

[Mark Schreiber]

Some code examples like this would be great on the biojava.org
cookbook.  If people could add their GUI code that would be excellent.

- Mark

On Fri, Mar 14, 2008 at 7:27 AM, Andrew Farmer <adf at ncgr.org> wrote:
> Eric-
> thanks very much for your insights, the phred -c trick might in fact be
> exactly what I need. If not, I will check out the other code you have
> sent and follow up off-list if I have further questions.
>
>
> Andrew
>
>
> Eric Haugen wrote:
> >
> > Hi Andrew,
> >
> > It looks like what I did three years ago was turn off the
> > ChromatogramGraphic's call boxes:
> >
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_SEPARATORS,
> > Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_A, Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_C, Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_G, Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_T, Boolean.FALSE );
> > graphic.setOption(ChromatogramGraphic.Option.DRAW_CALL_OTHER,
> > Boolean.FALSE );
> >
> > then set the range based on the chromat positions in the phred file:
> >
> > graphic.setOption(ChromatogramGraphic.Option.FROM_TRACE_SAMPLE,
> > startIndex );
> > graphic.setOption(ChromatogramGraphic.Option.TO_TRACE_SAMPLE, endIndex );
> >
> > and finally just draw Phred's base calls myself based on the chromat
> > position scale.
> >
> > I don't know if you'll find it useful, but I've attached
> > PhdSequence.java and support code which I use as an alternative to
> > PhredSequence currently in biojava, which I think ignores chromat
> > positions.
> >
> > But the easiest solution may be to have "phred -c" convert your ABI
> > chromats to SCF files containing the phred base calls.
> >
> > --
> > Eric Haugen
> > Software Engineer
> > University of Washington Genome Center
> > ehaugen at u.washington.edu
> > (206) 616-7582
> >
> > On Thu, 13 Mar 2008, Andrew Farmer wrote:
> >
> >> Hi all-
> >> I have been trying to use the ChromatogramGraphic class to display ABI
> >> chromatogram data, whilst relating this to alignments of sequences
> >> called from these trace files with phred. For example, if the user
> >> clicks a putatively polymorphic base in an alignment viewer, to scroll
> >> and highlight the region of the ChromatogramGraphic corresponding to
> >> the ase call. However, I seem to be having some difficulty in
> >> establishing correspondences between the phred base calls and the
> >> information shown in the graphic.
> >>
> >> As far as I understand what is being displayed by ChromatogramGraphic,
> >> it is drawing "callboxes" around peaks corresponding to calls that are
> >> stored by Chromatogram, which in turn is storing information about the
> >> base calls that was encoded in the ABI file. These tend to differ
> >> substantially (e.g. in lower-quality areas) from the calls made by
> >> phred- e.g. an untrimmed phred-called sequence might have 1300 bases
> >> to the abi-called version's 900 bases. So, I am trying to find some
> >> way to get the ChromatogramGraphic callboxes to reflect the calls made
> >> by phred.
> >>
> >> Has anyone else encountered this type of situation before? It appears
> >> that phred's phd output encodes a trace offset for each of its calls,
> >> so I would guess that one could conceivably overlay the phred calls
> >> into a chromatogram produced by the abi parser in order to get the
> >> callboxes to reflect phred's interpretation of the trace data.
> >>
> >> I could be way off-base (no pun intended) in my interpretation, and
> >> would appreciate any insights from the gurus out there. And if this is
> >> more or less correct, and there is not yet a canned solution, any
> >> advice on how to go about coding it in a way that could be contributed
> >> back to the project would be great.
> >>
> >> Thanks in advance
> >> --
> >>
> >> Andrew Farmer
> >> adf at ncgr.org
> >> (505) 995-4464
> >> Database Administrator/Software Developer
> >> National Center for Genome Resources
> >>
> >> ---
> >> "To live in the presence of great truths and eternal laws,
> >> to be led by permanent ideals-
> >> that is what keeps a man patient when the world ignores him,
> >> and calm and unspoiled when the world praises him."
> >> -Balzac
> >> ---
> >> _______________________________________________
> >> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/biojava-l
> >>
>
> --
>
> Andrew Farmer
> adf at ncgr.org
> (505) 995-4464
> Database Administrator/Software Developer
> National Center for Genome Resources
>
> ---
> "To live in the presence of great truths and eternal laws,
> to be led by permanent ideals-
> that is what keeps a man patient when the world ignores him,
> and calm and unspoiled when the world praises him."
> -Balzac
> ---
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