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Christopher Fields
Documentation
bp_einfo.pl - query einfo to find all available databases or information about a specific database (field information or links to other NCBI databases)
bp_genbank_ref_extractor - retrieves all related sequences for a list of searches on Entrez gene
Modules
Bio::DB::EUtilities - Webagent which interacts with and retrieves data from NCBI's eUtils.
Bio::Tools::EUtilities - NCBI eutil XML parsers.
Bio::Tools::EUtilities::EUtilDataI - EUtil data object interface.
Bio::Tools::EUtilities::EUtilParameters - Manipulation of NCBI eutil-based parameters for remote database requests.
Bio::Tools::EUtilities::History - Lightweight implementation of HistoryI interface (not bound to filehandles, extraneous methods, etc).
Bio::Tools::EUtilities::HistoryI - Simple extension of EUtilDataI interface class for classes which hold NCBI server history data.
Bio::Tools::EUtilities::Info - Interface class for storing einfo data.
Bio::Tools::EUtilities::Info::FieldInfo - Class for storing einfo field data.
Bio::Tools::EUtilities::Info::LinkInfo - Class for storing einfo link data.
Bio::Tools::EUtilities::Link - General API for accessing data retrieved from elink queries.
Bio::Tools::EUtilities::Link::LinkSet - Class for EUtils LinkSets.
Bio::Tools::EUtilities::Link::UrlLink - Class for EUtils UrlLinks.
Bio::Tools::EUtilities::Query - Parse and collect esearch, epost, espell, egquery information.
Bio::Tools::EUtilities::Query::GlobalQuery - Container class for egquery data.
Bio::Tools::EUtilities::Summary - Class for handling data output (XML) from esummary.
Bio::Tools::EUtilities::Summary::DocSum - Data object for document summary data from esummary.
Bio::Tools::EUtilities::Summary::Item - Simple layered object for DocSum item data.
Bio::Tools::EUtilities::Summary::ItemContainerI - Abtract interface methods for accessing Item information from any Item-containing class. This pertains to either DocSums or to Items themselves (which can be layered).
Changes for version 1.73
  • LWP::UserAgent is required for Bio::DB::EUtilities, now added
  • New script for download of all sequences from Entrez Gene queries



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