hi thomas
i have tried to update my biojava with the commands given at
cvs.biojava.org.I dont think the following lines were required when u want
to update the biojava but i still tried
cvs -d :pserver:[EMAIL PROTECTED]:/home/repository/biojava login
and
cvs -d :pserver:[EMAIL PROTECTED]
hi
I am sorry and that was my mistake in modifying the xml parsar and
not setting the class path back ..so now the problem is solved
sarath
On Tue, 12 Jun 2001, Thomas Down wrote:
> Sarath's right. This issue probably /IS/ more Genbank's
> fault than ours, but realistically the BioJava pars
Has anyone written something that fills out a sequence from the consensus
sequence found in the .ace files of phred/phrap?
If not, I will be writing one, I was thinking of doing something like being
able to do
BufferedReader reader = new BufferedReader( new FileReader(phredFile));
SequenceIterat
We have a full .ace parser. It was not written to the biojava API, so
sequences are strings. Our parser (which I have not worked with) uses Jlex
and Cup, and parses the entire .ace file into a really big Object with all
the data in it, in a structure just like the .ace file itself. For this
reason
I have given Mathieu my Phred classes which may be able to form the basis of
biojava API that could be used by your .ace parser
I attach it here for your interest
Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
PH: +64 3 489 9175
> -Original Message--
Hi -
I have written a number of files for dealing with Phred quality scores but
nothing as yet for the ace files. I have given them to Mat but I don't know
if he has had time to check them in. If not I could give you my copies
(which may be more up to date than the ones I gave Mat.)
Breif summar
