[ensembl-dev] $genomic_align->get_Slice returns UNDEF

[Benoit Ballester]

Hi, 

I am trying to get the EPO mammals coordinates of this regions in hg38  chr1:1287672-1287836


The API version used is 111
chr1	1287672	1287836	ENST00000325425.12_cds_7_0_chr1_1287673_f
	$VAR1 = undef;
Can't call method "seq_region_name" on an undefined value at wgaEnsemblEPO.pl line 103, <FH> line 1.



When using the Ensembl compara API, following the https://www.ensembl.org/info/docs/api/compara/compara_tutorial.html <https://www.ensembl.org/info/docs/api/compara/compara_tutorial.html> as example, I fetch the GAB from the human query slice, then restricting the $gab, then I get undef when trying to get the Slice from the genomic align.

The API doc for get_Slice says :
https://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1Locus.html#afbe22a62da57178280ca67b06eda9d5c <https://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1Locus.html#afbe22a62da57178280ca67b06eda9d5c> 
  Exceptions : return -undef- if slice cannot be created (this is likely to
               happen if the Registry <https://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Registry.html> is misconfigured)
Well, I am using the classic public registry in my script :
$registry->load_registry_from_db(
  -host => 'ensembldb.ensembl.org',
  -user => 'anonymous'
);


Is there something else I am missing somewhere ?
I am not sending the script here, as my email will get blocked like last time. 

Thanks for the feedback, 

Cheers, 

Ben


--
Benoît Ballester, PhD
Aix Marseille Univ, INSERM, TAGC, Marseille, France

+33 4 91 82 87 28
(1st)  benoit.ballester at inserm.fr
(2nd) benoit.ballester at univ-amu.fr 
ReMap2022: http://remap.univ-amu.fr/ <http://remap.univ-amu.fr/>


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