83 lines
2.3 KiB
Perl
83 lines
2.3 KiB
Perl
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#!/usr/bin/perl
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use strict;
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use warnings;
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my ($output_dir,$cancer_type)=@ARGV;
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die "useage:perl $0 output_dir cancer_type" unless @ARGV==2;
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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,"/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{$key}};
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}
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##靶向用药信息
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open THERAPY,"$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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}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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}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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for my $gene(sort keys %therapy){
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print OUT "$gene\t",join("/",@{$therapy{$gene}}),"\t未检出变异\t",join("/",@{$cancer{$gene}}),"\n";
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}
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