214 lines
8.6 KiB
Perl
Executable File
214 lines
8.6 KiB
Perl
Executable File
#!/usr/bin/perl
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use strict;
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use warnings;
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die "useage:perl $0 name output_dir project cancer_type" unless @ARGV==4;
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my ($name,$output_dir,$project,$cancer_type)=@ARGV;
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##将点突变信息记录到%mut
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open MUT, "/dataseq/jmdna/codes/reportbase/snv_indel_mutation.csv";
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<MUT>;
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my %mut;
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while (<MUT>){
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my @line=split(/,/);
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$mut{$line[0]}{$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,"/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[9] ne 'D' and $line[5] ne 'CSCO' 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}=$line[1];
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}
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}
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##疾病翻译信息
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open DIS,"/dataseq/jmdna/codes/reportbase/cancer_type.txt";
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my (%dis,%dis2);
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<DIS>;
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while(<DIS>){
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chomp;
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my @line=split(/\t/);
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$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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open IN,"$output_dir/mutation/${name}.target.mutation.txt";
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open POS,">$output_dir/mutation/${name}.snvindel.pos.txt";
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open NEG,">$output_dir/mutation/${name}.snvindel.neg.txt";
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open VUS,">$output_dir/mutation/${name}.snvindel.vus.txt";
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my $h2=<IN>;
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chomp $h2;
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my (@pos,@neg,@vus);
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while(<IN>){
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chomp;
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my @line=split("\t");
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$line[9]=~/:exon(\d+):c\.(\S+):p\.(\S+)$/;
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my $gene=$line[6];
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my $exon=$1;
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my $codon=$2;
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my $protein;
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if($3=~/\d+X$|\d+\*$/ or $line[8] eq 'stopgain' or $line[8] eq 'frameshift deletion' or $line[8] eq 'frameshift insertion'){
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$protein='Truncating Mutations';
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}else{
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$protein=$3;
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}
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my $mut_type=($codon=~/del/)?("Exon $exon deletion"):($codon=~/ins/)?("Exon $exon insertion"):("Exon $exon mutation");
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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 $mut{$gene}{$protein}){
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if ($line[15]=~/benign/i and $line[15]!~/sensitivity|pathogenic|uncertain|\./i and $line[14] ne '.'){
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push @neg,"$_\t.";
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}else{
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push @vus,"$_\t.";
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}
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}else{
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if ($mut{$gene}{$protein}=~/neutral/i){
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push @neg,"$_\t$mut{$gene}{$protein}";
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}elsif ($mut{$gene}{$protein}=~/Inconclusive/i){
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push @vus,"$_\t$mut{$gene}{$protein}";
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}else{
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if (not exists $therapy{$gene}){
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if ($line[15]=~/benign/i and $line[15]!~/sensitivity|pathogenic|uncertain|\./i and $line[14] ne '.'){
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push @neg,"$_\t$mut{$gene}{$protein}";
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}else{
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push @vus,"$_\t$mut{$gene}{$protein}";
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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}{$protein}){
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foreach my $entry(@{$therapy{$gene}{$protein}}){
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my @line=split("\t",$entry);
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if (($line[5] eq "FDA" or $line[5] eq "NCCN" or $line[5] eq "NMPA") and (lc$line[2] eq "solid tumor" or grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}})){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t适应症"."\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}elsif(($line[5] eq "FDA" or $line[5] eq "NCCN" or $line[5] eq "NMPA") and (lc$line[2] ne "solid tumor" and grep{lc$line[2] ne lc$_}@{$dis2{$cancer_type}})){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t非适应症"."\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}elsif(lc$line[2] eq "solid tumor" or grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}}){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t\.\t".&drug($line[3])."\t".$dis{lc$line[2]};$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}{'Mutation'}){
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foreach my $entry(@{$therapy{$gene}{'Mutation'}}){
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my @line=split("\t",$entry);
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if (($line[5] eq "FDA" or $line[5] eq "NCCN" or $line[5] eq "NMPA") and (lc$line[2] eq "solid tumor" or grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}})){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t适应症"."\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}elsif(($line[5] eq "FDA" or $line[5] eq "NCCN" or $line[5] eq "NMPA") and (lc$line[2] ne "solid tumor" and grep{lc$line[2] ne lc$_}@{$dis2{$cancer_type}})){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t非适应症"."\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}elsif(lc$line[2] eq "solid tumor" or grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}}){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t\.\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}
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}
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}
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##
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if($protein=~/^(\w\d+)\w$/ and exists $therapy{$gene}{$1}){
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foreach my $entry(@{$therapy{$gene}{$1}}){
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my @line=split("\t",$entry);
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if (($line[5] eq "FDA" or $line[5] eq "NCCN" or $line[5] eq "NMPA") and (lc$line[2] eq "solid tumor" or grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}})){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t适应症"."\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}elsif(($line[5] eq "FDA" or $line[5] eq "NCCN" or $line[5] eq "NMPA") and (lc$line[2] ne "solid tumor" and grep{lc$line[2] ne lc$_}@{$dis2{$cancer_type}})){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t非适应症"."\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}elsif(lc$line[2] eq "solid tumor" or grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}}){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t\.\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}
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}
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}
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#
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if($protein=~/^(\w\d+)\w$/ and exists $therapy{$gene}{$1."X"}){
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foreach my $entry(@{$therapy{$gene}{$1."X"}}){
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my @line=split("\t",$entry);
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if (($line[5] eq "FDA" or $line[5] eq "NCCN" or $line[5] eq "NMPA") and (lc$line[2] eq "solid tumor" or grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}})){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t适应症"."\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}elsif(($line[5] eq "FDA" or $line[5] eq "NCCN" or $line[5] eq "NMPA") and (lc$line[2] ne "solid tumor" and grep{lc$line[2] ne lc$_}@{$dis2{$cancer_type}})){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t非适应症"."\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}elsif(lc$line[2] eq "solid tumor" or grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}}){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t\.\t".&drug($line[3])."\t".$dis{lc$line[2]};$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}{$mut_type}){
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foreach my $entry(@{$therapy{$gene}{$mut_type}}){
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my @line=split("\t",$entry);
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if (($line[5] eq "FDA" or $line[5] eq "NCCN" or $line[5] eq "NMPA") and (lc$line[2] eq "solid tumor" or grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}})){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t适应症"."\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}elsif(($line[5] eq "FDA" or $line[5] eq "NCCN" or $line[5] eq "NMPA") and (lc$line[2] ne "solid tumor" and grep{lc$line[2] ne lc$_}@{$dis2{$cancer_type}})){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t非适应症"."\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}elsif(lc$line[2] eq "solid tumor" or grep{lc$line[2] eq lc$_}@{$dis2{$cancer_type}}){
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push @pos,"$_\t$mut{$gene}{$protein}\t".join("\t",@line[0..9,14])."\t\.\t".&drug($line[3])."\t".$dis{lc$line[2]};$bool=1;
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}
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}
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}
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if ($bool==0){
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if ($line[15]=~/benign/i and $line[15]!~/sensitivity|pathogenic|uncertain|\./i and $line[14] ne '.'){
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push @neg,"$_\t$mut{$gene}{$protein}";
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}else{
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push @vus,"$_\t$mut{$gene}{$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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}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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my $h=$h2."\tfun_change\t".join("\t",(split("\t",$h1))[0..9,14])."\t标签\t药物中文名\t疾病中文名";
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if(@pos){
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print POS "$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."\tfun_change\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."\tfun_change\n";
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print VUS join("\n",@vus)."\n";
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}
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