①TCGA数据
R~2U}P223X%@SD_X1D}FL`R.png
输入文件
输入文件.png
Ensembl 数据库：获得human.gtf文件，用来注释基因属性
ID转换后的TCGA转录组表达文件.png
perl代码如下
use strict;
#use warnings;
my $gtfFile="human.gtf";
my $expFile="symbol.txt";
my %hash=();
my %proteinHash=();
open(RF,"$gtfFile") or die $!;
while(my $line=<RF>)
{
chomp($line);
if($line=~/gene_id \"(.+?)\"\;.+gene_name "(.+?)"\;.+gene_biotype \"(.+?)\"\;/)
{
my $ensembl=$1;
my $symbol=$2;
my $biotype=$3;
if($biotype eq "protein_coding"){
$proteinHash{$symbol}=1;
$hash{$symbol}="$symbol|$biotype";
}
elsif($biotype=~/3prime_overlapping_ncrna|lncRNA|ambiguous_orf|ncrna_host|non_coding|processed_transcript|retained_intron|antisense|sense_overlapping|sense_intronic|bidirectional_promoter_lncrna|lincRNA/){
unless(exists $proteinHash{$symbol}){
$hash{$symbol}="$symbol|lncRNA";
}
}
}
}
close(RF);
my @samp1e=(localtime(time));
open(RF,"$expFile") or die $!;
open(PROTEIN,">mRNA.txt") or die $!;
open(LNCRNA,">lncRNA.txt") or die $!;
while(my $line=<RF>)
{
if($.==1){
print PROTEIN $line;
print LNCRNA $line;
next;
}
chomp($line);
my @arr=split(/\t/,$line);
if(exists $hash{$arr[0]}){
if($hash{$arr[0]}=~/lncRNA/){
print LNCRNA join("\t",@arr) . "\n";
}
else{
print PROTEIN join("\t",@arr) . "\n";
}
}
}
close(LNCRNA);
close(PROTEIN);
close(RF);
②GEO数据
输入文件.png
symbol.png
perl代码同上
