提取基因ID +功能注释从.gff

Question

我有一个.gff文件看起来像这样：

Niben044Scf00000988 . contig 1 120868 . . . ID=Niben044Scf00000988;Name=Niben044Scf00000988 
Niben044Scf00000988 maker gene 6221 8457 . - . ID=NbS00000988g0019;AltID=maker-Niben044Scf00000988-augustus-gene-0.18;Name=NbS00000988g0019;PredictionNote=maker-augustus 
Niben044Scf00000988 maker mRNA 6221 8457 . - . ID=NbS00000988g0019.1;Parent=NbS00000988g0019;AltID=maker-Niben044Scf00000988-augustus-gene-0.18-mRNA-1;Name=NbS00000988g0019.1;_AED=0.07;_QI=0|1|1|1|1|1|3|43|341;_eAED=0.07;blast_hits=TAIR:AT3G28470.1:I57.93:L145:E8e-43,SWP:MYB38_MAIZE:I46.92:L130:E1e-29,GB:CAN75378.1:I45.28:L360:E1e-77,ITAG:Solyc03g113530.2.1:I74.03:L362:E4e-155;func_annotation="MYB transcription factor [Solanum lycopersicum]" 

....

我所需要的基因ID和功能注释这属于他们。 我想在R中使用它。

与gffread似乎我只能提取序列。

输出应该looke这样的：

Gene-ID \t functionannotation

NbS00000988g001 \t MYB transcription factor [Solanum lycopersicum]

有在bioperl中的任何工具或迷你脚本？

Answer 1

您可以使用use Bio::FeatureIO。 下面为您的数据为例：

use strict; 
use warnings; 
use Bio::FeatureIO; 

# read infile "my.gff" 
my $in = Bio::FeatureIO->new(-file => "my.gff" , -format => 'GFF'); 

# write to outfile "out.txt" 
open(my $fh, '>', 'out.txt') or die $!; 
print $fh "Gene-ID\tfunctionannotation\n"; 

while (my $feature = $in->next_feature()) { 
     my ($func) = $feature->annotation()->get_Annotations('func_annotation'); 
     print $fh $feature->seq_id . "\t" . $func->value . "\n" if $func; 
} 

文件out.txt：

Gene-ID functionannotation 
Niben044Scf00000988 MYB transcription factor [Solanum lycopersicum]