From 778d55ed5b3fd9c023252be71f6a13855e118e17 Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Mon, 26 Feb 2024 10:06:23 +0800
Subject: [PATCH] =?UTF-8?q?hgvs=20=E9=87=87=E7=94=A8=E6=A0=87=E5=87=86?=
 =?UTF-8?q?=E8=BD=AC=E5=BD=95=E6=9C=AC?=
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---
 codes/filter_snpindel.pl | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/codes/filter_snpindel.pl b/codes/filter_snpindel.pl
index 5a7b453..c95b8a4 100755
--- a/codes/filter_snpindel.pl
+++ b/codes/filter_snpindel.pl
@@ -189,18 +189,22 @@ while (<IN>) {
             push @reason, 'not_need_spl_inron';
         }
         my @hgvs = split(/,/, $line[9]);
-        my $hgvs = $hgvs[0];
+        # my $hgvs = $hgvs[0];
         my $transcript_gene;
         $transcript_gene = $transcript{$gene} if (exists $transcript{$gene});
+        my $hgvs;
         if (grep {/$transcript_gene/} @hgvs) {
             $hgvs = (grep {/$transcript_gene/} @hgvs)[0];
-        }
-        $line[9] = $hgvs;
+            $line[9] = $hgvs;
 
-        $hgvs =~ /:(NM_\d+):exon\d+:(c\.\S+):p\.(\S+)$/;
-        $protein = $3;
-        if ($protein =~ /\d+X$|\d+\*$/ or $line[8] eq 'stopgain' or $line[8] eq 'frameshift deletion' or $line[8] eq 'frameshift insertion') {
-            $protein = 'Truncating Mutations';
+            $hgvs =~ /:(NM_\d+):exon\d+:(c\.\S+):p\.(\S+)$/;
+            $protein = $3;
+            if ($protein =~ /\d+X$|\d+\*$/ or $line[8] eq 'stopgain' or $line[8] eq 'frameshift deletion' or $line[8] eq 'frameshift insertion') {
+                $protein = 'Truncating Mutations';
+            }
+        }
+        else {
+            push @reason, 'not_correct_hgvs';
         }
 
     }