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Update ClinVar script to import somatic classifications + patch db schema 115 #1117

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@dglemos dglemos commented Aug 19, 2024

Ticket: https://www.ebi.ac.uk/panda/jira/browse/ENSVAR-5941

  • add db schema patches: patch_114_115_a.sql and patch_114_115_b.sql
  • add new clinvar attrib types to attrib_entries.sql (new attrib types were inserted in the production db on 2024-10-31)
  • update clinvar import
  • update clinvar post process
  • update API
  • add tests

This update should be merged before Ensembl/ensembl-vep#1794

@dglemos dglemos added the e115 label Aug 19, 2024
@dglemos dglemos changed the title Update ClinVar script to import somatic classifications Update ClinVar script to import somatic classifications + patch db schema Sep 3, 2024
@dglemos dglemos changed the title Update ClinVar script to import somatic classifications + patch db schema Update ClinVar script to import somatic classifications + patch db schema 115 Sep 3, 2024
@@ -727,7 +881,7 @@ sub get_submitters{
@{$mainXrefs->{'dbSNP'}} = keys {map { $_ => 1 } @{$mainXrefs->{'dbSNP'}} } if defined $mainXrefs->{'dbSNP'};
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Suggested change
@{$mainXrefs->{'dbSNP'}} = keys {map { $_ => 1 } @{$mainXrefs->{'dbSNP'}} } if defined $mainXrefs->{'dbSNP'};
@{$mainXrefs->{'dbSNP'}} = keys %{+{ map { $_ => 1 } @{$mainXrefs->{'dbSNP'}} }} if defined $mainXrefs->{'dbSNP'};

Need an anon hash constructor and then dereference the hash, otherwise with perl >5.14 getting the error -

Experimental keys on scalar is now forbidden at /hps/software/users/ensembl/variation/snhossain/ensembl-variation/scripts/import/import_clinvar_xml line 881.

Similar issue in Line 710 and 713.

modules/Bio/EnsEMBL/Variation/Utils/Config.pm Show resolved Hide resolved
@dglemos dglemos requested a review from nakib103 January 15, 2025 15:18
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2 participants