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

[Schreiber, Mark]

I'm not terribly happy about the way that I needed to wrap to symbol lists
in the same sequence. It just seems a bit ugly so if anyone has a suggestion
of how to avoid this let me know, otherwise I hope its useful to someone :)

Mark


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: Tuesday, June 26, 2001 3:03 AM
> To: 'Schreiber, Mark'
> Cc: 'Biojava-L (E-mail)
> Subject: RE: [Biojava-l]phred/phrap code
> 
> 
> 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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> > 
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