[Biopython] Bio.Sequencing.Ace

[Fungazid]

Hi Peter,

I compared the parameters with consed, and it seems to me the way to get the read strand is different:


for readn in range(len(contig.reads))
    strand=contig.af[readn].coru # strand 'C' is minus and 'U' is plus

Avi

--- On Sun, 6/28/09, Peter <biopython at maubp.freeserve.co.uk> wrote:

> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: Re: [Biopython] Bio.Sequencing.Ace
> To: "Fungazid" <fungazid at yahoo.com>
> Cc: biopython at lists.open-bio.org
> Date: Sunday, June 28, 2009, 4:17 PM
> On Sun, Jun 28, 2009 at 1:53 PM,
> Fungazid<fungazid at yahoo.com>
> wrote:
> >
> > Thanks Peter and David,
> >
> > contig.sequence and contig.quality parameters are more
> or less
> > the solution I basically wanted.
> >
> > Any additional tips are more than welcomed (For
> example:
> > getting specific qualities of reads. I think this
> requires parsing
> > the Phd file which is used as part of the assembly
> process. In
> > addition: getting read strand).
> 
> I'm not sure about the read qualities off hand, but you can
> get
> the read strand from the cryptically named property uorc,
> short
> for U (uncomplemented, i.e. forward) or C (complemented,
> i.e.
> reversed). This name reflects how the strand is stored in
> the
> raw Ace file.
> 
> from Bio.Sequencing import Ace
> handle = open("example.ace")
> for ace_contig in Ace.parse(handle) :
>     if ace_contig.uorc == "C" :
>         print ace_contig.name,
> "reverse"
>     else :
>         assert ace_contig.uorc == "U"
>         print ace_contig.name,
> "forward"
> 
> Peter
>