[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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