Fix for exonerate 2.2.0 that looks to have problems with target filename containing :

ProtoGene.pl

@@ -381,7 +381,7 @@ for(my $r=0; $r<=$#original_names; $r++){
                         download_seq($cache, $amont, $aval, $chr);
                         $intronStep = 1;
 
-                        unshift(@nt_GIs, "$chr:$amont-$aval");
+                        unshift(@nt_GIs, "$chr-$amont-$aval");
                     }
                 }
             }
@@ -1016,19 +1016,19 @@ sub download_seq{
         }
 
         if ( $amont =~ /^\d+$/ && $aval =~ /^\d+$/ ){
-            fetch_fasta("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$pacc2puid&rettype=fasta&retmode=text&from=$amont&to=$aval&tool=ProtoGene&email=smoretti\@unil.ch", "$cache/$acc[$a]:$from-$to.fas");
+            fetch_fasta("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$pacc2puid&rettype=fasta&retmode=text&from=$amont&to=$aval&tool=ProtoGene&email=smoretti\@unil.ch", "$cache/$acc[$a]-$from-$to.fas");
         }
         else{
             fetch_fasta("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$pacc2puid&rettype=fasta&retmode=text&tool=ProtoGene&email=smoretti\@unil.ch", "$cache/$acc[$a].fas");
         }
 
-        #FIXME: Don't remember exactly what all this function does
+        #FIXME Don't remember exactly what all this function does
         my $checkSeq = '';
-        $checkSeq    = `grep -v '>' "$cache/$acc[$a]:$from-$to.fas"` if ( $amont =~ /^\d+$/ && $aval =~ /^\d+$/ );
+        $checkSeq    = `grep -v '>' "$cache/$acc[$a]-$from-$to.fas"` if ( $amont =~ /^\d+$/ && $aval =~ /^\d+$/ );
         $checkSeq    = `grep -v '>' "$cache/$acc[$a].fas"`           if ( $amont !~ /^\d+$/ || $aval !~ /^\d+$/ );
         if ( $checkSeq !~ /^[A-Za-z]/ && $cp==0 ){
 #       if ( -s "$cache/$acc[$a]:$from-$to.fas" <120 && $cp==0){ #Instead of multiple downloads, only seq name and header
-            unlink("$cache/$acc[$a]:$from-$to.fas") if ( $amont =~ /^\d+$/ && $aval =~ /^\d+$/ );
+            unlink("$cache/$acc[$a]-$from-$to.fas") if ( $amont =~ /^\d+$/ && $aval =~ /^\d+$/ );
             unlink("$cache/$acc[$a].fas")           if ( $amont !~ /^\d+$/ || $aval !~ /^\d+$/ );
 #           $amont = '';
             $aval  = $aval - 5000 if ( $aval =~ /^\d+$/ );