downloadKalamari.pl: add in retmax 1

lskatz · Apr 10, 2024 · 7db4a76 · 7db4a76
1 parent 58a7c3e
commit 7db4a76
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/bin/downloadKalamari.pl b/bin/downloadKalamari.pl
@@ -79,7 +79,8 @@ sub downloadEntry{
   # Get the esearch xml in place for at least one downstream query
   my $esearchXml = "$dir/$acc.esearch.xml";
   if(! -e $esearchXml){
-    system("esearch -db nuccore -query '$acc' > $esearchXml.tmp");
+    # -retmax 1 to help avoid refseq/INSDC conflation
+    system("esearch -db nuccore -query '$acc' -retmax 1 > $esearchXml.tmp");
     if($?){
       die "ERROR running esearch: $!";
     }