[ensembl-dev] [ext] Re: accessing E. coli genes via API

[Sabine Reißer]

Yes! Thanks a lot.

Cheers

Sabine


On 27.05.20 10:59, Ameya Chaubal wrote:
> Hello Sabine,
>
> This should be fixed now.
>
> Thanks,
> Ameya
>
>> On 26 May 2020, at 19:59, Ameya Chaubal <ameya at ebi.ac.uk 
>> <mailto:ameya at ebi.ac.uk>> wrote:
>>
>> Hello Sabine,
>>
>> Thanks for bringing this up. We will look into it.
>>
>> Best,
>> Ameya
>>
>> On Mon, 25 May 2020 at 15:12, Sabine Rei?er 
>> <sabine.reisser at mdc-berlin.de <mailto:sabine.reisser at mdc-berlin.de>> 
>> wrote:
>>
>>     Hi everyone,
>>
>>     I'm trying to access E. coli genes via the API.
>>
>>     The output I get is
>>
>>     The API version used is 100
>>     chromosome:ASM584v2:Chromosome:1:4641652:1
>>     Slice: chromosome Chromosome 1-4641652 (1)
>>     DBD::mysql::st execute failed: Table
>>     'bacteria_0_collection_core_47_100_1.analysis' doesn't exist at
>>     /home/sabine/bin/ensembl_api/src/ensembl/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
>>     line 128.
>>     DBD::mysql::st execute failed: Table
>>     'bacteria_0_collection_core_47_100_1.analysis' doesn't exist at
>>     /home/sabine/bin/ensembl_api/src/ensembl/modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
>>     line 128.
>>
>>     If I run in verbose mode I get
>>
>>     Species 'escherichia_coli_str_k_12_substr_mg1655' (id:99) loaded
>>     from database 'bacteria_0_collection_core_47_100_1'.
>>
>>     Maybe I'm missing something in the installation?
>>
>>     It would be great if someone could give me a hint.
>>
>>     Please find my code below.
>>
>>     Cheers
>>
>>     Sabine
>>
>>
>>     use Bio::EnsEMBL::ApiVersion;
>>
>>     printf( "The API version used is %s", software_version() );
>>     use Bio::EnsEMBL::Registry;
>>
>>     my $registry = 'Bio::EnsEMBL::Registry';
>>     $registry->load_registry_from_db(
>>         -host => 'mysql-eg-publicsql.ebi.ac.uk
>>     <http://mysql-eg-publicsql.ebi.ac.uk>',
>>         -port => 4157,
>>     );
>>
>>     my $sp_EC = 'escherichia_coli_str_k_12_substr_mg1655';
>>     my $group = 'Core';
>>
>>     my $slice_adaptor = $registry->get_adaptor($sp_EC, $group, "slice");
>>     $slices = $slice_adaptor->fetch_all('toplevel');
>>     foreach my $slice (@$slices) {
>>         print $slice->name(), "\n";
>>             my $coord_sys  = $slice->coord_system()->name();
>>             my $seq_region = $slice->seq_region_name();
>>             my $start      = $slice->start();
>>             my $end        = $slice->end();
>>             my $strand     = $slice->strand();
>>
>>             print "Slice: $coord_sys $seq_region $start-$end
>>     ($strand)\n";
>>             foreach my $gene ( @{ $slice->get_all_Genes() } ) {
>>                     print $gene->stable_id(), "\n";
>>             }
>>      }
>>
>>
>>
>>     -- 
>>     Dr. Sabine Rei?er
>>     Postdoctoral researcher
>>
>>     Bioinformatics of RNA Structure and Transcriptome Regulation
>>     Berlin Institute for Medical Systems Biology
>>     Max Delbr?ck Center for Molecular Medicine in the Helmholtz Association
>>     Hannoversche Str. 28, 10115 Berlin, Germany
>>
>>     Tel.: +49 30 9406-3294
>>
>>     sabine.reisser at mdc-berlin.de  <mailto:sabine.reisser at mdc-berlin.de>
>>     www.mdc-berlin.de  <http://www.mdc-berlin.de/>
>>
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>
>
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-- 
Dr. Sabine Reißer
Postdoctoral researcher

Bioinformatics of RNA Structure and Transcriptome Regulation
Berlin Institute for Medical Systems Biology
Max Delbrück Center for Molecular Medicine in the Helmholtz Association
Hannoversche Str. 28, 10115 Berlin, Germany

Tel.: +49 30 9406-3294

sabine.reisser at mdc-berlin.de
www.mdc-berlin.de

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