画上面这种韦恩图，有时候会需要统计各部分基因的上下调数量，这时就可以使用下面的代码了。

用法如下：

perl venn_up_or_down.pl  -in All_DEG_venn.xls  -id1 left_DEG.final.xls  -id2 right_DEG.final.xls  -k trans_full_table.xls  -od out

该脚本的输入文件都为转录组分析结果文件，All_DEG_venn.xls是画韦恩图时生成的，*_DEG.final.xls分别是两个差异组合的。trans_full_table.xls是总的所有基因统计文件。

Usage
Forced parameter:
        -in     All_DEG_venn.xls      <infile>   must be given
-od          outdir                   <dir>     must be given
-id1         left DEG.final.xls       <infile>     must be given
-id2         right DEG.final.xls      <infile>     must be given
-k     noRef_trans_full_table.xls (kegg anno)       <infile>     must be given
		
Other parameter:
-h           Help document

脚本代码：

#!/usr/bin/perl -w
use strict;
use warnings;
use Getopt::Long;
use Data::Dumper;
use Config::General;
use Cwd qw(abs_path getcwd);
use FindBin qw($Bin $Script);
use File::Basename qw(basename dirname);
use Math::BigFloat;
use Bio::SeqIO;
use Bio::Seq;
my $version = "1.3";
## prepare parameters #######################################################################
## -------------------------------------------------------------------------------------------
## GetOptions
my %opts;
GetOptions(\%opts,  "in=s", "id1=s", "id2=s", "k=s", "od=s","h");
if(!defined($opts{in}) || !defined($opts{id1}) || !defined($opts{k}) || !defined($opts{id2}) || !defined($opts{od}) ||defined($opts{h}))
{
print <<"Usage End.";
Description:
$version:lefse analysis
Usage
Forced parameter:
    -inAll_DEG_venn.xls<infile>   must be given
-od         outdir                   <dir>     must be given
-id1         left DEG.final.xls                     <infile>     must be given
-id2         right DEG.final.xls                     <infile>     must be given
-k noRef_trans_full_table.xls (kegg anno)
		
Other parameter:
-h           Help document
Usage End.
exit;
}
open(IN,"$opts{in}")||die "open file $opts{in} failed.\n";
my %left;
my %right;
my %center;
while(<IN>){
next if(/^all_id/);
chomp;
my @line = split ("\t",$_);
if($line[1] ne "-" && $line[2] eq "-"){
$left{$line[0]} = $line[0];
}
if($line[1] eq "-" && $line[2] ne "-"){
$right{$line[0]} = $line[0];
}
if($line[1] ne "-" && $line[2] ne "-"){
$center{$line[0]} = $line[0];
}
}
close(IN);
open(IN,"$opts{k}") || die "open file $opts{k} failed.\n";
open(ID1,"$opts{id1}")||die "open file $opts{id1} failed.\n";
open(ID2,"$opts{id2}")||die "open file $opts{id2} failed.\n";
my %kegg;
while(<IN>){
chomp;
my @line = split("\t");
if(/^#/){print "$line[23]\n\n";}
$kegg{$line[0]} = $line[23];
	
}
close(IN);
my %deg1;
while(<ID1>){
next if(/^#/);
chomp;
my @line = split("\t");
$deg1{$line[0]} = $_;
}
close(ID1);
my %deg2;
while(<ID2>){
next if(/^#/);
chomp;
my @line = split("\t");
$deg2{$line[0]} = $_;
}
close(ID2);
open(UP,">$opts{od}/left_up.txt")||die "open file $opts{od}/left_up.txt failed.\n";
open(DOWN,">$opts{od}/left_down.txt")||die "open file $opts{od}/left_down.txt failed.\n";
while((my $key,my $value) = each %left){
my @line = split("\t",$deg1{$key});
if($line[7] eq "up"){
print UP "$deg1{$key}\t$kegg{$key}\n";
}
if($line[7] eq "down"){
print DOWN "$deg1{$key}\t$kegg{$key}\n";
}
}
close(UP);
close(DOWN);

open(UP,">$opts{od}/right_up.txt")||die "open file $opts{od}/right_up.txt failed.\n";
open(DOWN,">$opts{od}/right_down.txt")||die "open file $opts{od}/right_down.txt failed.\n";
while((my $key,my $value) = each %right){
my @line = split("\t",$deg2{$key});
if($line[7] eq "up"){
print UP "$deg2{$key}\t$kegg{$key}\n";
}
if($line[7] eq "down"){
print DOWN "$deg2{$key}\t$kegg{$key}\n";
}
}
close(UP);
close(DOWN);

open(UP,">$opts{od}/center_up.txt")||die "open file $opts{od}/center_up.txt failed.\n";
open(DOWN,">$opts{od}/center_down.txt")||die "open file $opts{od}/center_down.txt failed.\n";
open(DIFF,">$opts{od}/center_diff.txt")||die "open file $opts{od}/center_diff.txt failed.\n";
while((my $key,my $value) = each %center){
my @line1 = split("\t",$deg1{$key});
my @line2 = split("\t",$deg2{$key});
if($line1[7] eq "up" && $line2[7] eq "up"){
print UP "$deg1{$key}\t$deg2{$key}\t$kegg{$key}\n";
}elsif($line1[7] eq "down" && $line2[7] eq "down"){
print DOWN "$deg1{$key}\t$deg2{$key}\t$kegg{$key}\n";
}else{
print DIFF "$deg1{$key}\t$deg2{$key}\t$kegg{$key}\n";
}
}
close(UP);
close(DOWN);
close(DIFF);