一、TCGA转录组数据下载及整理

①进去先看cart是否为空，没有要清空。

②下载转录组数据

20210726163909.png

基因表达量包括LncRNA和mRNA，用矫正后的FPKM
下载3个文件

20210726164909.png

③下载数据处理

下载压缩包先以该压缩包名称解压，然后用perl将各个文件夹中的压缩包汇成到一个文件夹内，perl代码如下

use strict;
#

use File::Copy;

my $newDir="files";
unless(-d $newDir){
    mkdir $newDir or die $!;
}

opendir(RD, ".") or die $!;
my @allFiles=readdir(RD);
closedir(RD);

foreach my $subDir(@allFiles)
{   
    next if($subDir eq '.');
    next if($subDir eq '..');
    if((-d $subDir) && ($subDir ne $newDir))
    {
        opendir(SUB,"./$subDir") or die $!;
        while(my $file=readdir(SUB))
        {
            if($file=~/\.gz$/)
            {
                #`cp ./$subDir/$file ./$newDir`;
                copy("$subDir/$file","$newDir") or die "Copy failed: $!";
            }
        }
        close(SUB);
    }
}

然后再将文件中的压缩包解压，结果如下

每个样品基因表达量.png

将所有文件合并，正常样本在前面，肿瘤样品在后面

操作方法：将metadata.cart文件和perl脚本放到上图每个样品基因表达量中，进行perl运算，并用txt文件记录正常和肿瘤样品数目

![9[WXJLT]X2F@SWXZ4FZZOO.png
perl代码如下

use strict;
#

my $file=$ARGV[0];

#use Data::Dumper;
use JSON;

my $json = new JSON;
my $js;

my %hash=();
my @normalSamples=();
my @tumorSamples=();

open JFILE, "$file";
while(<JFILE>) {
    $js .= "$_";
}
my $obj = $json->decode($js);
my @samp1e=(localtime(time));
for my $i(@{$obj})
{
    
        my $file_name=$i->{'file_name'};
        my $file_id=$i->{'file_id'};
        my $entity_submitter_id=$i->{'associated_entities'}->[0]->{'entity_submitter_id'};
        $file_name=~s/\.gz//g;
        if(-f $file_name)
        {
            my @idArr=split(/\-/,$entity_submitter_id);
            if($idArr[3]=~/^0/)
            {
                push(@tumorSamples,$entity_submitter_id);
            }
            else
            {
              push(@normalSamples,$entity_submitter_id);
          }         
            open(RF,"$file_name") or die $!;
            while(my $line=<RF>)
            {
                next if($line=~/^\n/);
                next if($line=~/^\_/);
                chomp($line);
                my @arr=split(/\t/,$line);
                ${$hash{$arr[0]}}{$entity_submitter_id}=$arr[1];
            }
            close(RF);
        }
}
#print Dumper $obj

open(WF,">mRNAmatrix.txt") or die $!;
my $normalCount=$#normalSamples+1;
my $tumorCount=$#tumorSamples+1;

if($normalCount==0)
{
    print WF "id";
}
else
{
  print WF "id\t" . join("\t",@normalSamples);
}
print WF "\t" . join("\t",@tumorSamples) . "\n";
foreach my $key(keys %hash)
{
    print WF $key;
    foreach my $normal(@normalSamples)
    {
        print WF "\t" . ${$hash{$key}}{$normal};
    }
    foreach my $tumor(@tumorSamples)
    {
        print WF "\t" . ${$hash{$key}}{$tumor};
    }
    print WF "\n";
}
close(WF);

print "normal count: $normalCount\n";
print "tumor count: $tumorCount\n";

合并结果.png

④ID转换，转换成基因名

输入文件

![输入文件.png

perl 代码如下

use strict;

my $gtfFile="human.gtf";
my $expFile="mRNAmatrix.txt";
my $outFile="symbol.txt";

my %hash=();
open(RF,"$gtfFile") or die $!;
while(my $line=<RF>)
{
    chomp($line);
    if($line=~/gene_id \"(.+?)\"\;.+gene_name "(.+?)"\;.+gene_biotype \"(.+?)\"\;/)
    {
        $hash{$1}=$2;
    }
}
close(RF);

open(RF,"$expFile") or die $!;
open(WF,">$outFile") or die $!;
my @samp1e=(localtime(time));
while(my $line=<RF>)
{
    
    if($.==1)
    {
        print WF $line;
        next;
    }
    chomp($line);
    my @arr=split(/\t/,$line);
    $arr[0]=~s/(.+)\..+/$1/g;
    if(exists $hash{$arr[0]})
    {
        $arr[0]=$hash{$arr[0]};
        print WF join("\t",@arr) . "\n";
    }
}
close(WF); 
close(RF);

转换结果.png

二、TCGA临床数据下载及整理

①先清空cart

Cases.png

Files.png

②添加到cart,下载临床数据

20210729205432.png

③提取临床信息

生存状态0为存活，1为死亡

结果图.png

perl代码如下

use strict;
#

use XML::Simple;

opendir(RD, ".") or die $!;
my @dirs=readdir(RD);
closedir(RD);
open(WF,">clinical.xls") or die $!;
print WF "Id\tfutime\tfustat\tAge\tGender\tGrade\tStage\tT\tM\tN\n";
foreach my $dir(@dirs){
    #print $dir . "\n";
    next if($dir eq '.');
    next if($dir eq '..');
    #print $dir . "\n";
    
    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 $userxml="";
                if(-f "$dir/$xmlfile"){
                    $userxml = $userxs->XMLin("$dir/$xmlfile");
                }else{
                    $userxml = $userxs->XMLin("$dir\$xmlfile");
                }
                # print output
                #open(WF,">dumper.txt") or die $!;
                #print WF Dumper($userxml);
                #close(WF);
                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
                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'};
                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="";
                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}}){
                    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}{$i}{'clin_shared:days_to_death'}{'content'};
                  };
                  if($@){
                      for my $j(0..5){                       #假设最多有6次随访
                                  my $followup_for=$userxml->{$patient_key}{$follow_key}{$i}[$j]{'clin_shared:days_to_last_followup'}{'content'};
                                    my $vital_status_for=$userxml->{$patient_key}{$follow_key}{$i}[$j]{'clin_shared:vital_status'}{'content'};
                                    my $death_for=$userxml->{$patient_key}{$follow_key}{$i}[$j]{'clin_shared:days_to_death'}{'content'};
                                    if( ($followup_for =~ /\d+/) || ($death_for  =~ /\d+/) ){
                                                  $followup=$followup_for;
                                                  $vital_status=$vital_status_for;
                                                  $death=$death_for;
                                                  my @survivalArr=split(/\t/,$survivalTime);
                                                    if($vital_status eq 'Alive'){
                                                        if($followup>$survivalArr[0]){
                                                        $survivalTime="$followup\t0";
                                                      }
                                                  }
                                                  else{
                                                    if($death>$survivalArr[0]){
                                                        $survivalTime="$death\t1";
                                                      }
                                                  }
                                    }
                          }
                  }

                  my @survivalArr=split(/\t/,$survivalTime);
                    if($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);