311 lines
13 KiB
Perl
Executable File
311 lines
13 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 $0 input output cancer_type" unless @ARGV == 3;
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my ($input, $output, $cancer_type) = @ARGV;
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my $database_path = defined $ENV{'DATABASE'} ? $ENV{'DATABASE'} : "/dataseq/jmdna/codes/reportbase";
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print "SnpIndel药物注释使用路径：$database_path\n";
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##将点突变信息记录到%mut
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open MUT, "$database_path/snv_indel_mutation.csv";
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<MUT>;
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my %mut;
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while (<MUT>) {
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my @line = split(/,/);
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$mut{lc $line[0]}{lc $line[1]} = $line[2];
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}
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##将用药信息记录到%therapy
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open THERAPY, "$database_path/targetTherapy.txt";
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my $h1 = <THERAPY>;
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chomp $h1;
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my %therapy;
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while (<THERAPY>) {
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chomp;
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my @line = split("\t");
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push @{$therapy{lc $line[0]}{lc $line[1]}}, $_ if ($line[9] ne 'D' and $line[2] !~ /Leukemia|Lymphoma|Myeloid/i);
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}
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##药物翻译信息
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open DRUG, "$database_path/target_drug.txt";
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my %drug;
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<DRUG>;
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while (<DRUG>) {
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chomp;
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my @line = split(/\t/);
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next unless $line[1];
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foreach my $drug (split(/\|/, $line[0])) {
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$drug{lc $drug} = $line[1];
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}
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}
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##疾病翻译信息
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# 分两部分，向上匹配，和向下匹配
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open DIS, "$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{$key}};
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}
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open IN, "$input";
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open POS, ">$output.pos.txt";
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open NEG, ">$output.neg.txt";
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open VUS, ">$output.vus.txt";
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my $h2 = <IN>;
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chomp $h2;
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my $h = $h2 . "\tfun_change\t" . join("\t", (split("\t", $h1))[0 .. 9, 14]) . "\tLabel\tDrugCn\tIndication\treport_need_note";
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print POS "$h\n";
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print NEG $h2 . "\tfun_change\n";
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print VUS $h2 . "\tfun_change\n";
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my @column_names = split('\t', $h2);
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my (@pos, @neg, @vus);
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while (<IN>) {
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chomp;
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my @splitline = split("\t");
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# 将数据与表头对应
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my %record;
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@record{@column_names} = @splitline;
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my ($protein, $mut_type);
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my $gene = $record{'Gene_refGene'};
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if ($record{'AAChange_refGene'} =~ /(\w+):(\w+):exon(\d+):c\.(\S+):p\.(\S+)$/) {
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my $exon = $3;
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my $codon = $4;
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if ($5 =~ /\d+X$|\d+\*$/
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or $record{'ExonicFunc_refGene'} eq 'stopgain'
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or $record{'ExonicFunc_refGene'} eq 'frameshift deletion'
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or $record{'ExonicFunc_refGene'} eq 'frameshift insertion') {
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$protein = 'Truncating Mutations';
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}
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else {
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$protein = $5;
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}
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# $mut_type = ($codon =~ /del/) ? ("Exon $exon deletion") : ($codon =~ /ins/) ? ("Exon $exon insertion") : ("Exon $exon mutation");
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$mut_type = ($codon =~ /del/) ? ("Exon $exon deletion") :
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($codon =~ /ins/) ? ("Exon $exon insertion") :
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($codon =~ /dup/) ? ("Exon $exon insertion") :
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("Exon $exon mutation");
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}
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elsif ($record{'ExonicFunc_refGene'} =~ /skipping/) {
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$protein = 'Exon 14 Skipping Mutation';
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$mut_type = '';
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}
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elsif ($record{'Func_refGene'} =~ /splicing/) {
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$protein = 'Truncating Mutations';
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$mut_type = '';
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}
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else {
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print "药物注释未匹配到正确的protein或者mut_type";
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}
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##若突变不存在于%mut,写入@vus,若突变存在于%mut且neutral，写入@neg;若基因不存在于%therapy，写入@vus;
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if (not exists $mut{lc $gene}{lc $protein}) {
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if ($record{'CLNSIG'} =~ /benign/i and $record{'CLNSIG'} !~ /sensitivity|pathogenic|uncertain|\./i and $record{'cosmic91'} ne '.') {
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push @neg, "$_\t.";
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}
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else {
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push @vus, "$_\t.";
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}
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}
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else {
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if ($mut{lc $gene}{lc $protein} =~ /neutral/i) {
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push @neg, "$_\t$mut{lc $gene}{lc $protein}";
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}
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elsif ($mut{lc $gene}{lc $protein} =~ /Inconclusive/i) {
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push @vus, "$_\t$mut{lc $gene}{lc $protein}";
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}
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else {
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if (not exists $therapy{lc $gene}) {
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if ($record{'CLNSIG'} =~ /benign/i and $record{'CLNSIG'} !~ /sensitivity|pathogenic|uncertain|\./i and $record{'cosmic91'} ne '.') {
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push @neg, "$_\t$mut{lc $gene}{lc $protein}";
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}
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else {
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push @vus, "$_\t$mut{lc $gene}{lc $protein}";
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}
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}
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else {
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my $bool = 0;
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# 匹配 p.
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if (exists $therapy{lc $gene}{lc $protein}) {
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foreach my $entry (@{$therapy{lc $gene}{lc $protein}}) {
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my @line = split("\t", $entry);
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if (!defined($line[16])) {
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$line[16] = '';
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}
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if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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}
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}
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# 匹配 Mutation
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if (exists $therapy{lc $gene}{'mutation'}) {
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foreach my $entry (@{$therapy{lc $gene}{'mutation'}}) {
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my @line = split("\t", $entry);
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if (!defined($line[16])) {
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$line[16] = '';
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}
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if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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}
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}
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# 去掉最后一个字符 例如V600E 去掉之后 V600再去匹配
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if ($protein =~ /^(\w\d+)\w$/ and exists $therapy{lc $gene}{lc $1}) {
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foreach my $entry (@{$therapy{lc $gene}{lc $1}}) {
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my @line = split("\t", $entry);
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if (!defined($line[16])) {
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$line[16] = '';
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}
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if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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}
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}
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# 去掉最后一个字符 加上“.X”去匹配
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if ($protein =~ /^(\w\d+)\w$/ and exists $therapy{lc $gene}{lc $1 . "X"}) {
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foreach my $entry (@{$therapy{lc $gene}{lc $1 . "X"}}) {
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my @line = split("\t", $entry);
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if (!defined($line[16])) {
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$line[16] = '';
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}
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if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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}
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}
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# 外显子 模式去匹配
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if (exists $therapy{lc $gene}{lc $mut_type}) {
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foreach my $entry (@{$therapy{lc $gene}{lc $mut_type}}) {
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my @line = split("\t", $entry);
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if (!defined($line[16])) {
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$line[16] = '';
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}
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if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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elsif (($line[14] eq 'A') and (grep {lc $line[2] ne lc $_} @{$dis2{$cancer_type}})) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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elsif (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}}) {
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push @pos, "$_\t$mut{lc $gene}{lc $protein}\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]} . "\t" . $line[16];
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$bool = 1;
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}
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}
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}
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# 没有匹配上
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if ($bool == 0) {
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if ($record{'CLNSIG'} =~ /benign/i and $record{'CLNSIG'} !~ /sensitivity|pathogenic|uncertain|\./i and $record{'cosmic91'} ne '.') {
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push @neg, "$_\t$mut{lc $gene}{lc $protein}";
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}
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else {
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push @vus, "$_\t$mut{lc $gene}{lc $protein}";
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}
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}
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}
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}
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}
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}
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sub drug {
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my $drugs = shift @_;
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my @translation;
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foreach my $drug (split(/,/, $drugs)) {
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if ($drug =~ /\+/) {
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my $plus;
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foreach my $drug_c (split(/\s+\+\s+/, $drug)) {
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my $new = (exists $drug{lc $drug_c}) ? $drug{lc $drug_c} : ($drug_c);
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$plus .= " + $new";
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}
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$plus =~ s/^ \+ //;
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push @translation, $plus;
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}
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else {
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my $new = (exists $drug{lc $drug}) ? $drug{lc $drug} : ($drug);
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push @translation, $new;
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}
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}
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return (join(",", @translation));
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}
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if (@pos) {
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print POS join("\n", @pos) . "\n";
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}
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if (@neg) {
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print NEG join("\n", @neg) . "\n";
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}
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if (@vus) {
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print VUS join("\n", @vus) . "\n";
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}
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