[Bioperl-l] Parsing TGICL-CAP3 ACE result files

[Javier Forment Millet]

There is already a Bio::Assembly::IO::ace file in the Bioperl-1.4 distribution,
but it is not the same as the one you have sent. Actually, your ace.pm seems
not to be as phrap-oriented as the other one. For example, when searching for
the contig name, your file states

(/^CO (.*Contig\d+) (\d+) (\d+) (\d+) (\w+)/) && do {
       my $contigID = $1;

(so $contigID becomes, for example, 'CL2Contig14', for it is the way TGICL names
contigs)

whereas the one with the distribution does

(/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do {
       my $contigID = $1;

(so $contigID becomes, for example, '857', which is the way phrap names
contigs).

I don't know if there is other crucial changes, but I will try it.

Thanks a looooot,

Javier.




Cita de Marc Logghe <Marc.Logghe at devgen.com>:

> Hi Javier,
> It is already quite old now, don't know what changes have been done in the
> mean time.
> Have a try with the Bio::Assembly::IO::ace file attached.
> This package I used for exactly the same purpose as you.
> Good luck,
> Marc
>
> > -----Original Message-----
> > From: Javier Forment Millet [mailto:jforment at ibmcp.upv.es]
> > Sent: Tuesday, December 14, 2004 12:08 PM
> > To: bioperl-l at portal.open-bio.org
> > Subject: [Bioperl-l] Parsing TGICL-CAP3 ACE result files
> >
> >
> > Hi,...
> >
> > I have to parse CAP3 ACE result files obtained with the TGICL
> > pipeline (TIGR
> > Gene Indices clustering tools). I know about the
> > bioperl-1.4::Bio::Assembly
> > module for working with contig assemblies, but it seems to be
> > Phrap-orientated.
> > Has anybody parsed CAP3 ACE result files with this module or
> > a modification of
> > it? Is there another module available for parsing these files?
> >
> > Thanks a lot,
> >
> > Javier.
> >
> > --
> > Javier Forment Millet
> > Instituto de Biologia Molecular y Celular de Plantas (IBMCP)
> > UPV-CSIC
> > Avenida de los Naranjos, s/n
> > 46022 Valencia (SPAIN)
> > jforment at ibmcp.upv.es
> > Tlf.:+34-96-3877885
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
>


-- 
Javier Forment Millet
Instituto de Biologia Molecular y Celular de Plantas (IBMCP)
UPV-CSIC
Avenida de los Naranjos, s/n
46022 Valencia (SPAIN)
jforment at ibmcp.upv.es
Tlf.:+34-96-3877885