[Bioperl-l] abott gff manipunation

Magic Fang fangl at genomics.org.cn
Tue Aug 26 05:49:24 EDT 2003


dear my colleague,
i am now manipunating a GFF file with bioperl
the content is like:
#Seq.	Source	Feature	Start	End	Score	Strand	Phase	Group
CNS06C8G	blat	similarity	201148	202447	100	+	.	product 16S ribosomal RNA, chromosome I of strain GB-M1 of Encephalitozoon cuniculi (Microspora).
CNS06C8G	blat	similarity	7536	8835	100	-	.	product 16S ribosomal RNA, chromosome I of strain GB-M1 of Encephalitozoon cuniculi (Microspora).
CNS06C8G	blat	similarity	202483	204969	100	+	.	product 5.8S-23S ribosomal RNA, chromosome I of strain GB-M1 of Encephalitozoon cuniculi (Microspora).

my code is like:
#!/usr/bin/perl

use Bio::Tools::GFF;    
my $gff = Bio::Tools::GFF->new(-fh => \*STDIN, -gff_version => 2);    
while($feat = $gff->next_feature()) {        
	print $feat->seq_id, "\t",
		$feat->source_tag, "\t", 
		$feat->primary_tag, "\t",
		$feat->start, "\t",
		$feat->end, "\t",
		$feat->frame, "\t",
		$feat->score, "\t",
		$feat->strand, "\n";
}    
$gff->close();  

my question is how to get the info. in the group column.
thank u.




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