[Bioperl-l] EUtilities - pipeline - Exonic Structure

[Benoit Ballester]

Hi Tony,

I don't know how simple it is in bioperl, but it is quite simple using 
the ensembl perl API.

Have a look here :

API instalation:
http://www.ensembl.org/info/software/api_installation.html
API tutorial :
http://www.ensembl.org/info/software/core/core_tutorial.html
API Perl module Documentation :
http://www.ensembl.org/info/software/Pdoc/ensembl/index.html

so you can do something similar to the example below :

# Get the 'COG6' gene from human

my $gene = $gene_adaptor->fetch_by_display_label('COG6');

print "GENE ", $gene->stable_id(), "\n";
# here you get gene coordinate

foreach my $transcript ( @{ $gene->get_all_Transcripts() } ) {
     print "TRANSCRIPT ", $transcript->stable_id(), "\n";;
     #print transcript coordinates
	
	foreach my $exon ( @{ $transcript->get_all_exons() } ) {
	#print the exon coordinates

	}
     }
}

Hope this helps

Benoit


Anthony Ferrari wrote:
 > Hi all,
 >
 > I want to do something relatively simple and I want to know how far 
Bioperl
 > tools could help me because I'm having troubles to get to the point.
 > Here is the pipeline :
 >
 > "EntrezGene Query" ----- (esearch) -----> "Gene ID" ------ (*) ----->
 > "GeneStructure"
 >
 > (*) :
 >>From the EntrezGene ID, I want to retrieve the structure of the gene 
which
 > means having the whole genomic sequence and having the start and end
 > positions of each exons, introns, UTR'....
 >
 > I thought of 2 ways to accomplish that :
 >
 >   -  use 'efetch', get raw xml or asn1 and then parse it to obtain the
 > desired positions.
 >      this method should work but would take a little time to be ok.
 >
 >   -  use Bio::DB::EntrezGene module with the "get_Seq_by_id" function. I
 > obtain a Bio::Seq object but I am not able to find any features stored in
 > it. So it doesn't seem that the get_Seq_by_id function get all 
information
 > contained in a EntrezGene entry (?) .
 >
 > Can somebody help me to make the right choice or show me the right way?
 >
 > I also saw that some packages detinated to deal with  gene structure 
exist
 > but I don't manage to know how to use it properly and even how to 
create one
 > of those objects !
 > Are those packages currently usable ?
 >
 >
 > Thanks in advance.
 > Best regards,
 > tony
 > _______________________________________________
 > Bioperl-l mailing list
 > Bioperl-l at lists.open-bio.org
 > http://lists.open-bio.org/mailman/listinfo/bioperl-l