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

Jason Stajich jason at bioperl.org
Fri Apr 18 22:35:10 EDT 2008


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.
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
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