62 lines
1.6 KiB
Perl
Executable File
62 lines
1.6 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 $0 input output project\n" unless @ARGV == 3;
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open IN, "$ARGV[0]";
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open OUT, ">$ARGV[1]";
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my $project = $ARGV[2];
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# my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/";
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my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase";
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print "Cnv过滤使用database路径：$database_path\n";
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my $cnv = info();
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my @cnv_list = @$cnv;
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my $head = <IN>;
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chomp $head;
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my @head = split("\t", $head);
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print OUT join("\t", (@head[0 .. 4], "ref_gene", "copy", @head[5 .. 9])), "\n";
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while (<IN>) {
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chomp;
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my @line = split(/\t/, $_);
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my $cn = sprintf("%.1f", 2 ** (1 + $line[4]));
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my @gene_list = split(/,/, $line[3]);
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my %uniq;
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foreach my $element (@gene_list) {
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if (grep {$_ eq $element} @cnv_list) {
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$uniq{$element}++;
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next if $uniq{$element} > 1;
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if (($cn <= 1 or $cn >= 3.5)) {
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print OUT join("\t", (@line[0 .. 4], $element, $cn, @line[5 .. 9])), "\n";
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}
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}
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}
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}
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sub info {
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open INFO, "$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 (@cnvs);
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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{'cnv'} ne "NA") {
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@cnvs = split(/\//, $record{'cnv'});
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}
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}
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}
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return \@cnvs
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}
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