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TranscriptAnnotator.pm
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TranscriptAnnotator.pm
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=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=head1 CONTACT
Ensembl <http://www.ensembl.org/info/about/contact/index.html>
=cut
=head1 NAME
TranscriptAnnotator
=head1 SYNOPSIS
mv TranscriptAnnotator.pm ~/.vep/Plugins
./vep -i variations.vcf --plugin TranscriptAnnotator,file=/path/to/file.txt.gz
=head1 DESCRIPTION
A VEP plugin that annotates variant-transcript pairs based on a given file:
--plugin TranscriptAnnotator,file=${HOME}/file.tsv.gz
Example of a valid tab-separated annotation file:
```
#Chrom Pos Ref Alt Transcript SIFT_score SIFT_pred Comment
11 436154 A G NM_001347882.2 0.03 Deleterious Bad
11 1887471 C T ENST00000421485 0.86 Tolerated Good
```
Please bgzip and tabix the file with commands such as:
bgzip file.txt
tabix -b2 -e2 file.txt.gz
Options are passed to the plugin as key=value pairs:
file : (mandatory) Tabix-indexed file to parse. Must contain variant
location (chromosome, position, reference allele, alternative allele)
and transcript ID as the first 5 columns. Accepted transcript IDs
include those from Ensembl and RefSeq.
cols : Colon-delimited list with names of the columns to append. Column
names are based on the last header line. By default, all columns
(except the first 5) are appended.
prefix : String to prefix the name of appended columns (default: basename of
the filename without extensions). Set to 0 to avoid any prefix.
trim : Trim whitespaces from both ends of each column (default: 1).
The tabix and bgzip utilities must be installed in your path to read the
tabix-indexed annotation file: check https://github.com/samtools/htslib.git for
installation instructions.
=cut
package TranscriptAnnotator;
use strict;
use warnings;
use File::Basename;
use Bio::EnsEMBL::Variation::Utils::Sequence qw(get_matched_variant_alleles);
use Bio::EnsEMBL::Variation::Utils::BaseVepTabixPlugin;
use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepTabixPlugin);
sub _basename_without_ext {
my $file = basename shift;
$file =~ s/\.[^.]*?(.gz)?$//g;
return $file;
}
sub _trim_whitespaces {
my $text = shift;
$text =~ s/^\s+|\s+$//g;
return $text;
};
sub _get_colnames {
my $self = shift;
# Open file header
open IN, "tabix -f -h " . $self->{_files}[0] . " 1:1-1 |"
or die "ERROR: cannot open tabix file for " . $self->{_files}[0];
# Get last line
my $last;
$last = $_ while <IN>;
$last =~ s/(^#|\n$)//g;
close IN;
# Parse column names from header
my @cols = split /\t/, $last;
@cols = map { _trim_whitespaces $_ } @cols if $self->{trim};
# Check column names for variant location and transcript ID
my @var_cols = ("chr", "pos", "ref", "alt", "tr");
for my $i (0 .. scalar $#var_cols) {
unless (grep { /^$var_cols[$i]/i } @cols) {
warn sprintf "WARNING: Name of column %s ('%s') should start with '%s'\n",
$i, $cols[$i], $var_cols[$i];
}
}
# Return other columns
@cols = splice @cols, 5;
return @cols;
}
sub _get_selected_cols {
my $self = shift;
my @colnames = @_;
my @cols;
my $param_hash = $self->params_to_hash();
if ( $param_hash->{cols} ) {
# Check if user-selected columns are valid
my @invalid_cols;
for my $col ( split /:/, $param_hash->{cols} ) {
if (grep /^$col$/, @colnames) {
push @cols, $col;
} else {
push @invalid_cols, $col;
}
}
# Warn about invalid user-selected columns
my $msg_valid_cols = "Valid column names: " . join(", ", @colnames) . "\n";
if (not @cols) {
die "ERROR: no valid columns selected. " . $msg_valid_cols;
} elsif (@invalid_cols) {
my $file = $self->{_files}[0];
warn "WARNING: columns " . join(", ", @invalid_cols) .
" not found in $file. " . $msg_valid_cols;
}
} else {
@cols = @colnames;
}
return @cols;
}
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
$self->get_user_params();
my $param_hash = $self->params_to_hash();
$self->{trim} = defined($param_hash->{trim}) ? $param_hash->{trim} : 1;
# Check file
my $file = $param_hash->{file};
die "\nERROR: No file specified\nTry using 'file=path/to/file.txt.gz'\n"
unless defined($file);
$self->add_file($file);
# Prepare column names
my @colnames = $self->_get_colnames();
my @cols = $self->_get_selected_cols(@colnames);
# Add prefix to column names
unless (defined $param_hash->{prefix} && $param_hash->{prefix} eq 0) {
$self->{prefix} = ($param_hash->{prefix} || _basename_without_ext($file)) . "_";
@colnames = map($self->{prefix} . $_, @colnames);
@cols = map($self->{prefix} . $_, @cols);
}
$self->{colnames} = \@colnames;
$self->{cols} = \@cols;
return $self;
}
sub feature_types {
return ['Transcript'];
}
sub get_header_info {
my $self = shift;
my %header;
my @keys = @{ $self->{colnames} };
my @vals = map { "column from " . $self->{_files}[0] } @keys;
@header{ @keys } = @vals;
# Filter by user-selected columns
%header = map { $_ => $header{$_} } @{ $self->{cols} };
return \%header;
}
sub run {
my ($self, $tva) = @_;
my $tr = $tva->transcript;
# Get transcript ID for Ensembl and RefSeq
my @refseq = split(/,/, $tr->{_refseq}) unless $tr->{_refseq} eq '-';
my @tr_id = ( $tr->{stable_id}, @refseq );
my $vf = $tva->variation_feature;
# Get allele
my $alt_alleles = $tva->base_variation_feature->alt_alleles;
my $ref_allele = $vf->ref_allele_string;
my @data = @{ $self->get_data($vf->{chr}, $vf->{start} - 2, $vf->{end}) };
return {} unless(@data);
foreach my $var (@data) {
my $is_same_transcript = grep { $var->{transcript_id} eq $_ } @tr_id;
my $matches = get_matched_variant_alleles(
{
ref => $ref_allele,
alts => $alt_alleles,
pos => $vf->{start},
strand => $vf->strand
},
{
ref => $var->{ref},
alts => [$var->{alt}],
pos => $var->{start},
}
);
return $var->{result} if $is_same_transcript && (@$matches);
}
return {};
}
sub parse_data {
my ($self, $line) = @_;
my @data = split /\t/, $line;
@data = map(_trim_whitespaces($_), @data) if $self->{trim};
my ($seqname, $pos, $ref, $alt, $transcript_id, @vals) = @data;
my %res;
@res{ @{ $self->{colnames} } } = @vals;
# Filter by user-selected columns
%res = map { $_ => $res{$_} } @{ $self->{cols} };
return {
seqname => $seqname,
start => $pos,
end => $pos,
ref => $ref,
alt => $alt,
transcript_id => $transcript_id,
result => \%res
};
}
sub get_start {
return $_[1]->{start};
}
sub get_end {
return $_[1]->{end};
}
1;