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Remove POSIX ceil dep from Downstream #371

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merged 6 commits into from
Sep 6, 2021
Merged

Remove POSIX ceil dep from Downstream #371

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319cc0b
Die unless a FASTA file is provide in offline mode
stekaz Jul 26, 2020
dfdac88
Wrap long lines
stekaz Jul 26, 2020
078896c
Reduce indentation
stekaz Jul 26, 2020
4c196f8
Remove superfluous whitespace and comments
stekaz Jul 26, 2020
6305a9d
Remove ceil dependency
stekaz Aug 6, 2020
657fed8
Bump plugin version to 2.4
stekaz Aug 6, 2020
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120 changes: 65 additions & 55 deletions Downstream.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -55,12 +55,23 @@ use strict;
use warnings;

use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
use POSIX qw(ceil);

use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);

sub new {
my $class = shift;

my $self = $class->SUPER::new(@_);

if($self->{config}{offline} && !$self->{config}{fasta}) {
die("ERROR: cannot function in offline mode without a FASTA file\n");
}

return $self;
}

sub version {
return '2.3';
return '2.4';
}

sub feature_types {
Expand All @@ -80,61 +91,60 @@ sub get_header_info {

sub run {
my ($self, $tva) = @_;

my @ocs = @{$tva->get_all_OverlapConsequences};

if(grep {$_->SO_term eq 'frameshift_variant'} @ocs) {

# can't do it for splice sites
return {} if grep {$_->SO_term =~ /splice/} @ocs;

my $tv = $tva->transcript_variation;
my $tr = $tv->transcript;
my $cds_seq = defined($tr->{_variation_effect_feature_cache}) ? $tr->{_variation_effect_feature_cache}->{translateable_seq} : $tr->translateable_seq;

# get the sequence to translate
my ($low_pos, $high_pos) = sort {$a <=> $b} ($tv->cds_start, $tv->cds_end);
my $is_insertion = $tv->cds_start > $tv->cds_end ? 1 : 0;
my $last_complete_codon = (ceil($low_pos / 3) - 1) * 3;
my $before_var_seq = substr $cds_seq, $last_complete_codon, $low_pos - $last_complete_codon - ($is_insertion ? 0 : 1);
my $after_var_seq = substr $cds_seq, $high_pos - ($is_insertion ? 1 : 0);
my $to_translate = $before_var_seq.$tva->feature_seq.$after_var_seq;
my $three_prime_utr_seq = $tr->three_prime_utr->seq() if ($tr->three_prime_utr);
$to_translate = $to_translate.$three_prime_utr_seq if ($three_prime_utr_seq);
$to_translate =~ s/\-//g;

# create a bioperl object
my $codon_seq = Bio::Seq->new(
-seq => $to_translate,
-moltype => 'dna',
-alphabet => 'dna'
);

# get codon table
my $codon_table;
if(defined($tr->{_variation_effect_feature_cache})) {
$codon_table = $tr->{_variation_effect_feature_cache}->{codon_table} || 1;
}
else {
my ($attrib) = @{$tr->slice->get_all_Attributes('codon_table')};
$codon_table = $attrib ? $attrib->value || 1 : 1;
}

# translate
my $new_pep = $codon_seq->translate(undef, undef, undef, $codon_table)->seq();
$new_pep =~ s/\*.*//;

# compare lengths
my $translation = defined($tr->{_variation_effect_feature_cache}) && defined($tr->{_variation_effect_feature_cache}->{peptide}) ? $tr->{_variation_effect_feature_cache}->{peptide} : $tr->translation->seq;
my $new_length = ($tv->translation_start < $tv->translation_end ? $tv->translation_start : $tv->translation_end) + length($new_pep);

return {
DownstreamProtein => $new_pep,
ProteinLengthChange => $new_length - length($translation),
};

my @SO_terms = map { $_->SO_term } @{$tva->get_all_OverlapConsequences};

return {} unless grep { $_ eq 'frameshift_variant' } @SO_terms;

return {} if grep { /splice/ } @SO_terms;

my $tv = $tva->transcript_variation;
my $tr = $tv->transcript;

my $cds_seq = defined($tr->{_variation_effect_feature_cache})
? $tr->{_variation_effect_feature_cache}->{translateable_seq}
: $tr->translateable_seq;

my ($start, $end) = ($tv->cds_start, $tv->cds_end);

substr($cds_seq, $start - 1, $end - $start + 1) = $tva->seq_length > 0 ? $tva->feature_seq : '';

my $low_pos = $start > $end ? $end : $start;
my $last_complete_codon = $low_pos - ( ( ( $low_pos - 1 ) % 3 ) + 1 );

my $downstream_seq = substr($cds_seq, $last_complete_codon > 0 ? $last_complete_codon : 0);
my $three_prime_utr = $tr->three_prime_utr ? $tr->three_prime_utr->seq() : '';

my $codon_seq = Bio::Seq->new(
-seq => $downstream_seq . $three_prime_utr,
-moltype => 'dna',
-alphabet => 'dna'
);

my $codon_table;
if(defined($tr->{_variation_effect_feature_cache})) {
$codon_table = $tr->{_variation_effect_feature_cache}->{codon_table} || 1;
}
else {
my ($attrib) = @{$tr->slice->get_all_Attributes('codon_table')};
$codon_table = $attrib ? $attrib->value || 1 : 1;
}

return {};
my $new_pep = $codon_seq->translate(undef, undef, undef, $codon_table)->seq();
$new_pep =~ s/\*.*//;

my $translation = defined($tr->{_variation_effect_feature_cache}->{peptide})
? $tr->{_variation_effect_feature_cache}->{peptide}
: $tr->translation->seq;

my ($pep_start, $pep_end) = ($tv->translation_start, $tv->translation_end);

my $new_length = ($pep_start < $pep_end ? $pep_start : $pep_end) + length($new_pep);

return {
DownstreamProtein => $new_pep,
ProteinLengthChange => $new_length - length($translation),
};
}

1;
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