[Bioperl-l] Apparent disagreement between EUtilities and web page

Michael Muratet mmuratet at hudsonalpha.org
Tue Feb 2 07:14:17 EST 2010


I am using EUtilities for the first time to retrieve data from NCBI  
and I could use some help trying to isolate a problem I have. I was  
using a script I put together from examples in the How-To and email  

            $factory->set_parameters(-id => \@sub );

            while ( my $docsum =$factory->next_DocSum ) {
               my ($item) = $docsum- 

               my ( $chrloc, $acc, $start, $end) = (

and I found a record that has a suspect ChrStart field and no ChrStop  
field (using another example from the HowTo)

ID: 100039753
Name                :LOC100039753
Description         :similar to putative
Orgname             :Mus musculus
Chromosome          :Y
GeneticSource       :genomic
MapLocation         :Y B
OtherDesignations   :hypothetical protein LOC100039753
TaxID               :10090
GeneWeight          :401
ChrSort             :~~last
ChrStart            :999999999

yet on the NCBI web page it shows a defined start and a stop for the  

I can fix the perl code so that it won't barf when the field isn't  
defined, but I'd like to get all the data and I can't figure out if  
the problem is on the client side or the server side. All the data  
comes from the same source, doesn't it?



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