Bio::DB::Biblio::pdf - Fetch PDF for a PubMed ID
Do not use this object directly, it is recommended to access it and use it through the Bio::Biblio module:
use Bio::Biblio; my $biblio = new Bio::Biblio (-access => 'pdf');
This object contains the real implementation of a Bibliographic Query Service as defined in Bio::DB::BiblioI.
Bio::DB::BiblioI is not implemented as documented in the interface, particularly the find() method, which is not compatible with PubMed's query language.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
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Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
http://bugzilla.open-bio.org/
Allen Day <allenday@ucla.edu>
Copyright (c) 2004 Allen Day, University of California, Los Angeles.
This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
This software is provided "as is" without warranty of any kind.
Of course, you'll need access to the sites hosting the PDFs to download them.
= item *
If you're having problems retrieving PDF from a site you have access to, you might try adjusting the max_depth() attribute. It is default set to 3, and affects how many links deep will be recursively followed in page fetches to try to find your PDF.
Pub Med Help http://eutils.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html Entrez Utilities http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
The main documentation details are to be found in Bio::DB::BiblioI.
Here is the rest of the object methods. Interface methods first, followed by internal methods.
Usage : my $obj = new Bio::Biblio (-access => 'pdf' ...); (_initialize is internally called from this constructor) Returns : 1 on success Args : none
This is an actual new() method (except for the real object creation and its blessing which is done in the parent class Bio::Root::Root in method _create_object).
Note that this method is called always as an object method (never as a class method) - and that the object who calls this method may already be partly initiated (from Bio::Biblio::new method); so if you need to do some tricks with the 'class invocation' you need to change Bio::Biblio::new method, not this one.
Title : get_next Usage : $xml = $biblio->get_next(); Function: return next record as xml Returns : an xml string Args : none
Title : find Usage : $biblio = $biblio->find(1234); Function: perform a PubMed query by PubMed ID Returns : a reference to the object on which the method was called Args : a PubMed ID
Title : exists Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
Title : destroy Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
Title : get_vocabulary_names Usage : do not use Function: no-op. this is here only for interface compatibility Returns : empty arrayref Args : none
Title : contains Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
Title : get_entry_description Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
Title : get_all_values Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
Title : get_all_entries Usage : do not use Function: no-op. this is here only for interface compatibility Returns : undef Args : none
Usage : $obj->depth($newval) Function: track link recursion depth Example : Returns : value of depth (a scalar) Args : on set, new value (a scalar or undef, optional)
Usage : $obj->max_depth($newval) Function: how far should link recursion go? Example : Returns : value of max_depth (a scalar) Args : on set, new value (a scalar or undef, optional)
Usage : $obj->ua($newval) Function: holds an LWP::UserAgent instance Example : Returns : value of ua (a scalar) Args : on set, new value (a scalar or undef, optional)
Usage : $obj->pdf($newval) Function: holds pdf data Example : Returns : value of pdf (a scalar) Args : on set, new value (a scalar or undef, optional)
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.