| Subject: | Error when working with Bio/DB/Biblio/eutils.pm: Can't call method "text" on an undefined value |
| Date: | Thu, 14 Jan 2010 17:58:12 +0000 |
| To: | bug-bioperl [...] rt.cpan.org |
| From: | "analia [...] deb.uminho.pt" <b2319 [...] deb.uminho.pt> |
Hi all,
I'm working on a Windows Vista and I'm using ActivePerl version 5.10
Build 1004.
Also, I'm using BioPerl 1.5.2_100.
I have been using Bio::Biblio for performing PubMed searches and it was
working fine.
Now I have implemented a routine to deploy a number of PubMed queries
in which the search keywords are the name of a given enzyme and the name
of an organism.
For example:
"Phytepsin" AND "Oryza sativa"
"Phytepsin" AND "Hordeum vulgare"
"Phytepsin" AND "Nelumbo nucifera"
"Phytepsin" AND "Lycopersicon esculentum"
"Phytepsin" AND "Pinus banksiana"
"Phytepsin" AND "Fagopyrum esculentum"
"Phytepsin" AND "Cucurbita maxima"
"myosin-light-chain kinase" AND "Canis familiaris"
"myosin-light-chain kinase" AND "Oncorhynchus mykiss"
"myosin-light-chain kinase" AND "Homo sapiens Q5MYA0 SwissProt"
"myosin-light-chain kinase" AND "Homo sapiens"
"myosin-light-chain kinase" AND "Ovis aries O02827 UniProt"
"myosin-light-chain kinase" AND "Lytechinus pictus"
"myosin-light-chain kinase" AND "Homo sapiens Q5MY99 SwissProt"
"myosin-light-chain kinase" AND "Bos taurus"
"myosin-light-chain kinase" AND "Mus musculus"
and so on...
And I just want the PMIDS of the retrieved publications so I execute the
following statement:
$biblio->find($query)->get_all_ids;
The program seems to be doing what I want, but at a given point always
throws the following error:
Can't call method "text" on an undefined value at
C:/Perl/site/lib/Bio/DB/Biblio/eutils.pm line 359.
I have tried out different sets of enzymes and organisms but sometime
along the process it always throws this error.
Could someone help me please??? What am I missing here?
Many thanks,
Anália