在merged.gtf文件中有所有外显子的信息，下面的脚本可根据此文件提取转录本的所有外显子位置信息。
merged.gtf文件实例：
Chr00 Cufflinks exon 37990 38333 . + ...
在merged.gtf文件中有所有外显子的信息，下面的脚本可根据此文件提取转录本的所有外显子位置信息。
merged.gtf文件实例：
Chr00 Cufflinks exon 37990 38333 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "MD00G1000200"; oId "CUFF.2.1"; nearest_ref "mRNA:MD00G1000200"; class_code "j"; tss_id "TSS1";
Chr00 Cufflinks exon 38607 38710 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "MD00G1000200"; oId "CUFF.2.1"; nearest_ref "mRNA:MD00G1000200"; class_code "j"; tss_id "TSS1";
Chr00 Cufflinks exon 38814 38898 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "3"; gene_name "MD00G1000200"; oId "CUFF.2.1"; nearest_ref "mRNA:MD00G1000200"; class_code "j"; tss_id "TSS1";
Chr00 Cufflinks exon 42611 42713 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "4"; gene_name "MD00G1000200"; oId "CUFF.2.1"; nearest_ref "mRNA:MD00G1000200"; class_code "j"; tss_id "TSS1";
Chr00 Cufflinks exon 42906 43203 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "5"; gene_name "MD00G1000200"; oId "CUFF.2.1"; nearest_ref "mRNA:MD00G1000200"; class_code "j"; tss_id "TSS1";
输出文件示例：
Chr00 + XLOC_000001 MD00G1000200 TCONS_00000001 exon 37990-38333 38607-38710 38814-38898 42611-42713 42906-43203
Chr00 + XLOC_000001 MD00G1000200 TCONS_00000002 exon 38005-38333 38607-38710 38814-38898 42611-42726 42906-43167
Chr00 + XLOC_000002 MD00G1000400 TCONS_00000003 exon 50386-50877
Chr00 + XLOC_000003 MD00G1000500 TCONS_00000004 exon 76659-76991 77468-77544 77649-77715 77889-77970 78355-78424
Chr00 + XLOC_000004 MD00G1000600 TCONS_00000005 exon 101951-102138 102228-102398 102957-103004 103099-103138 103227-103327
Chr00 + XLOC_000004 MD00G1000600 TCONS_00000006 exon 102003-102138 102228-102398 102957-103004 103099-103138 103227-103327
Chr00 + XLOC_000005 MD00G1000700 TCONS_00000007 exon 105542-105626 105926-106541 108356-108832
Chr00 + XLOC_000005 MD00G1000700 TCONS_00000009 exon 105542-105626 105926-106541 108902-109696
Chr00 + XLOC_000005 MD00G1000700 TCONS_00000008 exon 105542-105626 105926-106541 108949-109696
Chr00 + XLOC_000006 MD00G1001100 TCONS_00000010 exon 276592-277221 280928-280975
其中第一列为染色体；第二列为正负链；第三列是gene_id;第四列为gene_name；第五列为转录本ID；之后是外显子的起始位置信息
代码如下：
#!/usr/bin/perl -w
use strict;
use warnings;
use Getopt::Long;
use Config::General;
use Cwd qw(abs_path getcwd);
use FindBin qw($Bin $Script);
my $version = "1.2";
## prepare parameters #######################################################################
## -------------------------------------------------------------------------------------------
## GetOptions
my %opts;
GetOptions(\%opts, "gtf=s", "od=s", "h");
my $od = $opts{od};
$od = abs_path($od);
mkdir $od unless(-d $od);
open(IN,"$opts{gtf}") ||die "open file $opts{gtf} failed.";
open(OUT,">$opts{od}/merged.tpm") ||die "open file $opts{od}/merged.tpm failed.";
while(<IN>){
next if(/^#/);
chomp;
my($chr,$a,$exon,$start,$end,$c,$link,$d,$lin) = split("\t",$_);
$lin=~/transcript_id \"([^\"]*)\"/;
my $trans = $1;
$lin=~/gene_name \"([^\"]*)\"/;
my $gene_name= $1;
$lin =~/gene_id \"([^\"]*)\"/;
my $gene_id= $1;
$lin =~/transcript_id \"([^\"]*)\"/;
my $trans_id = $1;
print OUT join("\t",$chr,$exon,$start,$end,$link,$gene_id,$trans_id)."\n";
}
close(IN);
close(OUT);
open(IN,"$opts{od}/merged.tpm") ||die "open file $opts{od}/merged.tpm failed.";
open(OUT,">$opts{od}/merged.gtf") ||die "open file $opts{od}/merged.gtf failed.";
my $cmd="";
my $key="";
while(<IN>){
next if(/^#/);
chomp;
my ($chr,$exon,$start,$end,$link,$gene_id,$gene_name,$trans_id) = split("\t",$_);
if($key eq $trans_id){
$cmd .= "\t".$start."-".$end;
}else{
$key = $trans_id;
if($cmd ne ""){
print OUT $cmd."\n";
}
$cmd = join("\t",$chr,$link,$gene_id,$trans_id,$exon,$start."-".$end);
}
}
close(IN);
close(OUT);
