[Biojava-l] SCF Parser issues with gaps and unread peak values ?
Ashika Umanga Umagiliya
aumanga at biggjapan.com
Thu Jun 18 02:51:44 UTC 2009
Please refer to image at: http://i43.tinypic.com/sfdjs6.png
As shown in Figure1 , I am drawing bases using Phrap ACE file and
drawing chromatographs using
Biojava 'ChromatoGraphics' . I use .SCF file generated by phrep.
As can be seen in Figure 1 , the alignment breaks from the 'Magenta
callbase-box'.The reason is may be the 'SCF parser' has ignored one of
the peaks which should be a 'T'.
Figure 2 : Shows what need to be happen.If somehow if I can fill it with
a T (or may be sometimes a Gap) I can save the alignment between sequences.
Figure 3 : Shows the same Chromatograph using ChromasPro , It has
identified the peak as a T.
I went throught the biojavas SCF parser , I noticed that it finally
creates a 'SimpleAlignment'.Can I utilize 'GappedSymbolList' and fix this?
Is there a way to read the gaps (or incases like this , the correct base
T) and make these two align.
Thanks in advance,
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