[Bioperl-l] IOManager

Brian Osborne brian_osborne at cognia.com
Mon May 17 08:47:31 EDT 2004


It sounds like you want to read some sort of data file, not a sequence file,
is that right?

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of luisa pugliese
Sent: Monday, May 17, 2004 7:19 AM
To: Bioperl-l at portal.open-bio.org
Subject: [Bioperl-l] IOManager

Hi Bioperler,
 I would like to read a text file within bioperl and I found that the
IOManager module should do it. However I looked at the doc and I didn't
understand completely what should I do. The doc says:
$myIO = new Bio::Root::IOManager(-WHERE   =>'/usr/tmp/data.out',
                                     -PARENT =>$self);
If I do this it works, but then I don't know how to get the informations
from $myIO.

Or it says:
 Usage     : $object->read(<named parameters>);
 Purpose   : Read raw textual data from a file or STDIN.
           : Optionally process each record it as it is read.
 Example   : $data = $object->read(-FILE    =>'usr/people/me/data.txt',
    :      -REC_SEP =>"\n:",
    :      -FUNC    =>\&process_rec);
           : $data = $object->read(-FILE  =>\*FILEHANDLE);
           : $data = $object->read(-FILE  =>new FileHandle $file, 'r');
that would be perfect, but I didn't understand what how I should define
$object, since when I try to use this syntax it says that it cannot use read
on an undefined variable.

Thanking everybody, I send you my best regards

Luisa Pugliese, Ph.D.
luisa.pugliese at safan-bioinformatics.it
Corso Tazzoli 215/13 -10137 Torino - ITALY
tel +39 011 3026230
cell. +39 333 6130644

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