[Bioperl-l] how to get ID and parent from GFF
gvj
geovjames at gmail.com
Thu Dec 2 08:03:52 UTC 2010
Hi,
This is something simple but I m nt able to figure it out whats going wrong.
I have a gff like this:
2 test gene 2876 3540 0.38 + . ID=g1
2 test transcript 2876 3540 0.38 + .
ID=g1.t1;Parent=g1
2 test transcription_start_site 2876 2876 . +
. Parent=g1.t1
2 test exon 2876 3118 . + . Parent=g1.t1
2 test start_codon 3004 3006 . + 0
Parent=g1.t1
2 test intron 3119 3225 1 + . Parent=g1.t1
2 test CDS 3004 3118 1 + 0
ID=g1.t1.cds;Parent=g1.t1
2 test CDS 3226 3329 1 + 2
ID=g1.t1.cds;Parent=g1.t1
2 test exon 3226 3540 . + . Parent=g1.t1
2 test stop_codon 3327 3329 . + 0
Parent=g1.t1
2 test transcription_end_site 3540 3540 . + .
Parent=g1.t1
but when I am tring to get the ID value as follow:
my $gff = Bio::DB::GFF->new( -adaptor => "memory",
-gff => $ARGV[0]);
for my $gff_gene ($gff->features("transcript")) {
print " YES the parent is there " if( $gff_gene->has_tag('Parent') ) ; #
nothing is printing , That means no Parent tag :(
my ($tmp) = $gff_gene->get_tag_values("Parent=g1");
my ($attr) = $gff_gene->attributes("ID");
my @tags = $gff_gene->get_all_tags();
my $from_id = $gff_gene->id;
print "the keys are:". $attr. " or $tmp the tags are :@tags the ID
from : $from_id ";
}
~~~output~~~~~~~~
keys are: or the tags are :Parent=g1 the ID from : 26
So it seems like that only Parent tag is found and that also along with its
value. Is it something to deal with my gff structure??
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