[BioPython] Checked in Parsers for Phred and Ace files

[Andrew Nunberg]

Perhaps the phred.py should just be called Phd.py and be added to SeqIO ?
Phred can output different file formats, scf, phd, fasta ....
Well I should actually look at the code first before making such suggestions
:)
Andy

I am currently up to my ears in ensembl-pipeline/ensembl/apollo stuff
I don¹t suppose anyone is working on a python API for ensembl... Hey there
is a nice project for some students :)


-- 
Andrew Nunberg
Bioinformagician
Orion Genomics
(314)-615-6989
www.oriongenomics.com


> From: Brad Chapman <chapmanb at uga.edu>
> Date: Sun, 25 Jan 2004 19:22:07 -0500
> To: biopython at biopython.org
> Subject: [BioPython] Checked in Parsers for Phred and Ace files
> 
> Hello all;
> Thanks to Frank Kauff's generous contributions, I've just checked
> parsers for Phred and Ace files (from the whole Phred/Phrap/Consed
> distribution).
> 
> They are checked in as:
> 
> Bio/Sequencing/Ace.py
> Bio/Sequencing/Phred.py
> 
> They work in the same way as standard Biopython parsers so you could
> get a Phred iterator and parser with:
> 
> from Bio.Sequencing import Phred
> 
> parser = Phred.RecordParser()
> iterator = Phred.Iterator(open("your_phred_file.phd"), parser)
> 
> while 1:
>   rec = iterator.next()
>   if not rec:
>       break
>   # do something with the record
> 
> The one caveat is that the Ace parser does not support RT, CT and WA
> tags. But, it does do lots of other useful things and if you need
> these tags (or know more about them) feel free to provide patches
> adding them.
> 
> I'd appreciate it if people who are using Phred and Ace files could
> test drive the code and make sure it works with their code. I'll try
> to get some phred and ace files from our own lab and add at least a
> quick test suite for them later this week.
> 
> Thanks to Frank for the contribution!
> Brad
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