<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hello Sabine,<div class=""><br class=""></div><div class="">This should be fixed now. </div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Ameya<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 26 May 2020, at 19:59, Ameya Chaubal <<a href="mailto:ameya@ebi.ac.uk" class="">ameya@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class=""><div dir="auto" class="">Hello Sabine,</div><div dir="auto" class=""><br class=""></div><div dir="auto" class="">Thanks for bringing this up. We will look into it. </div><div dir="auto" class=""><br class=""></div><div dir="auto" class="">Best,</div><div dir="auto" class="">Ameya</div></div><div class=""><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 25 May 2020 at 15:12, Sabine Rei?er <<a href="mailto:sabine.reisser@mdc-berlin.de" class="">sabine.reisser@mdc-berlin.de</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; padding-left: 1ex; border-left-color: rgb(204, 204, 204);"><div class=""><p class="">Hi everyone,</p><p class="">I'm trying to access E. coli genes via the API. <br class="">
</p><p class="">The output I get is</p><p class="">The API version used is 100<br class="">
chromosome:ASM584v2:Chromosome:1:<wbr class="">4641652:1<br class="">
Slice: chromosome Chromosome 1-4641652 (1)<br class="">
DBD::mysql::st execute failed: Table
'bacteria_0_collection_core_47_100_<wbr class="">1.analysis' doesn't exist at
/home/sabine/bin/ensembl_api/src/<wbr class="">ensembl/modules/Bio/EnsEMBL/DBSQL/<wbr class="">AnalysisAdaptor.pm
line 128.<br class="">
DBD::mysql::st execute failed: Table
'bacteria_0_collection_core_47_100_<wbr class="">1.analysis' doesn't exist at
/home/sabine/bin/ensembl_api/src/<wbr class="">ensembl/modules/Bio/EnsEMBL/DBSQL/<wbr class="">AnalysisAdaptor.pm
line 128.</p><p class="">If I run in verbose mode I get</p><p class="">Species 'escherichia_coli_str_k_12_substr_<wbr class="">mg1655' (id:99) loaded
from database 'bacteria_0_collection_core_47_100_1'.</p><p class="">Maybe I'm missing something in the installation?</p><p class="">It would be great if someone could give me a hint.</p><p class="">Please find my code below. <br class="">
</p><p class="">Cheers</p><p class="">Sabine<br class="">
</p><p class=""><font face="Courier New, Courier, monospace" style="font-family: "Courier New", Courier, monospace;" class=""><br class="">
</font></p><p class=""><font size="-1" face="Courier New, Courier, monospace" style="font-family: "Courier New", Courier, monospace;" class="">use
Bio::EnsEMBL::ApiVersion;</font></p>
<font size="-1" face="Courier New, Courier, monospace" style="font-family: "Courier New", Courier, monospace;" class="">printf( "The
API version used is %s", software_version() ); <br class="">
use Bio::EnsEMBL::Registry;<br class="">
<br class="">
my $registry = 'Bio::EnsEMBL::Registry';<br class="">
$registry->load_registry_from_db(<br class="">
-host => '<a href="http://mysql-eg-publicsql.ebi.ac.uk" class="">mysql-eg-publicsql.ebi.ac.uk</a>',<br class="">
-port => 4157,<br class="">
);<br class="">
<br class="">
my $sp_EC = 'escherichia_coli_str_k_12_substr_<wbr style="font-family: "Courier New", Courier, monospace;" class="">mg1655';<br class="">
my $group = 'Core';<br class="">
<br class="">
my $slice_adaptor = $registry->get_adaptor($sp_EC, $group,
"slice");<br class="">
$slices = $slice_adaptor->fetch_all('toplevel');<br class="">
foreach my $slice (@$slices) {<!-- --><br class="">
print $slice->name(), "\n";<br class="">
my $coord_sys = $slice->coord_system()->name();<br class="">
my $seq_region = $slice->seq_region_name();<br class="">
my $start = $slice->start();<br class="">
my $end = $slice->end();<br class="">
my $strand = $slice->strand();<br class="">
<br class="">
print "Slice: $coord_sys $seq_region $start-$end
($strand)\n"; <br class="">
foreach my $gene ( @{ $slice->get_all_Genes() } ) {<!-- --><br class="">
print $gene->stable_id(), "\n";<br class="">
}<br class="">
}</font><br class="">
<br class=""><p class=""><br class="">
</p><p class=""><br class="">
</p>
<pre style="font-family: monospace;" class="">--
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
<a href="mailto:sabine.reisser@mdc-berlin.de" style="font-family: monospace;" class="">sabine.reisser@mdc-berlin.de</a>
<a href="http://www.mdc-berlin.de/" style="font-family: monospace;" class="">www.mdc-berlin.de</a></pre>
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