Skip to content

Phylogenetic Profile fix #97

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
rdemko2332 wants to merge 2 commits into from
+10 −2
Closed

Phylogenetic Profile fix #97

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
38984dd
Resolving issue with incorrect profile string
rdemko2332 Nov 10, 2025
44e2742
Minor syntax change
rdemko2332 Nov 10, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 10 additions & 2 deletions Load/plugin/perl/InsertPhylogeneticProfile.pm
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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) = $idSth->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";
Expand All @@ -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;
}

Expand Down