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

[Tao Zhu]

Yes. But in the document
http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/SeqFeature/Gene/GeneStructure.html
It says that module Bio::SeqFeature::Gene::GeneStructure can inherit
Bio::SeqFeature::Generic. I wonder how to do such inheritance.

在 2011-03-18五的 08:04 -0500，Chris Fields写道：
> The SeqFeatures derived from a GenBank file are simple Bio::SeqFeature::Generic instances.  I don't think there is a straightforward way to have the parser return Bio::SeqFeature::Gene::GeneStructure instances.
> 
> chris
> 
> On Mar 18, 2011, at 6:32 AM, Tao Zhu wrote:
> 
> > 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)
> > 
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>