[ensembl-dev] Use of uninitialized value in print at HZ254_genedata.pl line .

[mag]

Hi Pengfei,

Depending on the species and data, it is not always possible to have an
official gene name and/or description.

As more proteins and cDNAs are submitted to public databases, we will be
able to use these to name the gene models.


Regards,
Magali

On 11/02/2014 01:25, 刘鹏飞 wrote:
> Thanks, now I am analyzing RNAseq data and want to download the gene
> information of the species, so briefly now I need the gene name,
> production function or description, stable id and gene length data.
>
>
> 2014-02-10 17:10 GMT+08:00 mag <mr6 at ebi.ac.uk <mailto:mr6 at ebi.ac.uk>>:
>
>     Hi Pengfei,
>
>     I am not entirely sure which data you are looking at, but
>     depending on the databases, not all genes will have a description
>     or an external_name.
>
>     For a given gene, we assign a display xref if we find an external
>     reference from a trusted source matching the ensembl gene.
>     That xref (external reference) is then used to assign a display
>     name to the gene.
>     If there is no such external reference, the gene will have no
>     display name and we will use the ensembl stable id instead.
>
>     A similar rule applies to assigning descriptions.
>
>
>     Hope that helps,
>     Magali
>
>
>     On 10/02/2014 05:22, 刘鹏飞 wrote:
>>     Hi Magali and
>>     Hi all,
>>
>>     I use following code to fetch all information of genes for a
>>     bacteria, but get some errors (althouth I could get all data I
>>     wanted), but I could not figure out where goes wrong, thanks:
>>     errors:
>>     Use of uninitialized value in print at HZ254_genedata.pl line 20.
>>
>>     scripts:
>>     # methanocella_conradii_hz254
>>     #HZ254_genedata.pl
>>     #!/usr/bin/perl
>>     use strict;
>>     use warnings;
>>     use Bio::EnsEMBL::LookUp;
>>     # load the lookup from the main Ensembl Bacteria public server
>>     my $lookup = Bio::EnsEMBL::LookUp->new(
>>     -URL => "http://bacteria.ensembl.org/registry.json",
>>     -NO_CACHE => 1
>>     );
>>     # find the correct database adaptor using a unique name
>>     my ($dba) = @{$lookup->get_by_name_exact(
>>     'methanocella_conradii_hz254'
>>     )};
>>     my $genes = $dba->get_GeneAdaptor()->fetch_all();
>>     # get all gene infomation
>>     open (MYFILE, '>>HZ254gene_data.txt');
>>     foreach my $gene (@$genes){
>>     print $gene->stable_id,"\t",
>>     $gene->display_id,"\t",
>>     $gene->description,"\t",
>>     $gene->start, " - ",
>>     $gene->end, "\t",
>>     $gene->external_name, "\t",
>>     $gene->length,"\n";
>>     };
>>     close (MYFILE);
>>     ##API version 74
>>
>>
>>     -- 
>>     Pengfei Liu, PhD Candidate
>>
>>     Lab of Microbial Ecology
>>     College of Resources and Environmental Sciences
>>     China Agricultural University
>>     No.2 Yuanmingyuanxilu, Beijing, 100193
>>     P.R. China
>>
>>     Tel: +86-10-62731358
>>     Fax: +86-10-62731016
>>
>>     E-mail: liupfskygre at gmail.com <mailto:liupfskygre at gmail.com>
>>     If you are afraid of tomorrow, how can you enjoy today!
>>     Keep hungry, Keep foolish!
>>     Moving forward!
>
>
>
>
> -- 
> Pengfei Liu, PhD Candidate
>
> Lab of Microbial Ecology
> College of Resources and Environmental Sciences
> China Agricultural University
> No.2 Yuanmingyuanxilu, Beijing, 100193
> P.R. China
>
> Tel: +86-10-62731358
> Fax: +86-10-62731016
>
> E-mail: liupfskygre at gmail.com <mailto:liupfskygre at gmail.com>
> If you are afraid of tomorrow, how can you enjoy today!
> Keep hungry, Keep foolish!
> Moving forward!

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140211/d4bd4e1a/attachment.html>