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Commit 20d5e0fc authored by Marek Szuba's avatar Marek Szuba
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RFAMParser: relax selection criteria on analysis.logic_name

Due to changes in the structure of the production database, since
release 98 the value of analysis.logic_name corresponding to non-coding
RNA can be either 'ncrna' (which is what we used before) or
'ncrna_species_name'. Change the SQL query used to map RFAM IDs to
Ensembl stable IDs so that it can correctly handle species using the
latter syntax, i.e. human, mouse and zebrafish.

Issue: ENSINT-402
parent 3a6aa7cd
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2 merge requests!469Yearly copyright update [feature/xref_sprint],!466RFAMParser: relax selection criteria on analysis.logic_name
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in 17 minutes and 23 seconds
......@@ -105,7 +105,7 @@ sub run_script {
$dba = $registry->get_DBAdaptor($species_name, 'core');
}
my $rfam_sql = "select distinct t.stable_id, hit_name from analysis a join transcript t on (a.analysis_id = t.analysis_id and a.logic_name = 'ncRNA' and t.biotype != 'miRNA') join exon_transcript et on (t.transcript_id = et.transcript_id) join supporting_feature sf on (et.exon_id = sf.exon_id and sf.feature_type = 'dna_align_feature' ) join dna_align_feature df on (sf.feature_id = df.dna_align_feature_id) order by hit_name";
my $rfam_sql = "select distinct t.stable_id, hit_name from analysis a join transcript t on (a.analysis_id = t.analysis_id and a.logic_name like 'ncrna%' and t.biotype != 'miRNA') join exon_transcript et on (t.transcript_id = et.transcript_id) join supporting_feature sf on (et.exon_id = sf.exon_id and sf.feature_type = 'dna_align_feature' ) join dna_align_feature df on (sf.feature_id = df.dna_align_feature_id) order by hit_name";
my $sth = $dba->dbc->prepare($rfam_sql);
$sth->execute();
......
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