=head1 LICENSE Copyright (c) 1999-2013 The European Bioinformatics Institute and Genome Research Limited. All rights reserved. This software is distributed under a modified Apache license. For license details, please see http://www.ensembl.org/info/about/code_licence.html =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =cut =head1 NAME =head1 SYNOPSIS =head1 DESCRIPTION =head1 METHODS =cut package Bio::EnsEMBL::Utils::VegaCuration::Transcript; use strict; use warnings; no warnings 'uninitialized'; use vars qw(@ISA); use Bio::EnsEMBL::Utils::VegaCuration::Gene; use Data::Dumper; @ISA = qw(Bio::EnsEMBL::Utils::VegaCuration::Gene); =head2 find_non_overlaps Args : arrayref of B::E::Transcripts Example : find_non_overlaps($all_transcripts) Description: identifies any non-overlapping transcripts Returntype : array refs of stable IDs Exceptions : none =cut sub find_non_overlaps { my $self = shift; my ($all_transcripts) = @_; my $non_overlaps = []; foreach my $transcript1 (@{$all_transcripts}) { foreach my $transcript2 (@{$all_transcripts}) { if ($transcript1->end < $transcript2->start) { push @{$non_overlaps}, $transcript1->stable_id; push @{$non_overlaps}, $transcript2->stable_id; } } } return $non_overlaps; } =head2 check_remarks_and_update_names Arg[1] : B::E::Gene (with potentially duplicated transcript names) Arg[2] : counter 1 (no. of patched genes) Arg[3] : counter 2 (no. of patched transcripts) Example : $support->update_names($gene,\$c1,\$c2) Description: - checks remarks and patches transcripts with identical names according to CDS and length Returntype : true | false (depending on whether patched or not), counter1, counter2 =cut sub check_remarks_and_update_names { my $self = shift; my ($gene,$gene_c,$trans_c) = @_; my $action = ($self->param('dry_run')) ? 'Would add' : 'Added'; my $aa = $gene->adaptor->db->get_AttributeAdaptor; my $dbh = $gene->adaptor->db->dbc->db_handle; #get list of IDs that have previously been sent to annotators my $seen_genes = $self->get_havana_fragmented_loci_comments; my $gsi = $gene->stable_id; my $gid = $gene->dbID; my $g_name; my $study_more = 1; eval { $g_name = $gene->display_xref->display_id; }; if ($@) { $g_name = $gene->get_all_Attributes('name')->[0]->value; } #get existing gene remarks my $remarks = [ map {$_->value} @{$gene->get_all_Attributes('remark')} ]; #shout if there is no remark to identify this as being fragmented if ( grep {$_ eq 'fragmented locus' } @$remarks) { $study_more = 0; } else { $self->log_warning("Gene $gsi should have a fragmented locus remark\n"); } ##patch transcript names according to length and CDS $gene_c++; #separate coding and non_coding transcripts my $coding_trans = []; my $noncoding_trans = []; foreach my $trans ( @{$gene->get_all_Transcripts()} ) { if ($trans->translate) { push @$coding_trans, $trans; } else { push @$noncoding_trans, $trans; } } #sort transcripts coding > non-coding, then on length my $c = 0; $self->log("\nPatching names according to CDS and length:\n",1); foreach my $array_ref ($coding_trans,$noncoding_trans) { foreach my $trans ( sort { $b->length <=> $a->length } @$array_ref ) { $trans_c++; my $tsi = $trans->stable_id; my $t_name; eval { $t_name = $trans->display_xref->display_id; }; if ($@) { $t_name = $trans->get_all_Attributes('name')->[0]->value; } $c++; my $ext = sprintf("%03d", $c); my $new_name = $g_name.'-'.$ext; $self->log(sprintf("%-20s%-3s%-20s", "$t_name ", "-->", "$new_name")."\n",1); if (! $self->param('dry_run')) { # update transcript display xref $dbh->do(qq(UPDATE xref x, external_db edb SET x.display_label = "$new_name" WHERE x.external_db_id = edb.external_db_id AND x.dbprimary_acc = "$tsi" AND edb.db_name = "Vega_transcript")); } } } return ($study_more,$gene_c,$trans_c); } =head2 check_names_and_overlap Arg[1] : arayref of arrayrefs of duplicated names Arg[2] : B::E::Gene (with potentially duplicated transcript names) Arg[3] : FH (to log new duplicates) Example : $support->check_names_and_overlap($transcripts,$gene,$fh) Description: checks pairs of transcripts identified as having duplicate Vega names: - to see if they have identical names in loutre (shouldn't have) - distinguish between overlapping and non overlapping transcripts Returntype : none =cut sub check_names_and_overlap { my $self = shift; my ($transcript_info,$gene,$n_flist_fh) = @_; my $ta = $gene->adaptor->db->get_TranscriptAdaptor; my $gsi = $gene->stable_id; my $g_name = $gene->get_all_Attributes('name')->[0]->value; foreach my $set (values %{$transcript_info} ) { next if (scalar @{$set} == 1); my $transcripts = []; my $all_t_names; my %ids_to_names; foreach my $id1 (@{$set}) { my ($name1,$tsi1) = split /\|/, $id1; $ids_to_names{$tsi1} = $name1; $all_t_names .= "$tsi1 [$name1] "; my $t = $ta->fetch_by_stable_id($tsi1); push @{$transcripts}, $t; } my $non_overlaps; eval { $non_overlaps = $self->find_non_overlaps($transcripts); }; if ($@) { $self->log_warning("Problem looking for overlapping transcripts for gene $gsi (is_current = 0 ?). Skipping this bit\n"); } #if the transcripts don't overlap elsif (@{$non_overlaps}) { my $tsi_string; foreach my $id (@{$non_overlaps}) { my $string = " $id [ $ids_to_names{$id} ] "; $tsi_string .= $string; } $self->log_warning("NEW: Non-overlapping: $gsi ($g_name) has non-overlapping transcripts ($tsi_string) with duplicated Vega names, and it has no \'fragmented locus\' gene remark. Neither has it been OKeyed by Havana before. Transcript names are being patched but this needs checking by Havana.\n"); #log gsi (to be sent to Havana) print $n_flist_fh "$gsi\n"; } #...otherwise if the transcripts do overlap else { $self->log_warning("NEW: Overlapping: $gsi ($g_name) has overlapping transcripts ($all_t_names) with duplicated Vega names and it has no \'fragmented locus\' gene_remark. Neither has it been OKeyed by Havana before. Transcript names are being patched but this could be checked by Havana if they were feeling keen.\n"); print $n_flist_fh "$gsi\n"; } } } =head2 get_havana_fragmented_loci_comments Args : none Example : my $results = $support->get_havana_fragmented_loci_comments Description: parses the HEREDOC containing Havana comments in this module Returntype : hashref =cut sub get_havana_fragmented_loci_comments { my $seen_genes; while () { next if /^\s+$/ or /#+/; my ($obj,$comment) = split /=/; $obj =~ s/^\s+|\s+$//g; $comment =~ s/^\s+|\s+$//g; $seen_genes->{$obj} = $comment; } return $seen_genes; } #details of genes with duplicated transcript names that have already been reported to Havana #identified as either fragmented or as being OK to patch __DATA__ OTTMUSG00000005478 = fragmented OTTMUSG00000001936 = fragmented OTTMUSG00000017081 = fragmented OTTMUSG00000011441 = fragmented OTTMUSG00000013335 = fragmented OTTMUSG00000011654 = fragmented OTTMUSG00000001835 = fragmented OTTHUMG00000035221 = fragmented OTTHUMG00000037378 = fragmented OTTHUMG00000060732 = fragmented OTTHUMG00000132441 = fragmented OTTHUMG00000031383 = fragmented OTTHUMG00000012716 = fragmented OTTHUMG00000031102 = fragmented OTTHUMG00000148816 = fragmented OTTHUMG00000149059 = fragmented OTTHUMG00000149221 = fragmented OTTHUMG00000149326 = fragmented OTTHUMG00000149644 = fragmented OTTHUMG00000149574 = fragmented OTTHUMG00000058101 = fragmented OTTHUMG00000150119 = OK OTTHUMG00000149850 = OK OTTHUMG00000058101 = OK OTTHUMG00000058907 = OK OTTMUSG00000011654 = fragmented OTTMUSG00000019369 = fragmented OTTMUSG00000017081 = fragmented OTTMUSG00000001835 = fragmented OTTMUSG00000011499 = fragmented OTTMUSG00000013335 = fragmented OTTMUSG00000008023 = fragmented OTTMUSG00000019369 = fragmented OTTMUSG00000022266 OTTMUSG00000006697 OTTMUSG00000012302 = OTTMUSG00000013368 = OTTMUSG00000015766 = OTTMUSG00000016025 = OTTMUSG00000001066 = OTTMUSG00000016331 = OTTMUSG00000006935 = OTTMUSG00000007263 = OTTMUSG00000000304 = OTTMUSG00000009150 = OTTMUSG00000008023 = OTTMUSG00000017077 = OTTMUSG00000003440 = OTTMUSG00000016310 = OTTMUSG00000026199 = OTTMUSG00000028423 = OTTMUSG00000007427 =