adapted phylogenomics code to changes in Compara TSV files

phylogenomics/PlantCompUtils.pm

@@ -1,7 +1,7 @@
 package PlantCompUtils;
 require Exporter;
 
-# Copyright [2019-2023] EMBL-European Bioinformatics Institute
+# Copyright [2019-2025] EMBL-European Bioinformatics Institute
 
 @ISA       = qw(Exporter);
 @EXPORT_OK = qw(
@@ -23,8 +23,7 @@ use Time::HiRes;
 use HTTP::Tiny;
 use DBI;
 
-# Fungi Protists Metazoa have collections and one all-vs-all TSV file
-# This code won't work there
+# Only tested in Plants; Fungi Protists Metazoa have collections, code will need tweaking
 our @DIVISIONS  = qw( Plants );
 our $FTPURL     = 'ftp.ensemblgenomes.org';
 our $COMPARADIR = '/pub/xxx/current/tsv/ensembl-compara/homologies';
@@ -180,11 +179,11 @@ sub get_gene_coords_GTF_file {
       || die "# ERROR(get_gene_coords_GTF_file): cannot open $GTF_filename\n";
     while ( my $line = <GTF> ) {
 
-        #1 araport11 gene 3631 5899 . + . gene_id "AT1G01010";...
+        #1  araport11 gene 3631 5899 . + . gene_id "AT1G01010";...
+        #C3 brad      gene 4809 5027 . - . gene_id "Bo3g025160";...
         if ( $line =~
-               m/^([^#])\t[^\t]+\tgene\t(\d+)\t(\d+)\t[^\t]\t(\S+)\t[^\t]\tgene_id "([^";]+)/
-          )
-        {
+               m/^([^#]+)\t[^\t]+\tgene\t(\d+)\t(\d+)\t[^\t]\t(\S+)\t[^\t]\tgene_id "([^";]+)/) {
+
             ( $chr, $start, $end, $strand, $geneid ) = ( $1, $2, $3, $4, $5 );
             push( @chr_sorted_gene_ids,
                 [ $geneid, $chr, $start, $end, $strand ] );
@@ -258,7 +257,7 @@ sub download_GTF_file {
 
 # download compressed TSV file from FTP site, renames it
 # and saves it in $targetdir; uses FTP globals defined above
-# NOTE: if species file is not found it tries the bulky all-vs-all file
+# NOTE: tries only the bulky all-vs-all file (GBs)
 sub download_compara_TSV_file {
 
     my ( $dir, $ref_genome, $targetdir ) = @_;
@@ -274,32 +273,18 @@ sub download_compara_TSV_file {
           || die "# ERROR(download_compara_TSV_file): cannot change working directory to $dir "
           . $ftp->message();
 
-        # find out which file is to be downloaded
-        if ( $ftp->cwd($ref_genome) ) {
-            foreach my $file ( $ftp->ls() ) {
-                if ( $file =~ m/protein_default.homologies.tsv.gz/ ) {
-                    $compara_file        = $file;
-                    $stored_compara_file = "$targetdir/$compara_file";
-                    $stored_compara_file =~ s/tsv.gz/$ref_genome.tsv.gz/;
-                    last;
-                }
-            }
-        }
-        else {    # try all-vs-all file instead (Fungi, Protists, Metazoa)
-
-            print "# WARNING(download_compara_TSV_file): cannot find ".
-			    "$ref_genome in $dir, try all-vs-all\n";
-
-            foreach my $file ( $ftp->ls() ) {
-                if ( $file =~ m/protein_default.homologies.tsv.gz/ ) {
-                    $compara_file        = $file;
-                    $stored_compara_file = "$targetdir/$compara_file";
-                    foreach my $div (@DIVISIONS) {
-                        if ( $dir =~ m/($div)/i ) {
-                            $div = $1;
-                            $stored_compara_file =~ s/tsv.gz/$div.tsv.gz/;
-                            last;
-                        }
+        # find file to be downloaded
+        print "# WARNING(download_compara_TSV_file): try all-vs-all\n";
+
+        foreach my $file ( $ftp->ls() ) {
+            if ( $file =~ m/protein_default.homologies.tsv.gz/ ) {
+                $compara_file        = $file;
+                $stored_compara_file = "$targetdir/$compara_file";
+                foreach my $div (@DIVISIONS) {
+                    if ( $dir =~ m/($div)/i ) {
+                        $div = $1;
+                        $stored_compara_file =~ s/tsv.gz/$div.tsv.gz/;
+                        last;
                     }
                 }
             }

phylogenomics/ens_sequences.pl

@@ -18,7 +18,7 @@
 # Uses canonical transcripts, used in the gene tree analysis,
 # which usually are the longest translation with no stop codons
 #
-# Copyright [2019-2021] EMBL-European Bioinformatics Institute
+# Copyright [2019-2025] EMBL-European Bioinformatics Institute
 
 # Ensembl Genomes
 my $RESTURL   = 'http://rest.ensembl.org';

phylogenomics/ens_single-copy_core_genes.pl

@@ -15,10 +15,10 @@
 );
 
 # Retrieves single-copy orthologous genes/proteins shared by (plant) species in clade
-# by querying pre-computed Compara data from Ensembl Genomes with a reference genome.
+# by querying pre-computed Compara data from Ensembl with a reference genome.
 # Multiple copies are optionally allowed for selected or all species.
 #
-# Copyright [2019-2023] EMBL-European Bioinformatics Institute
+# Copyright [2019-2025] EMBL-European Bioinformatics Institute
 
 # Ensembl Genomes
 my $RESTURL   = 'http://rest.ensembl.org';
@@ -273,15 +273,23 @@ sub help_message {
         $wga_coverage,       $high_confidence
     ) = split(/\t/);
 
-    if ( $species ne $ref_genome ) {
+    next if( !$supported{$species} || !$supported{$hom_species} );
+
+    # ref genome forced to be species as opposed to hom_species
+    if( $hom_species eq $ref_genome ) {
+        ($gene_stable_id, $hom_gene_stable_id) = ($hom_gene_stable_id, $gene_stable_id);
+        ($prot_stable_id, $hom_prot_stable_id) = ($hom_prot_stable_id, $prot_stable_id);
+        ($species, $hom_species) = ($hom_species, $species);
+        ($identity, $hom_identity) = ($hom_identity, $identity);
+    }
+
+    if ( $species ne $ref_genome ) { 
         if ( keys(%present) == $n_of_species ) {
             last;
         }    # in case all-vs-all file is used
         else { next }
     }
 
-    next if ( !$supported{$hom_species} || $hom_species eq $ref_genome );
-
     if ( defined($high_confidence) ) {
         next
           if ( $LOWCONF == 0
@@ -298,7 +306,6 @@ sub help_message {
             && $homology_type eq 'ortholog_one2many' )
       )
     {
-
         # add $ref_genome protein
         if ( !$core{$gene_stable_id} ) {
 

phylogenomics/ens_syntelogs.pl

@@ -16,9 +16,9 @@
 );
 
 # Retrieves orthologous, syntenic genes (syntelogs) shared by (plant) species in clade
-# by querying pre-computed Compara data from Ensembl Genomes with a reference genome.
+# by querying pre-computed Compara data from Ensembl with a reference genome.
 #
-# Copyright [2019-2023] EMBL-European Bioinformatics Institute
+# Copyright [2019-2025] EMBL-European Bioinformatics Institute
 
 # Ensembl Genomes
 my $RESTURL   = 'http://rest.ensembl.org';
@@ -255,15 +255,23 @@ sub help_message {
         $wga_coverage,       $high_confidence
     ) = split(/\t/);
 
+    next if( !$supported{$species} || !$supported{$hom_species} );
+
+    # ref genome forced to be species as opposed to hom_species
+    if( $hom_species eq $ref_genome ) {
+        ($gene_stable_id, $hom_gene_stable_id) = ($hom_gene_stable_id, $gene_stable_id);
+        ($prot_stable_id, $hom_prot_stable_id) = ($hom_prot_stable_id, $prot_stable_id);
+        ($species, $hom_species) = ($hom_species, $species);
+        ($identity, $hom_identity) = ($hom_identity, $identity);
+    }
+
     if ( $species ne $ref_genome ) {
         if ( keys(%present) == $n_of_species ) {
             last;
         }    # in case all-vs-all file is used
         else { next }
     }
 
-    next if ( !$supported{$hom_species} || $hom_species eq $ref_genome );
-
     if ( defined($high_confidence) ) {
         next
           if ( $LOWCONF == 0
@@ -273,8 +281,7 @@ sub help_message {
     next if ( $goc_ssynt eq 'NULL' || $goc_ssynt < $GOC );
 
     if (   $homology_type eq 'ortholog_one2one'
-        || $homology_type eq 'ortholog_one2many' )
-    {
+        || $homology_type eq 'ortholog_one2many' ) {
 
         # add $ref_genome protein
         if ( !$synt{$gene_stable_id} ) {