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
[EMAIL PROTECTED]
(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
[EMAIL PROTECTED]
(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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http://lists.open-bio.org/mailman/listinfo/biojava-l
--
Andrew Farmer
[EMAIL PROTECTED]
(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 - [email protected]
http://lists.open-bio.org/mailman/listinfo/biojava-l
