[Bioperl-l] ORF FInder

[Brian Osborne]

Lynn,

You must be referring to the Docs Web page, and you're right,
Bio::Factory::EMBOSS is not mentioned there since those pages only go as far
as version 0.7.2. My guess is that this page is not created automatically,
so it's not up-to-date. For more current documentation see
http://doc.bioperl.org/bioperl-live/ but it looks like these pages aren't
absolutely current either, but they're close and Bio::Factory::EMBOSS is
mentioned (I don't see the Bio/Biblio directory, for example).

For the most recent code you might want to get a CVS account and download
bioperl-live. I can't vouch for every single thing in bioperl-live but the
code I've used works. Plus you'll be able to contribute!

Brian O.

----- Original Message -----
From: "Lynn Stevens" <lynn_m_stevens@hotmail.com>
To: <b_i_osborne@hotmail.com>
Sent: Thursday, February 14, 2002 8:04 PM
Subject: Re: [Bioperl-l] ORF FInder


>
> Hi Brian,
> I don't see Bio::Factory::EMBOSS on the BioPerl documents page.  Is this
new?
>
>
> >From: "Brian Osborne" <b_i_osborne@hotmail.com>
> >To: "Lynn Stevens" <lynn_m_stevens@hotmail.com>
> >CC: <bioperl-l@bioperl.org>
> >Subject: Re: [Bioperl-l] ORF FInder
> >Date: Thu, 14 Feb 2002 16:16:14 -0500
> >
> >Lynn,
> >
> >Jason is also saying that you can use EMBOSS programs from within
Bioperl.
> >Here's an example using EMBOSS's getorf program :
> >
> >use Bio::SeqIO;
> >use Bio::Factory::EMBOSS;
> >
> >$factory = new Bio::Factory::EMBOSS;
> >$app = $factory->program("getorf");
> >%input = ( -sequence => "input.fasta", -minsize => 22, -outseq =>
> >"orfs.fasta" );
> >$app->run(\%input);
> >$seqio = Bio::SeqIO->new(-file => "orfs.fasta");
> >$seqobj = $seqio->next;
> >
> >Or something....
> >
> >True, it's not strictly Bioperl-ish but you have tremendous amount of
> >functionality in the EMBOSS suite, and this makes it all available
easily.
> >My understanding is that the EMBOSS modules will return Bioperl objects
> >someday, rather than just create files for you as in the example above.
To
> >get the positions of the ORFs you're going to have parse the
> >header/description line yourself, it's provided by the Seq object's
desc()
> >method.
> >
> >I'll add this to the new FAQ, something about functionality not found in
> >Bioperl might be found in EMBOSS, which is accessible through Bioperl.
> >
> >Brian O.
> >
> >
> >----- Original Message -----
> >From: "Jason Stajich" <jason@cgt.mc.duke.edu>
> >To: "Lynn Stevens" <lynn_m_stevens@hotmail.com>
> >Cc: <bioperl-l@bioperl.org>
> >Sent: Sunday, February 10, 2002 3:04 PM
> >Subject: Re: [Bioperl-l] ORF FInder
> >
> >
> > > Not in bioperl directly but you can use emboss's getorf program.
> > >
> > > On Sun, 10 Feb 2002, Lynn Stevens wrote:
> > >
> > > > Is there a module in BioPerl which allows you to take a sequence and
get
> > > > back a list of all the ORFs (or even just the largest ORF) in all
six
> >frames
> > > > (or even just one frame) indexed by sequence position.
> > > >
> > > > In other words you would submit a seq object and you would get back
a
> >set of
> > > > numbers which tell you where the ORFs are located in the sequence.
> > > >
> > > > I have looked through all the documentation and still can not find
this
> > > > feature even though it seem like an extremely common task.
> > > >
> > > > Thanks for any help,
> > > >
> > > > Lynn
> > > >
> > > >
> > > > _________________________________________________________________
> > > > Get your FREE download of MSN Explorer at
> >http://explorer.msn.com/intl.asp.
> > > >
> > > > _______________________________________________
> > > > Bioperl-l mailing list
> > > > Bioperl-l@bioperl.org
> > > > http://bioperl.org/mailman/listinfo/bioperl-l
> > > >
> > >
> > > --
> > > Jason Stajich
> > > Duke University
> > > jason@cgt.mc.duke.edu
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l@bioperl.org
> >http://bioperl.org/mailman/listinfo/bioperl-l
>
>