[Biojava-l] RE: [Biojava-l]phred/phrap code

[Wiepert, Mathieu]

All the files have been put.  Note that Mark called this experimental code.
I have not yet added any new functionality.  Have at it...

-----Original Message-----
From: 	Schreiber, Mark [mailto:mark.schreiber@agresearch.co.nz] 
Sent:	Thursday, June 14, 2001 4:12 PM
To:	'Wiepert, Mathieu'
Cc:	'Biojava-L (E-mail)
Subject:	RE: [Biojava-l] Reading consensus sequence from phred/phrap
ace files

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 summary:

 * Title:        PhredSequence.java
 * Description:  An extension of SimpleSequence that implements Qualitative
to hold Phred quality scores
 *               Consideration was made of using a CrossProduct alphabet to
hold both the quality and DNA
 *               within the same sequence, however the CrossProduct
alphabets cannot use an Infinite Alphabet
 *               such as the IntegerAlphabet.

 * Title:        Qualitative.java
 * Description:  An interface for Classes wanting to hold quality data in
symbolic form such as Phred scores

 * Title:        GappedPhredSequence
 * Description:  A Class that wraps two GappedSymbolLists, one for sequence
data and one for
 *               quality data. All changes in sequence are reflected in the
quality data. The two
 *               SymbolLists can be though of as a single sequence. The
class provides a safer
 *               alternative to building a PhredSequence with two
GappedSymbolLists (although this
 *               can be done).<p>
 *               The class may be particularly useful for sequence assembly
projects where the
 *               quality of the sequence information must be taken into
account.<p>
 *               A Number of the methods are <code>synchronized</code> to
add integrety to the
 *               underlying symbol lists. If performance rather than saftey
is an issue then
 *               implement a PhredSequence with two GappedSymbolLists and
take care!

 * Title:        PhredTools
 * Description:  Static methods for working with phred quality data

I also had to implement some previously unimplemented methods from the
IntegerAlphabet class.
Also I added some methods to SeqIOTools (I can't remember if I needed these
for the phred stuff or not..

And I made the following for working with alignments

 * Title:        DistributionTools.java
 * Description:  A static class to hold static methods for calculations and
 * maniputlations using Distributions.


If you want some of these let me know. I have had some serious issues with
CVS so this is why they are not committed, also they should be considered
experimental,I have tested most of this but not intensively.

Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand

PH: +64 3 489 9175

 

> -----Original Message-----
> From: Wiepert, Mathieu [mailto:Wiepert.Mathieu@mayo.edu]
> Sent: Friday, June 15, 2001 3:24 AM
> To: 'biojava-l@biojava.org'
> Subject: [Biojava-l] Reading consensus sequence from phred/phrap ace
> files
> 
> 
> 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...
> 
> -Mat
> 
> 
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