chaopower
/
pipeline
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

hgvs 采用标准转录本

master
chaopower 2024-02-26 10:06:23 +08:00
parent 157fa94ef8
commit 778d55ed5b
1 changed files with 11 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
codes/filter_snpindel.pl
View File

@ -189,12 +189,12 @@ while (<IN>) {
push @reason, 'not_need_spl_inron'; push @reason, 'not_need_spl_inron';
} }
my @hgvs = split(/,/, $line[9]); my @hgvs = split(/,/, $line[9]);
my $hgvs = $hgvs[0]; # my $hgvs = $hgvs[0];
my $transcript_gene; my $transcript_gene;
$transcript_gene = $transcript{$gene} if (exists $transcript{$gene}); $transcript_gene = $transcript{$gene} if (exists $transcript{$gene});
my $hgvs;
if (grep {/$transcript_gene/} @hgvs) { if (grep {/$transcript_gene/} @hgvs) {
$hgvs = (grep {/$transcript_gene/} @hgvs)[0]; $hgvs = (grep {/$transcript_gene/} @hgvs)[0];
}
$line[9] = $hgvs; $line[9] = $hgvs;
$hgvs =~ /:(NM_\d+):exon\d+:(c\.\S+):p\.(\S+)$/; $hgvs =~ /:(NM_\d+):exon\d+:(c\.\S+):p\.(\S+)$/;
@ -202,6 +202,10 @@ while (<IN>) {
if ($protein =~ /\d+X$|\d+\*$/ or $line[8] eq 'stopgain' or $line[8] eq 'frameshift deletion' or $line[8] eq 'frameshift insertion') { if ($protein =~ /\d+X$|\d+\*$/ or $line[8] eq 'stopgain' or $line[8] eq 'frameshift deletion' or $line[8] eq 'frameshift insertion') {
$protein = 'Truncating Mutations'; $protein = 'Truncating Mutations';
} }
}
else {
push @reason, 'not_correct_hgvs';
}
} }