[ensembl-dev] accessing E. coli genes via API
Sabine Reißer
sabine.reisser at mdc-berlin.de
Mon May 25 15:12:09 BST 2020
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',
-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 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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