diff --git a/DESCRIPTION b/DESCRIPTION index 57f18c4..13a0902 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: ensembldb Type: Package Title: Utilities to create and use Ensembl-based annotation databases -Version: 2.21.2 +Version: 2.21.3 Authors@R: c(person(given = "Johannes", family = "Rainer", email = "johannes.rainer@eurac.edu", role = c("aut", "cre"), diff --git a/inst/NEWS b/inst/NEWS index fc567b3..d496c8f 100644 --- a/inst/NEWS +++ b/inst/NEWS @@ -1,3 +1,8 @@ +Changes in version 2.21.3 + +- Add minimal required Ensembl API version for certain data fields + (stable_id_version). Issue https://github.com/jorainer/ensembldb/issues/139 + Changes in version 2.21.1 - Since *is circular* flag for chromosomes extracted using the Ensembl Perl API diff --git a/inst/perl/get_gene_transcript_exon_tables.pl b/inst/perl/get_gene_transcript_exon_tables.pl index c19093c..ecc62d3 100644 --- a/inst/perl/get_gene_transcript_exon_tables.pl +++ b/inst/perl/get_gene_transcript_exon_tables.pl @@ -1,5 +1,6 @@ #!/usr/bin/perl ##################################### +## version 0.3.9: * Don't query stable_id_version for Ensembl release < 75. ## version 0.3.8: * Add column tx_is_canonical to transcript table. ## version 0.3.7: * Add column tx_external_name to transcript table. ## version 0.3.6: * Add column canonical_transcript to gene table. @@ -38,6 +39,7 @@ use List::MoreUtils qw/ uniq /; my $script_version = "0.3.7"; my $min_tsl_version = 87; ## The minimal required Ensembl version providing support for the tsl method. +my $min_stable_id_version_version = 87; # minimal Ensembl version for ->stable_id_version ## connecting to the ENSEMBL data base use Bio::EnsEMBL::Registry; @@ -227,7 +229,10 @@ if(!defined($gene_external_name)){ $gene_external_name=""; } - my $gene_id_version = $gene->stable_id_version; + my $gene_id_version = "NULL"; + if ($ensembl_version_num >= $min_stable_id_version_version) { + $gene_id_version = $gene->stable_id_version; + } my $gene_biotype = $gene->biotype; my $gene_seq_start = $gene->start; my $gene_seq_end = $gene->end; @@ -270,7 +275,10 @@ $tx_cds_end = "NULL"; } my $tx_id = $transcript->stable_id; - my $tx_id_version = $transcript->stable_id_version; + my $tx_id_version = "NULL"; + if ($ensembl_version_num >= $min_stable_id_version_version) { + $tx_id_version = $transcript->stable_id_version; + } my $tx_biotype = $transcript->biotype; my $tx_seq_start = $transcript->start; my $tx_seq_end = $transcript->end;