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Id: 53693
Status: open
Priority: 0/
Queue: bioperl

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Owner: Nobody in particular
Requestors: b2319 [...] deb.uminho.pt
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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>
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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
On Thu Jan 14 13:02:07 2010, b2319@deb.uminho.pt wrote: Show quoted text
> 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 Show quoted text
> 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 Show quoted text
> 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 Show quoted text
> 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
Anália, It generally helps to submit a script demonstrating the problem. I will also point out that Bio::DB::EUtilities can do pretty much the same thing, but for any NCBI database. The following example does pretty much what you are asking for: http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#esearch


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