orgBase

scripts/downloadOrg.pl

@@ -0,0 +1,47 @@
+# This script downloads all viral genomes in RefSeq and puts them in viruses.fa
+# Script is taken from: http://www.ncbi.nlm.nih.gov/books/NBK25498/#chapter3.Application_3_Retrieving_large 
+# BY INTERFACE NCBI: http://www.ncbi.nlm.nih.gov/nuccore?term=%22Viruses%22[PORG]+AND+srcdb_refseq[PROP] , then sent to file: fasta.
+
+use LWP::Simple;
+
+
+$organism = 'Escherichia coli';
+
+$query = $organism.'[orgn]';
+#$query = $organism.'[orgn]+AND+srcdb_refseq[prop]';
+print STDERR "Searching RefSeq for $organism: $query\n";
+#assemble the esearch URL
+$base = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/';
+$url = $base . "esearch.fcgi?db=genome&term=$query&usehistory=y";
+
+#post the esearch URL
+$output = get($url);
+
+#parse WebEnv, QueryKey and Count (# records retrieved)
+$web = $1 if ($output =~ /<WebEnv>(\S+)<\/WebEnv>/);
+$key = $1 if ($output =~ /<QueryKey>(\d+)<\/QueryKey>/);
+$count = $1 if ($output =~ /<Count>(\d+)<\/Count>/);
+
+print STDERR "Found: $count records for $organism\n";
+if($count == 0) {
+    exit(0);
+}
+
+#open output file for writing
+open(OUT, ">tmp.$organism.fa") || die "Can't open file!\n";
+
+#retrieve data in batches of 500
+$retmax = 1;
+for ($ret = 0; $ret < $count; ) {
+    $efetch_url = $base ."efetch.fcgi?dbfrom=genome&db=nuccore&WebEnv=$web";
+    $efetch_url .= "&query_key=$key&retstart=$ret";
+    $efetch_url .= "&retmax=$retmax&rettype=fasta&retmode=text";
+    $efetch_out = get($efetch_url);
+    $actual_sequences_returned = $efetch_out =~ s/>/\n>/g;  # count number of sequences returned
+    $ret += $actual_sequences_returned;
+    print OUT "$efetch_out";
+    print STDERR "Fetched $ret\n";
+}
+close OUT;
+
+rename("tmp.$organism.fa", "$organism.fa");