From f38ab4003882763b224faa17401b55c4829ce82e Mon Sep 17 00:00:00 2001
From: chaopower <chao.zhang@jmdna.com>
Date: Mon, 25 Dec 2023 14:43:56 +0800
Subject: [PATCH] longindel bug

---
 codes/target_therapy_longindel.pl | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/codes/target_therapy_longindel.pl b/codes/target_therapy_longindel.pl
index 13aae43..a467028 100755
--- a/codes/target_therapy_longindel.pl
+++ b/codes/target_therapy_longindel.pl
@@ -98,8 +98,7 @@ open POS, ">$output.pos.txt";
 my $h2 = <IN>;
 chomp $h2;
 
-my $h = $h2 . "\tHGVS\tAAChange.refGene\tFreq\t" . join("\t", (split("\t", $h1))[0 .. 9]) . "\tLabel\tDrugCn\tIndication";
-print POS "$h\n";
+print POS $h2 . "\tOncogenic\t" . join("\t", (split("\t", $h1))[0 .. 9, 14]) . "\tLabel\tDrugCn\tIndication\n";
 
 my @pos;
 while (<IN>) {
@@ -115,15 +114,15 @@ while (<IN>) {
             my @line = split("\t", $entry);
             if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
                 # push @pos, "$_\t.\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
-                push @pos, "$_\tc\.394+1479_394+4381del\tBCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del\t" . $freq . "\t" . join("\t", @line[0 .. 9]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
+                push @pos, "$_\t.\tc\.394+1479_394+4381del\tBCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del\t" . $freq . "\t" . join("\t", @line[0 .. 9]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
             }
             elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
                 # push @pos, "$_\t.\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
-                push @pos, "$_\tc\.394+1479_394+4381del\tBCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del\t" . $freq . "\t" . join("\t", @line[0 .. 9]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
+                push @pos, "$_\t.\tc\.394+1479_394+4381del\tBCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del\t" . $freq . "\t" . join("\t", @line[0 .. 9]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
             }
             elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
                 # push @pos, "$_\t.\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
-                push @pos, "$_\tc\.394+1479_394+4381del\tBCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del\t" . $freq . "\t" . join("\t", @line[0 .. 9]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
+                push @pos, "$_\t.\tc\.394+1479_394+4381del\tBCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del\t" . $freq . "\t" . join("\t", @line[0 .. 9]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
             }
 
             # my @line = split("\t", $entry);