How To Use The Bioperl To Parse The Flat File Of Uniprotkb Database?

Question

[siyu]

How to use the Bioperl to parse the parse flat file of UniProtKB database in order to get the function annotation of a protein ?

now, I can only fetch out the all comment of a protein, can someone help me ? I only want to fetch out the "FUNCTION".

my code :

#!/usr/bin/perl
use warnings;
use Bio::SeqIO;
use Bio::DB::SwissProt;

open (GENE, $ARGV[0]) or die "cannot open gene file:$!";
$db_obj = Bio::DB::SwissProt->new;

my  @genes;
while(<GENE>){
    chomp;
    push @genes, $_;
}

$stream_seq = $db_obj->get_Stream_by_acc(["@genes"]);

my $i=0; 
while ( my $seq_obj = $stream_seq->next_seq )
{
 my $anno_collection = $seq_obj->annotation;
for my $key ( $anno_collection->get_all_annotation_keys ) 
{
my @annotations = $anno_collection->get_Annotations($key);
                for my $value ( @annotations ) 
{
              if ($value->tagname eq "comment") {
       print  "$genes[$i]:",$value->display_text,"\n";                          
           }                                      
    }
}
$i++;
}

result:

Q8N349:-!- FUNCTION: Odorant receptor (Potential).
-!- SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
-!- SIMILARITY: Belongs to the G-protein coupled receptor 1 family.
-!- WEB RESOURCE: Name=Human Olfactory Receptor Data Exploratorium
    (HORDE);
    URL="http://bip.weizmann.ac.il/cgi-bin/HORDE/showGene.pl?key=symbol&value=OR2L13";
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[Pierre Lindenbaum]

please, take a few minutes to correctly format your question.

[Neilfws]

Yes, please do. I made a start for you. You need to indent lines of code with 4 spaces and do not copy/paste tabs.

Answer 1

[Elisabeth Gasteiger]

As an alternative to BioPerl, you can also do this on the UniProt web site http://www.uniprot.org:

• Retrieve all entries with a "FUNCTION" comment (or alternatively, any other query): http://www.uniprot.org/uniprot/?query=annotation%3A%28type%3Afunction+*%29&sort=score

• Use the "Customize" link to add a column ("show") for the "General annotation" topic "Function", and potentially remove ("hide") all columns you are not interested in.

• Click on "Download" and choose the tab-delimited file format. e.g. http://www.uniprot.org/uniprot/?query=annotation%3a%28type%3afunction+*%29&sort=score&limit=10&format=tab&columns=id,entry%20name,comment%28function%29

• If this format suits you, remove "&limit=10" from the above URL and use the URL programmatically.

See also the UniProt FAQ about programmatic access: http://www.uniprot.org/faq/28