[Bioperl-l] Trace coordinates from scf files

[SRMD, Col - Underwood, Anthony]

Hi Bioperlers and Chad

As a follow up to my last message on the bioperl-mailing list:

I can see that the follwing methods do the following
$seq->length() returns the length in bases of the sequence held within the
scf file
$seq->trace_length() this returns the number of points for the trace data
print $seq->baseat("64") returns the base at position 64 in the sequence
print $seq->qualat("64") returns the quality at position 64 in the sequence
$seq->peak_indices() returns the peaks heights at each of the sequence
positions


however I find the $seq->trace("G") method a bit mysterious
the array returned has $seq->trace_length() elements and the values are
cumulative ( I think I may be dealing with a version 2 scf file). I
understand that the trace values should be calculated based on delta values.

something like $current_delta=$current_value-$previous_value
		$delta_delta=$current_delta-$previous_delta

This doesn't quite work. Please could anybody enlighten me on how the trace
values can be convrted into points that plotted as sequential "Y" values
would represent points on  a curve that resemble the traces when viewed in a
an application such as Chromas.

Many thanks,

Anthony

Dr Anthony Underwood
Bioinformatics Group
Genomics, Proteomic and Bioinformatics Unit
Central Public Health Laboratory
Health Protection Agency
61 Colindale Avenue
London
NW9 5HT
t:    0208 2004400 ext. 3618
f:    0208 3583138
e: anthony.underwood at hpa.org.uk