[Biojava-l] Reading consensus sequence from phred/phrap ace files

Wiepert, Mathieu Wiepert.Mathieu@mayo.edu
Thu, 14 Jun 2001 10:23:32 -0500

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));
SequenceIterator si = SeqIOTools.readPhred(reader);
Sequence sequence = si.getConsensusSequence();

Don't really need a sequence iterator I suppose, there is only one consensus
in the file, though there are all the sample sequences in the file.  And I
don't want to add a method to the sequence iterator either.  SO perhaps some
sort of sequencebuilder child or factory method?  Anyway, please advise...