[Bioperl-l] index::abstract on win and unix

Frédéric Romagné frederic.romagne at gmail.com
Mon Apr 21 11:53:11 EDT 2008


In fact, i want the whole Bio::Seq object, but the i verified the
ACCESSION and the LOCUS are the same in my genbank files.
I saw that the program sometimes tells that it cannot find the entry :

 if( !defined $seq ) {
	warn("Sequence $id in Database $db is not present\n");
    }

i suspect the make_index function not to work properly on windows
instead of the get_Seq_by_acc function...

Le vendredi 18 avril 2008 à 19:35 -0700, Jason Stajich a écrit :
> do you want the LOCUS or the ACCESSION?
> Do you mean the result is the completely wrong record or just the  
> wrong field?
> accession number is available from the seq's accession_number() method.
> -jason
> On Apr 16, 2008, at 2:39 PM, Frédéric Romagné wrote:
> 
> > Well, if with input file you mean the database used, it's created
> > with Bio::Index::GenBank from a ncbi FTP's genbank file.
> >
> > $id is an accession number read from a file but i chomp the line...
> >
> > I am trying to install the svn version of bioperl under windows to see
> > if there is an improvement.
> >
> > Le jeudi 17 avril 2008 à 08:49 +1200, Smithies, Russell a écrit :
> >> Did you check the format of your input file?
> >> i.e. DOS or UNIX line endings?
> >>
> >>> -----Original Message-----
> >>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l- 
> >>> bounces at lists.open-
> >>> bio.org] On Behalf Of Frédéric Romagné
> >>> Sent: Thursday, 17 April 2008 5:25 a.m.
> >>> To: bioperl-l at lists.open-bio.org
> >>> Subject: [Bioperl-l] [bioperl-l] index::abstract on win and unix
> >>>
> >>> Hello,
> >>> i made a program which use Bio::Index::GenBank and i tested it under
> >>> unix, that worked well.
> >>>
> >>> But i have to launch it under windows and it seems not to work on.
> >>>
> >>> Here is the problem :
> >>>
> >>> my $dbobj = Bio::Index::Abstract->new("Data/$db");
> >>> my $seq = $dbobj->get_Seq_by_acc($id);
> >>> print $seq->display_id."\n";
> >>>
> >>> did not print the same number than $id !!! So i don't work on the
> >>> sequence expected...
> >>>
> >>> I use the SVN sources on unix and the Perl package manager for
> >>> windows...
> >>>
> >>> Thanks.
> >>>
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