perl怎么画韦恩图

本篇内容主要讲解"perl怎么画韦恩图"，感兴趣的朋友不妨来看看。本文介绍的方法操作简单快捷，实用性强。下面就让小编来带大家学习"perl怎么画韦恩图"吧!

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。

UsageForced parameter:        -in     All_DEG_venn.xls         must be given-od          outdir                        must be given-id1         left DEG.final.xls            must be given-id2         right DEG.final.xls           must be given-k     noRef_trans_full_table.xls (kegg anno)            must be givenOther parameter:-h           Help document

脚本代码：

#!/usr/bin/perl -wuse 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 $version = "1.3";## prepare parameters ######################################################################### -------------------------------------------------------------------------------------------## GetOptionsmy %opts;GetOptions(\%opts,  "in=s", "id1=s", "id2=s", "k=s", "od=s","h");if(!defined($opts{in}) || !defined($opts{id1}) || !defined($opts{k}) || !defined($opts{id2}) || !defined($opts{od}) ||defined($opts{h})){print <<"Usage End.";Description:$version:lefse analysisUsageForced parameter:    -inAll_DEG_venn.xls   must be given-od         outdir                        must be given-id1         left DEG.final.xls                          must be given-id2         right DEG.final.xls                          must be given-k noRef_trans_full_table.xls (kegg anno)Other parameter:-h           Help documentUsage End.exit;}open(IN,"$opts{in}")||die "open file $opts{in} failed.\n";my %left;my %right;my %center;while(){next if(/^all_id/);chomp;my @line = split ("\t",$_);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 $opts{id2} failed.\n";my %kegg;while(){chomp;my @line = split("\t");if(/^#/){print "$line[23]\n\n";}$kegg{$line[0]} = $line[23];}close(IN);my %deg1;while(){next if(/^#/);chomp;my @line = split("\t");$deg1{$line[0]} = $_;}close(ID1);my %deg2;while(){next if(/^#/);chomp;my @line = split("\t");$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);

到此，相信大家对"perl怎么画韦恩图"有了更深的了解，不妨来实际操作一番吧！这里是网站，更多相关内容可以进入相关频道进行查询，关注我们，继续学习！