From 38984dd1fb3744caef5adf03adf1aac311abd350 Mon Sep 17 00:00:00 2001 From: Richard Demko Date: Mon, 10 Nov 2025 18:39:29 -0500 Subject: [PATCH 1/2] Resolving issue with incorrect profile string --- Load/plugin/perl/InsertPhylogeneticProfile.pm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/Load/plugin/perl/InsertPhylogeneticProfile.pm b/Load/plugin/perl/InsertPhylogeneticProfile.pm index 1bc98937d..b2ed3fe6a 100644 --- a/Load/plugin/perl/InsertPhylogeneticProfile.pm +++ b/Load/plugin/perl/InsertPhylogeneticProfile.pm @@ -90,6 +90,15 @@ sub run { $allTaxa{$orthomclAbbrev} = 1; } + my %proteinIdToOrthomclAbbrev; + + my $idSql = "select org.orthomcl_abbrev, aas.source_id from dots.aasequence aas, apidb.organism org where aas.taxon_id = org.taxon_id"; + my $idSth = $self->prepareAndExecute($idSql); + + while (my ($orthoAbbrev,$source_id) = $sth->fetchrow_array()) { + $proteinIdToOrthomclAbbrev{$source_id} = $orthoAbbrev; + } + my @allTaxaSorted = sort(keys(%allTaxa)); open(FILE, $self->getArg('groupsFile')) || die "Could Not open Ortholog File for reading: $!\n"; @@ -103,8 +112,7 @@ sub run { my %taxaInThisGroup; foreach my $member (@members) { - # pfal|PF11_0987 - my ($taxonCode, $sourceId) = split(/\|/, $member); + my $taxonCode = $proteinIdToOrthomclAbbrev{$member}; $taxaInThisGroup{$taxonCode} = 1; } From 44e2742ddbbc91ea92792232e7c82552c918430c Mon Sep 17 00:00:00 2001 From: Richard Demko Date: Mon, 10 Nov 2025 18:41:50 -0500 Subject: [PATCH 2/2] Minor syntax change --- Load/plugin/perl/InsertPhylogeneticProfile.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Load/plugin/perl/InsertPhylogeneticProfile.pm b/Load/plugin/perl/InsertPhylogeneticProfile.pm index b2ed3fe6a..b1c40fbfd 100644 --- a/Load/plugin/perl/InsertPhylogeneticProfile.pm +++ b/Load/plugin/perl/InsertPhylogeneticProfile.pm @@ -95,7 +95,7 @@ sub run { my $idSql = "select org.orthomcl_abbrev, aas.source_id from dots.aasequence aas, apidb.organism org where aas.taxon_id = org.taxon_id"; my $idSth = $self->prepareAndExecute($idSql); - while (my ($orthoAbbrev,$source_id) = $sth->fetchrow_array()) { + while (my ($orthoAbbrev,$source_id) = $idSth->fetchrow_array()) { $proteinIdToOrthomclAbbrev{$source_id} = $orthoAbbrev; }