72 lines
1.9 KiB
Perl
Executable File
72 lines
1.9 KiB
Perl
Executable File
#!/usr/bin/perl
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use strict;
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use warnings;
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die "usage:perl $0 input out project" unless @ARGV == 3;
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my ($input, $out, $project) = @ARGV;
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# my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/";
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#
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# print "LongIndel过滤使用public路径：$public_path\n";
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my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase";
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print "longindel过滤使用database路径：$database_path\n";
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open IN, "$input";
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open LONGINDEL, "> $out";
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my ($longindel) = info();
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my @longindels = @$longindel;
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my $h2;
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while (<IN>) {
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chomp;
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next if /^##/;
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if (/^#CHROM/) {
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$h2 = $_;
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print LONGINDEL "$h2\tHGVS\tfreq\n";
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next;
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}
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my @line = split(/\t/);
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$line[7] =~ /Gene.refGene=(.*?);/;
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my $gene = $1;
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if ((grep {$gene =~ /$_/} @longindels) && ($_ =~ /SVTYPE=DEL/ || $_ =~ /SVTYPE=DUP/ || $_ =~ /SVTYPE=INS/)) {
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my $freq = (split(/:/, $line[9]))[9] / (split(/:/, $line[9]))[7];
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my $hgvs = '.';
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if ($gene eq "BCL2L11") {
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if ($line[1] == '111883194') {
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$hgvs = "BCL2L11:NM_001204106:intron2:c\.394+1479_394+4381del";
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print LONGINDEL $_ . "\t$hgvs\t$freq\n";
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}
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}
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else {
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print LONGINDEL $_ . "\t$hgvs\t$freq\n";
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}
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}
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}
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sub info {
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open INFO, "$database_path/info.csv";
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# 读取并解析表头
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my $header = <INFO>;
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chomp($header);
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my @column_names = split(',', $header);
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my (@fusion, @longindel);
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while (<INFO>) {
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chomp;
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my @line = split(/,/, $_);
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# 将数据与表头对应
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my %record;
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@record{@column_names} = @line;
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if ($record{'project'} eq $project) {
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if ($record{'long_indel'} ne "NA") {
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@longindel = split(/\//, $line[12]);
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}
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}
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}
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return \@longindel
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}
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