FlankingSequence

FlankingSequence.pm

@@ -0,0 +1,123 @@
+=head1 NAME
+
+FlankingSequence - a plugin for VEP that annotates the surrounding sequence of a variant with [ref/alt] notation.
+
+=head1 SYNOPSIS
+
+  vep -i input.vcf -o output.txt --fasta hg38.fa --plugin FlankingSequence,10
+
+=head1 DESCRIPTION
+
+This plugin retrieves the sequence surrounding a variant, based on a specified number of flanking bases on either side. It inserts the variant in the format [ref/alt] in the middle of the sequence. The flanking length can be specified as a parameter.
+
+=head1 PARAMETERS
+
+This plugin takes one parameter, which specifies the number of bases to retrieve upstream and downstream of the variant. The default is 10 bases.
+
+=head1 LICENSE
+
+MIT License
+
+Copyright (c) 2024 pzweuj
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+=head1 AUTHOR
+
+pzweuj, pzweuj@live.com
+
+=cut
+
+# FlankingSequence.pm
+package FlankingSequence;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
+
+# 继承BaseVepPlugin
+use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
+
+sub new {
+    my $class = shift;
+    my $self = $class->SUPER::new(@_);
+
+    # 读取参数
+    my $params = $self->params;
+    $self->{flank_length} = $params->[0] || 10;  # 默认提取10个碱基作为上下游序列
+
+    return $self;
+}
+
+sub feature_types {
+    return ['Transcript'];
+}
+
+sub get_header_info {
+    return {
+        'FlankingSequence' => "Sequence surrounding the variant with [ref/alt] notation",
+    };
+}
+
+sub run {
+    my ($self, $tva) = @_;
+
+    # 提取位置信息和变异信息
+    my $vf = $tva->variation_feature;
+    my $chrom = $vf->seq_region_name;
+    my $pos = $vf->seq_region_start;
+    my $ref = $vf->ref_allele_string;
+
+    # 获取 alt 等位基因，确保只取第一个变异碱基
+    my $alt = $vf->alt_alleles ? join(',', @{$vf->alt_alleles}) : '';
+    if (!$alt) {
+        warn "No alternative allele found for variant at $chrom:$pos\n";
+        return {};
+    }
+
+    # 获取参考序列的长度
+    my $ref_length = length($ref);
+
+    # 获取上下游序列的长度
+    my $flank_length = $self->{flank_length};
+
+    # 计算左侧序列的起始位置，确保从ref的前一位开始
+    my $left_start_pos = $pos - $flank_length;
+    $left_start_pos = 1 if $left_start_pos < 1;  # 防止左侧起始位置小于1
+
+    # 计算右侧序列的结束位置，确保从ref的最后一位之后的下一位开始
+    my $right_end_pos = $pos + $ref_length + $flank_length - 1;
+
+    # 获取左侧和右侧序列
+    my $slice_left = $vf->slice->sub_Slice($left_start_pos, $pos - 1); # 上游为pos-1
+    my $slice_right = $vf->slice->sub_Slice($pos + $ref_length, $right_end_pos); # 下游为pos+ref_length
+
+    my $flanking_seq_left = $slice_left ? $slice_left->seq : '';
+    my $flanking_seq_right = $slice_right ? $slice_right->seq : '';
+
+    # 拼接左侧、变异部分和右侧序列
+    my $mutated_seq = $flanking_seq_left . "[$ref/$alt]" . $flanking_seq_right;
+
+    return {
+        FlankingSequence => $mutated_seq,
+    };
+}
+
+1;