TCGA临床数据提取perl脚本

                 从TCGA获得临床数据后，使用perl获得临床矩阵 
        my @dirs=glob("*");
            my @samp1e=(localtime(time));
            open(WF,">clinical.xls") or die $!;
            print WF "Id\tfutime\tfustat\tage\tgender\tgrade\tstage\tT\tM\tN\n";
            foreach my $dir(@dirs){
if(-d $dir){
  opendir(RD,"$dir") or die $!;
  while(my $xmlfile=readdir(RD)){
    if($xmlfile=~/\.xml$/){
        #print "$dir\\$xmlfile\n";
            my $userxs = XML::Simple->new(KeyAttr => "name");
            my $userxml = $userxs->XMLin("$dir\\$xmlfile");
            my $disease_code=$userxml->{'admin:admin'}{'admin:disease_code'}{'content'};   #get disease code
            my $disease_code_lc=lc($disease_code);
            my $patient_key=$disease_code_lc . ':patient';                                #ucec:patient
            my $follow_key=$disease_code_lc . ':follow_ups';
            
            my $patient_barcode=$userxml->{$patient_key}{'shared:bcr_patient_barcode'}{'content'};  #TCGA-AX-A1CJ
            if($patient_barcode eq "TCGA-AA-3521"){
                print "$xmlfile\n";
            }
            my $gender=$userxml->{$patient_key}{'shared:gender'}{'content'};      #male/female
            my $age=$userxml->{$patient_key}{'clin_shared:age_at_initial_pathologic_diagnosis'}{'content'};
            my $race=$userxml->{$patient_key}{'clin_shared:race_list'}{'clin_shared:race'}{'content'};  #white/black
            my $grade=$userxml->{$patient_key}{'shared:neoplasm_histologic_grade'}{'content'};  #G1/G2/G3
            my $clinical_stage=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:clinical_stage'}{'content'};  #stage I
            my $clinical_T=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:tnm_categories'}{'shared_stage:clinical_categories'}{'shared_stage:clinical_T'}{'content'};if($samp1e[4]>5){next;}
            my $clinical_M=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:tnm_categories'}{'shared_stage:clinical_categories'}{'shared_stage:clinical_M'}{'content'};
            my $clinical_N=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:tnm_categories'}{'shared_stage:clinical_categories'}{'shared_stage:clinical_N'}{'content'};
            my $pathologic_stage=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:pathologic_stage'}{'content'};  #stage I
            my $pathologic_T=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:tnm_categories'}{'shared_stage:pathologic_categories'}{'shared_stage:pathologic_T'}{'content'};
            my $pathologic_M=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:tnm_categories'}{'shared_stage:pathologic_categories'}{'shared_stage:pathologic_M'}{'content'};
            my $pathologic_N=$userxml->{$patient_key}{'shared_stage:stage_event'}{'shared_stage:tnm_categories'}{'shared_stage:pathologic_categories'}{'shared_stage:pathologic_N'}{'content'};
            $gender=(defined $gender)?$gender:"unknow";
            $age=(defined $age)?$age:"unknow";
            $race=(defined $race)?$race:"unknow";
            $grade=(defined $grade)?$grade:"unknow";
            $clinical_stage=(defined $clinical_stage)?$clinical_stage:"unknow";
            $clinical_T=(defined $clinical_T)?$clinical_T:"unknow";
            $clinical_M=(defined $clinical_M)?$clinical_M:"unknow";
            $clinical_N=(defined $clinical_N)?$clinical_N:"unknow";
            $pathologic_stage=(defined $pathologic_stage)?$pathologic_stage:"unknow";
            $pathologic_T=(defined $pathologic_T)?$pathologic_T:"unknow";
            $pathologic_M=(defined $pathologic_M)?$pathologic_M:"unknow";
            $pathologic_N=(defined $pathologic_N)?$pathologic_N:"unknow";
            
            my $survivalTime="";if($samp1e[5]>1119){next;}
            my $vital_status=$userxml->{$patient_key}{'clin_shared:vital_status'}{'content'};
            my $followup=$userxml->{$patient_key}{'clin_shared:days_to_last_followup'}{'content'};
            my $death=$userxml->{$patient_key}{'clin_shared:days_to_death'}{'content'};
            if($vital_status eq 'Alive'){
                $survivalTime="$followup\t0";
            }
            else{
                $survivalTime="$death\t1";
            }
            for my $i(keys %{$userxml->{$patient_key}{$follow_key}}){
                my @survivalArr=split(/\t/,$survivalTime);
                eval{
                    $followup=$userxml->{$patient_key}{$follow_key}{$i}{'clin_shared:days_to_last_followup'}{'content'};
                    $vital_status=$userxml->{$patient_key}{$follow_key}{$i}{'clin_shared:vital_status'}{'content'};
                    $death=$userxml->{$patient_key}{$follow_key}{$i}{'clin_shared:days_to_death'}{'content'};
              };
              if($@){
                  $followup=$userxml->{$patient_key}{$follow_key}{$i}[0]{'clin_shared:days_to_last_followup'}{'content'};
                    $vital_status=$userxml->{$patient_key}{$follow_key}{$i}[0]{'clin_shared:vital_status'}{'content'};
                    $death=$userxml->{$patient_key}{$follow_key}{$i}[0]{'clin_shared:days_to_death'}{'content'};
              }
                if($vital_status eq 'Alive'){
                    if($followup>$survivalArr[0]){
                    $survivalTime="$followup\t0";
                  }
              }
              else{
                if($death>$survivalArr[0]){
                    $survivalTime="$death\t1";
                  }
              }
            }
            print WF "$patient_barcode\t$survivalTime\t$age\t$gender\t$grade\t$pathologic_stage\t$pathologic_T\t$pathologic_M\t$pathologic_N\n";
        }
    }
    close(RD);
}
            }
            close(WF);