47 lines
1.5 KiB
Perl
47 lines
1.5 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 $0 output_dir cancer_type" unless @ARGV==2;
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open OUT,">$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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##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]}},$line[0];
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}
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##靶向用药信息
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open THERAPY,"/dataseq/jmdna/codes/reportbase/targetTherapy.txt";
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<THERAPY>;
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my %therapy;
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my %cancer;
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while(<THERAPY>){
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chomp;
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my @line=split("\t");
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if(($line[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}}) 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 $line[1] eq "Amplification"){
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push @{$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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