241 lines
7.9 KiB
Perl
Executable File
241 lines
7.9 KiB
Perl
Executable File
#!/usr/bin/env perl
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use strict;
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use warnings;
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die "useage:perl $0 input longvcf_input output longvcf_output project cancer_type" unless @ARGV == 6;
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my ($input, $longvcf_input, $output, $longvcf_output, $project, $cancer_type) = @ARGV;
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my $public_path = defined $ENV{'PUBLIC'} ? $ENV{'PUBLIC'} : "/dataseq/jmdna/codes/public/";
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open INFO, "$public_path/info.csv";
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<INFO>;
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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(/,/, $_);
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if ($line[0] eq $project) {
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if ($line[6] ne "NA") {
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@fusion = split(/\//, $line[6]);
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}
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if ($line[7] ne "NA") {
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@longindel = split(/\//, $line[7]);
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}
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}
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}
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open THERAPY, "/dataseq/jmdna/codes/reportbase/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{$line[0]}{$line[1]}}, $_ if ($line[1] =~ /fusion/i and $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, "/dataseq/jmdna/codes/reportbase/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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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, $new;
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}
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}
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return (join(",", @translation));
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}
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=pod
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##疾病翻译信息
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open DIS,"/dataseq/jmdna/codes/reportbase/cancer_type.txt";
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my (%dis,%dis2);
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<DIS>;
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while(<DIS>){
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chomp;
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my @line=split(/\t/);
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$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, "/dataseq/jmdna/codes/reportbase/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{$key}};
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}
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if (@fusion) {
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open MUT, "/dataseq/jmdna/codes/reportbase/fusion.csv";
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<MUT>;
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my %mut;
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while (<MUT>) {
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my @line = split(/,/);
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$mut{$line[1]}{$line[0]} = $line[2];
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}
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open IN, "$input";
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open POS, ">$output.fusion.pos.txt";
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open NEG, ">$output.fusion.neg.txt";
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open VUS, ">$output.fuison.vus.txt";
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my (@pos, @neg, @vus);
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my $h2;
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while (<IN>) {
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next if /^##/;
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if (/^#CHROM/) {
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$h2 = $_;
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chomp $h2;
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}
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chomp;
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my @line = split(/\t/);
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if (grep {$_ eq $line[13]} @fusion or grep {$_ eq $line[14]} @fusion) {
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my ($gene1, $gene2, $alt) = @line[13, 14, 15];
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if (not exists $mut{"$alt Fusion"}{$gene1} and not exists $mut{"$alt Fusion"}{$gene2}) {
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push @vus, "$_\t.";
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}
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else {
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my $gene = (keys %{$mut{"$alt Fusion"}})[0];
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my $sig = $mut{"$alt Fusion"}{$gene};
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if ($sig =~ /neutral/i) {
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push @neg, "$_\t$sig";
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}
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else {
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if (not exists $therapy{$gene}) {
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push @vus, "$_\t$sig";
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}
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else {
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my $bool = 0;
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##
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if (exists $therapy{$gene}{"$alt Fusion"}) {
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foreach my $entry (@{$therapy{$gene}{"$alt Fusion"}}) {
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my @line = split("\t", $entry);
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if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
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push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
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$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$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
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$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$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
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$bool = 1;
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}
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}
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}
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##
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if (exists $therapy{$gene}{"Fusion"}) {
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foreach my $entry (@{$therapy{$gene}{"Fusion"}}) {
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my @line = split("\t", $entry);
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if (($line[14] eq 'A') and (grep {lc $line[2] eq lc $_} @{$dis2{$cancer_type}})) {
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push @pos, "$_\t$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
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$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$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t非适应症" . "\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
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$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$sig\t" . join("\t", @line[0 .. 9, 14]) . "\t\.\t" . &drug($line[3]) . "\t" . $dis{lc $line[2]};
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$bool = 1;
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}
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}
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}
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push @vus, "$_\t$sig" if $bool == 0;
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}
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}
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}
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}
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}
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my $h = $h2 . "\tOncogenic\t" . join("\t", (split("\t", $h1))[0 .. 9, 14]) . "\tLabel\tDrugCn\tIndication";
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if (@pos) {
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print POS "$h\n";
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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 $h2 . "\tOncogenic\n";
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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 $h2 . "\tOncogenic\n";
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print VUS join("\n", @vus) . "\n";
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}
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}
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if (@longindel) {
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my @pos;
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open LONGINDEL, ">$longvcf_output";
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open IN2, "$longvcf_input";
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my $h2;
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while (<IN2>) {
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chomp;
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next if /^##/;
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if (/^#CHROM/) {
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$h2 = $_;
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next;
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}
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my @line = split(/\t/);
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$line[7] =~ /Gene.refGene=(.*?);/;
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if (grep {$1 =~ /$_/} @longindel) {
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if ($1 eq "BCL2L11") {
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push @pos, $_ if $line[1] == '111883194';
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}
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else {
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push @pos, $_;
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}
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}
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}
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if (@pos) {
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print LONGINDEL "$h2\n";
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print LONGINDEL join("\n", @pos) . "\n";
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}
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}
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