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#!/usr/bin/perl
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# PREP (Perl RegExps for Pubmed) is a script that allows the use of
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# Perl regexs in the searching of Pubmed records, providing the ability to search
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# records for textual patterns as well as keywords
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# Copyright 2005- Christopher M. Frenz
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# This script is free sofware it may be used, copied, redistributed, and/or modified
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# under the terms laid forth in the Perl Artisic License
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# Please cite this script in any publication in which literature cited within the
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# publication was located using the PREP.pl script.
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# Usage: perl PREPv1-0.pl PubmedQueryTerms
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# Usage of this script requires the LWP and XML::LibXML modules are installed
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use LWP;
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use XML::LibXML; #Version 1.58 used for development and testing
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# Change the variable below to set the text pattern that Perl
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# will seek to match in the returned results
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my $regex='[ARNDCEQGHILKMFPSTWYV]\d+[ARNDCEQGHILKMFPSTWYV]'; |
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my $request;
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my $response;
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my $query;
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# Concatenates arguments passed to script to form Pubmed query
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$query=join(" ", @ARGV);
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# Creates the URL to search Pubmed
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my $baseurl="http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?";
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my $url=$baseurl . "db=Pubmed&retmax=1&usehistory=y&term=" . $query;
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# Searches Pubmed and Returns the number of results
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# as well as the session information needed for results retrieval
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$request=LWP::UserAgent->new();
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$response=$request->get($url);
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my $results= $response->content;
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die unless $response->is_success;
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print "PubMed Search Results \n";
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$results=~/<Count>(\d+)<\/Count>/;
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my $NumAbstracts=$1;
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$results=~/<QueryKey>(\d+)<\/QueryKey>/;
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my $QueryKey=$1;
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$results=~/<WebEnv>(.*?)<\/WebEnv>/;
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my $WebEnv=$1;
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print "$NumAbstracts are Available \n";
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print "Query Key= $QueryKey \n";
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print "WebEnv= $WebEnv \n";
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# Opens a file for output
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open(OFile, ">PREPout.html");
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my $parser=XML::LibXML->new;
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my $retmax=500; #Number of records to be retrieved per request-Max 500
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my $retstart=0; #Record number to start retreival from
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# Creates the URL needed to retrieve results
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$baseurl="http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?"; |
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my $url2="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids="; |
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my $Count=0;
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# Retreives results in XML format
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for($retstart=0;$retstart<=$NumAbstracts;$retstart+=$retmax){
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print "Processing record # $retstart \n";
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$url=$baseurl . "rettype=abstract&retmode=xml&retstart=$retstart&retmax=$retmax&db=Pubmed&query_key=$QueryKey&WebEnv=$WebEnv";
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$response=$request->get($url);
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$results=$response->content;
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die unless $response->is_success;
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# Uses a DOM based XML parser to process returned results
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my $domtree=$parser->parse_string($results);
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@Records=$domtree->getElementsByTagName("PubmedArticle"); |
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my $i=0;
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foreach(@Records){ |
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# Extracts element data for regex processing and output formatting |
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$titles=$Records[$i]->getElementsByTagName("ArticleTitle"); |
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$journals=$Records[$i]->getElementsByTagName("MedlineTA"); |
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$volumes=$Records[$i]->getElementsByTagName("Volume"); |
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$pgnums=$Records[$i]->getElementsByTagName("MedlinePgn"); |
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$abstracts=$Records[$i]->getElementsByTagName("AbstractText"); |
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$IDS=$Records[$i]->getElementsByTagName("PMID"); |
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# Processes title and abstract for pattern match and if a match occurs
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# data is written to output
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if($titles=~/($regex)/ or $abstracts=~/($regex)/){
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print OFile "<h1>Pattern Match: $1 </h1>\n";
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print OFile "<h3><a href=\"$url2$IDS\">$titles </a></h3> \n";
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print OFile "<p>$journals $volumes, $pgnums </p>\n";
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print OFile "<p>$abstracts </p>\n\n";
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$Count=$Count+1;
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}
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$i=$i+1;
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}
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}
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close OFile;
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print "$Count records matched the pattern";
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