From 388296bffa1794ac9f6bf865263899e5ee6f493a Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Mon, 11 Dec 2023 13:49:59 +0800
Subject: [PATCH] =?UTF-8?q?splicing=20=E4=BD=8D=E7=82=B9=20exon=20?=
 =?UTF-8?q?=E5=B1=95=E7=A4=BA?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 script/filter_snpindel.pl | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/script/filter_snpindel.pl b/script/filter_snpindel.pl
index 57efe45..7fd3ef3 100755
--- a/script/filter_snpindel.pl
+++ b/script/filter_snpindel.pl
@@ -123,8 +123,16 @@ while (<IN>) {
             }
             $hgvs =~ /(\S+):exon(\d+):c\.(\S+)$/;
             my $spl = $3;
+            my $exon = $2;
             # splicing 位点 的前后 1-2bp 的 或者 MET的基因
-            if ($spl =~ /\d+[\+|\-][1|2]\D+/) {
+            if ($spl =~ /\d+\+[1|2]\D+/) {
+                my $intron = $exon;
+                $hgvs =~ s/exon(\d+)/exon$exon;intron$intron/;
+                $line[9] = join(":", ($gene, $hgvs));
+            }
+            elsif ($spl =~ /\d+\-[1|2]\D+/) {
+                my $intron = $exon-1;
+                $hgvs =~ s/exon(\d+)/intron$intron;exon$exon/;
                 $line[9] = join(":", ($gene, $hgvs));
             }
             elsif ($gene eq "MET") {