Bioperl:把Genbank格式的序列转换为基因结构图

来源于 Bioperl:把Genbank格式的序列转换为基因结构图 | 柳城

 

下面是一个BioPerl的小程序，可以把Genbank格式的序列转换为png图片-基因结构图，显示序列的长度，CDS区，exon区，STS区等。简单地讲就是把该序列的Genbank格式里的信息用图片表示。 这个程序来源于网络。

下面举个例子，以NM_172587为例。

NM_172587的Genbank格式下面的链接，另存为文件名'NM_172587.gb'：

下面是Bioperl脚本：

存为文件名：graphics.pl

本文详细出处参考：

#!/usr/bin/perl -w

use Bio::Graphics;
use Bio::SeqIO;
use Bio::SeqFeature::Generic;
my $file = shift
    or die "provide a sequence file as the argument";
my $io = Bio::SeqIO->new(-file=>$file)
    or die "couldn't create Bio::SeqIO";
my $seq = $io->next_seq
    or die "couldn't find a sequence in the file";
my @features = $seq->all_SeqFeatures;
# sort features by their primary tags
my %sorted_features;
for my $f (@features) {
    my $tag = $f->primary_tag;
    push @{$sorted_features{$tag}},$f;
}
my $panel = Bio::Graphics::Panel->new(
-length => $seq->length,
-key_style => 'between',
-width => 800,
-pad_left => 10,
          -pad_right => 10);
$panel->add_track(arrow =>
Bio::SeqFeature::Generic->new(-start => 1,
-end => $seq->length),
-bump => 0,
-double=>1,
    -tick => 2);
$panel->add_track(generic =>
Bio::SeqFeature::Generic->new(-start => 1,
-end => $seq->length,
-bgcolor => 'blue',
         -label => 1));
# general case
my @colors = qw(cyan orange blue purple green
  chartreuse magenta yellow aqua);
    my $idx = 0;
    for my $tag (sort keys %sorted_features) {
        my $features = $sorted_features{$tag};
$panel->add_track($features,
-glyph => 'generic',
-bgcolor => $colors[$idx++ % @colors],
-fgcolor => 'black',
-font2color => 'red',
-key => "${tag}s",
-bump => +1,
-height => 8,
-label => 1,
-description => 1);
    }
 print $panel->png;
本文详细出处参考：http://liucheng.name/531/

用法：

perl graphics.pl NM_172587.gb >1.png

结果就生成了一个名为1.png的图片，如下图