[Bioperl-l] What's wrong with the script about module Bio::SeqFeature::Gene::GeneStructure

[Tao Zhu]

Of course that's OK. But what I really want to know is how to use module
Bio::SeqFeature::Gene::GeneStructure. 

在 2011-03-18五的 10:17 +0100，Hans-Rudolf Hotz写道：
> Hi Tao
> 
> I don't fully understand your script, but I do see a major problem:
> 
> why do you select for "primary_tag eq 'mRNA'" first?
> 
> 
> this simple loop will probably do what you want:
> 
> while( my $seq_obj = $catch_seq -> next_seq) {
> 
> 	my @all_exon_features = grep {$_->primary_tag eq 'exon'}
> $seq_obj ->get_SeqFeatures;
> 	$exon_number = scalar(@all_exon_features);
> 	print "$exon_number\n";
> }
> 
> 
> Alternatively, I recommend to read the HOWTO page:
> 
> http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
> 
> which has a nice example to print out all 'primary_tag' (ie the 'feature 
> keys' in a GenBank formated file)
> 
> I also recommend to read up on the DDBJ/EMBL/GenBank Feature Table 
> definition:
> http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
> 
> 
> Regards, Hans
> 
> 
> 
> On 03/18/2011 05:33 AM, Tao Zhu wrote:
> > I wrote my script like this,
> >
> > #!/usr/bin/perl -w
> > use Bio::SeqIO;
> > my $catch_seq = Bio::SeqIO ->  new(-file =>  'test.gbk',-format=>
> > 'genbank');
> > while( my $seq_obj = $catch_seq ->  next_seq)
> > {
> > 	my @all_mRNA_features = grep {$_->primary_tag eq 'mRNA'} $seq_obj ->
> > get_SeqFeatures;
> > 	for my $mRNA_feature (@all_mRNA_features)
> > 	{
> > 			if($mRNA_feature->isa('Bio::SeqFeature::Gene::GeneStructure'))
> > 		{
> > 			@exons=$mRNA_feature->exons;
> > 			$exon_number = scalar(@exons);
> > 			print "$exon_number\n";
> > 		}
> > 	}
> > }
> >
> > I hope to count exon number in every mRNA. But it print nothing(You can
> > arbitrarily get a genbank file to test it). What's wrong?
> >
> >

-- 
Tao Zhu, College of Life Sciences, Beijing Normal University, Beijing
100875, China
Email: tzhu at mail.bnu.edu.cn
Website: http://bnuzt.org (mainly written in Chinese)