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jaudoux
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Correct bug in GFF annotation loading due to UTR having unusual id<->parent IDs
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3 files changed

+57
-5
lines changed

3 files changed

+57
-5
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‎dist.ini‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@ license = MIT
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copyright_holder = Jérôme Audoux
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copyright_year = 2018
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7-
version = 0.004
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version = 0.005
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[@Basic]
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[PkgVersion]

‎lib/DEkupl/Annotations.pm‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -79,8 +79,7 @@ sub loadFromGFF {
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$parent = DEkupl::Utils::getAtomicGeneID($parent) if defined $parent;
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# Add the id to parent relationship
82-
if(defined $parent && defined $id) {
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# Todo we should only store that information fore transcript_id to gene_id
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if($annot->{feature} eq 'transcript' && defined $parent && defined $id) {
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$id_to_parents{$id} = $parent;
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}
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# next if !defined $id;

‎t/DEkupl-Analyzer-Annotations.t‎

Lines changed: 55 additions & 2 deletions
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@@ -1,12 +1,16 @@
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use strict;
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use warnings;
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4-
use Test::More tests => 12;
5-
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use Test::More tests => 15;
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use DEkupl::IntervalQuery;
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use DEkupl::GenomicInterval;
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use DEkupl::Annotations;
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use DEkupl::Annotations::Exon;
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use DEkupl::Annotations::Gene;
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use DEkupl::Analyzer::Annotations;
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use Inline::Files 0.68;
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use File::Temp;
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use Test::Exception;
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my $query = DEkupl::GenomicInterval->new(
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'chr' => '12',
@@ -104,3 +108,52 @@ my $geneC_exon1 = DEkupl::Annotations::Exon->new(
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is($candidate->{is_exonic}, 1);
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is($candidate->{is_intronic}, 0);
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}
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# Test on real GFF file
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{
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my ($fh, $gff_file) = File::Temp::tempfile( SUFFIX => '.gff', UNLINK => 0);
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while(<GFF>) {print $fh $_;}
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$fh->close;
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my $annotations = DEkupl::Annotations->new();
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$annotations->loadFromGFF($gff_file);
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my $interval_query = DEkupl::IntervalQuery->new();
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$interval_query->loadAnnotations($annotations);
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# chr11:5,225,504-5,225,560
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my $query = DEkupl::GenomicInterval->new(
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'chr' => 'chr11',
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'start' => 5225504,
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'end' => 5225560,
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'strand' => '-',
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);
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my $results = $interval_query->fetchByRegion($query);
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my $candidate = DEkupl::Analyzer::Annotations::_selectBestCandidate($results, $query);
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is($candidate->{gene}->id, 'ENSG00000244734');
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is($candidate->{is_exonic}, 1);
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is($candidate->{is_intronic}, 0);
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}
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__GFF__
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##gff-version 3
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#description: evidence-based annotation of the human genome (GRCh38), version 31 (Ensembl 97)
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#provider: GENCODE
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#contact: gencode-help@ebi.ac.uk
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#format: gff3
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#date: 2019-06-27
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##sequence-region chr1 1 248956422
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chr11 HAVANA gene 5225464 5229395 . - . ID=ENSG00000244734.4;gene_id=ENSG00000244734.4;gene_type=protein_coding;gene_name=HBB;level=2;hgnc_id=HGNC:4827;havana_gene=OTTHUMG00000066678.8
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chr11 HAVANA transcript 5225464 5227071 . - . ID=ENST00000335295.4;Parent=ENSG00000244734.4;gene_id=ENSG00000244734.4;transcript_id=ENST00000335295.4;gene_type=protein_coding;gene_name=HBB;transcript_type=protein_coding;transcript_name=HBB-201;level=2;protein_id=ENSP00000333994.3;transcript_support_level=1;hgnc_id=HGNC:4827;tag=CAGE_supported_TSS,basic,MANE_Select,appris_principal_1,CCDS;ccdsid=CCDS7753.1;havana_gene=OTTHUMG00000066678.8;havana_transcript=OTTHUMT00000495006.2
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chr11 HAVANA exon 5226930 5227071 . - . ID=exon:ENST00000335295.4:1;Parent=ENST00000335295.4;gene_id=ENSG00000244734.4;transcript_id=ENST00000335295.4;gene_type=protein_coding;gene_name=HBB;transcript_type=protein_coding;transcript_name=HBB-201;exon_number=1;exon_id=ENSE00001829867.2;level=2;protein_id=ENSP00000333994.3;transcript_support_level=1;hgnc_id=HGNC:4827;tag=CAGE_supported_TSS,basic,MANE_Select,appris_principal_1,CCDS;ccdsid=CCDS7753.1;havana_gene=OTTHUMG00000066678.8;havana_transcript=OTTHUMT00000495006.2
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chr11 HAVANA CDS 5226930 5227021 . - 0 ID=CDS:ENST00000335295.4;Parent=ENST00000335295.4;gene_id=ENSG00000244734.4;transcript_id=ENST00000335295.4;gene_type=protein_coding;gene_name=HBB;transcript_type=protein_coding;transcript_name=HBB-201;exon_number=1;exon_id=ENSE00001829867.2;level=2;protein_id=ENSP00000333994.3;transcript_support_level=1;hgnc_id=HGNC:4827;tag=CAGE_supported_TSS,basic,MANE_Select,appris_principal_1,CCDS;ccdsid=CCDS7753.1;havana_gene=OTTHUMG00000066678.8;havana_transcript=OTTHUMT00000495006.2
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chr11 HAVANA start_codon 5227019 5227021 . - 0 ID=start_codon:ENST00000335295.4;Parent=ENST00000335295.4;gene_id=ENSG00000244734.4;transcript_id=ENST00000335295.4;gene_type=protein_coding;gene_name=HBB;transcript_type=protein_coding;transcript_name=HBB-201;exon_number=1;exon_id=ENSE00001829867.2;level=2;protein_id=ENSP00000333994.3;transcript_support_level=1;hgnc_id=HGNC:4827;tag=CAGE_supported_TSS,basic,MANE_Select,appris_principal_1,CCDS;ccdsid=CCDS7753.1;havana_gene=OTTHUMG00000066678.8;havana_transcript=OTTHUMT00000495006.2
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chr11 HAVANA exon 5226577 5226799 . - . ID=exon:ENST00000335295.4:2;Parent=ENST00000335295.4;gene_id=ENSG00000244734.4;transcript_id=ENST00000335295.4;gene_type=protein_coding;gene_name=HBB;transcript_type=protein_coding;transcript_name=HBB-201;exon_number=2;exon_id=ENSE00001057381.1;level=2;protein_id=ENSP00000333994.3;transcript_support_level=1;hgnc_id=HGNC:4827;tag=CAGE_supported_TSS,basic,MANE_Select,appris_principal_1,CCDS;ccdsid=CCDS7753.1;havana_gene=OTTHUMG00000066678.8;havana_transcript=OTTHUMT00000495006.2
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chr11 HAVANA CDS 5226577 5226799 . - 1 ID=CDS:ENST00000335295.4;Parent=ENST00000335295.4;gene_id=ENSG00000244734.4;transcript_id=ENST00000335295.4;gene_type=protein_coding;gene_name=HBB;transcript_type=protein_coding;transcript_name=HBB-201;exon_number=2;exon_id=ENSE00001057381.1;level=2;protein_id=ENSP00000333994.3;transcript_support_level=1;hgnc_id=HGNC:4827;tag=CAGE_supported_TSS,basic,MANE_Select,appris_principal_1,CCDS;ccdsid=CCDS7753.1;havana_gene=OTTHUMG00000066678.8;havana_transcript=OTTHUMT00000495006.2
155+
chr11 HAVANA exon 5225464 5225726 . - . ID=exon:ENST00000335295.4:3;Parent=ENST00000335295.4;gene_id=ENSG00000244734.4;transcript_id=ENST00000335295.4;gene_type=protein_coding;gene_name=HBB;transcript_type=protein_coding;transcript_name=HBB-201;exon_number=3;exon_id=ENSE00001600613.2;level=2;protein_id=ENSP00000333994.3;transcript_support_level=1;hgnc_id=HGNC:4827;tag=CAGE_supported_TSS,basic,MANE_Select,appris_principal_1,CCDS;ccdsid=CCDS7753.1;havana_gene=OTTHUMG00000066678.8;havana_transcript=OTTHUMT00000495006.2
156+
chr11 HAVANA CDS 5225598 5225726 . - 0 ID=CDS:ENST00000335295.4;Parent=ENST00000335295.4;gene_id=ENSG00000244734.4;transcript_id=ENST00000335295.4;gene_type=protein_coding;gene_name=HBB;transcript_type=protein_coding;transcript_name=HBB-201;exon_number=3;exon_id=ENSE00001600613.2;level=2;protein_id=ENSP00000333994.3;transcript_support_level=1;hgnc_id=HGNC:4827;tag=CAGE_supported_TSS,basic,MANE_Select,appris_principal_1,CCDS;ccdsid=CCDS7753.1;havana_gene=OTTHUMG00000066678.8;havana_transcript=OTTHUMT00000495006.2
157+
chr11 HAVANA stop_codon 5225598 5225600 . - 0 ID=stop_codon:ENST00000335295.4;Parent=ENST00000335295.4;gene_id=ENSG00000244734.4;transcript_id=ENST00000335295.4;gene_type=protein_coding;gene_name=HBB;transcript_type=protein_coding;transcript_name=HBB-201;exon_number=3;exon_id=ENSE00001600613.2;level=2;protein_id=ENSP00000333994.3;transcript_support_level=1;hgnc_id=HGNC:4827;tag=CAGE_supported_TSS,basic,MANE_Select,appris_principal_1,CCDS;ccdsid=CCDS7753.1;havana_gene=OTTHUMG00000066678.8;havana_transcript=OTTHUMT00000495006.2
158+
chr11 HAVANA five_prime_UTR 5227022 5227071 . - . ID=UTR5:ENST00000335295.4;Parent=ENST00000335295.4;gene_id=ENSG00000244734.4;transcript_id=ENST00000335295.4;gene_type=protein_coding;gene_name=HBB;transcript_type=protein_coding;transcript_name=HBB-201;exon_number=1;exon_id=ENSE00001829867.2;level=2;protein_id=ENSP00000333994.3;transcript_support_level=1;hgnc_id=HGNC:4827;tag=CAGE_supported_TSS,basic,MANE_Select,appris_principal_1,CCDS;ccdsid=CCDS7753.1;havana_gene=OTTHUMG00000066678.8;havana_transcript=OTTHUMT00000495006.2
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chr11 HAVANA three_prime_UTR 5225464 5225597 . - . ID=UTR3:ENST00000335295.4;Parent=ENST00000335295.4;gene_id=ENSG00000244734.4;transcript_id=ENST00000335295.4;gene_type=protein_coding;gene_name=HBB;transcript_type=protein_coding;transcript_name=HBB-201;exon_number=3;exon_id=ENSE00001600613.2;level=2;protein_id=ENSP00000333994.3;transcript_support_level=1;hgnc_id=HGNC:4827;tag=CAGE_supported_TSS,basic,MANE_Select,appris_principal_1,CCDS;ccdsid=CCDS7753.1;havana_gene=OTTHUMG00000066678.8;havana_transcript=OTTHUMT00000495006.2

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