[BioPython] Checked in Parsers for Phred and Ace files

[Frank Kauff]

Andrew Nunberg schrieb:

> Perhaps the phred.py should just be called Phd.py and be added to SeqIO ?
> Phred can output different file formats, scf, phd, fasta ....

I'm in favour of that. Actually that was the name it had when I submitted it :-)
, and it makes clear which of the different filetypes of phred the parser is
dealing with.

Frank



>
> 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
> > _______________________________________________
> > BioPython mailing list  -  BioPython at biopython.org
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> >
>
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