114 lines
3.1 KiB
Perl
Executable File
114 lines
3.1 KiB
Perl
Executable File
#!/usr/bin/perl
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use strict;
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use warnings;
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die "useage:perl $0 output_dir cancer_type project" unless @ARGV == 3;
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my ($output_dir, $cancer_type, $project) = @ARGV;
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my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase";
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print "Indication药物注释使用路径：$database_path\n";
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open OUT, ">$output_dir/mutation/indication.txt";
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print OUT "基因\t检测内容\t检测情况\t肿瘤类型\n";
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##本癌种FDA/NMPA/NCCN批准基因检测
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=pod
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##疾病翻译信息
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open DIS,"/dataseq/jmdna/codes/reportbase/cancer_type.txt";
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my (%dis,%dis2);
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<DIS>;
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while(<DIS>){
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chomp;
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my @line=split(/\t/);
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$dis{lc$line[0]}=$line[1];
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push @{$dis2{$line[3]}},$line[0];
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push @{$dis2{$line[4]}},$line[0];
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}
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=cut
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open DIS, "$database_path/oncotree.cancertype.20230801.txt";
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<DIS>;
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my (%dis, @id, %dis2);
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while (<DIS>) {
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chomp;
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my @line = split(/\t/);
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$dis{lc $line[2]} = $line[3];
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# $dis{lc $line[4]} = $line[5];
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push @{$dis2{$line[0]}}, lc $line[2];
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# push @{$dis2{$line[0]}}, lc $line[4];
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push @id, $line[0];
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}
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foreach my $ID ($cancer_type) {
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my @family;
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my @ids = split("", $ID);
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for (my $i = 1; $i < @ids; $i = $i + 2) {
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push @family, join("", @ids[0 .. $i]);
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}
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push @family, (grep {/^$ID/} @id);
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foreach my $t (@family) {
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push @{$dis2{$ID}}, @{$dis2{$t}};
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}
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}
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foreach my $key (keys(%dis2)) {
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my %uniq;
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@{$dis2{$key}} = grep {++$uniq{$_} < 2} @{$dis2{$key}};
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}
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##靶向用药信息
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open THERAPY, "$database_path/targetTherapy.txt";
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<THERAPY>;
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my %therapy;
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my %cancer;
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while (<THERAPY>) {
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chomp;
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my @line = split("\t");
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if ($line[9] eq 'V' and $line[14] eq 'A' and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) and $line[0] !~ /,/) {
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push @{$cancer{$line[0]}}, $dis{lc $line[2]} if !(grep {$_ eq $dis{lc $line[2]}} @{$cancer{$line[0]}});
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if ($line[1] =~ /fusion/i) {
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push @{$therapy{$line[0]}}, '融合' if !(grep {$_ eq '融合'} @{$therapy{$line[0]}});
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}
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elsif ($line[1] eq "Deletion" or $line[1] =~ /Amplification/) {
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push @{$therapy{$line[0]}}, '扩增' if !(grep {$_ eq '扩增'} @{$therapy{$line[0]}});
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}
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else {
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push @{$therapy{$line[0]}}, '突变' if !(grep {$_ eq '突变'} @{$therapy{$line[0]}});;
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}
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}
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}
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my $muts_ref = info();
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my @muts = @$muts_ref;
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for my $gene (sort keys %therapy) {
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# 是否检测
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if (grep {$_ eq $gene} @muts) {
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print OUT "$gene\t", join("/", @{$therapy{$gene}}), "\t未检出变异\t", join("/", @{$cancer{$gene}}), "\n";
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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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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{'mutation'} ne "NA") {
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@muts = split(/\//, $record{'mutation'});
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}
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}
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}
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return \@muts
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}
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