Fixes for blast db name change at IGS

runblast.pl

@@ -114,7 +114,7 @@ sub Usage{
     print {*STDERR} "
 
 
- $0 -d refprot -p blastp -i fasta_file
+ $0 -d refseq_protein -p blastp -i fasta_file
 
     Options disponibles:
       -i input multifasta file
@@ -141,7 +141,7 @@ sub Usage{
             mtimonensis
             nr
             pdbaa
-            refprot
+            refseq_protein
             sprot
             sptr
             sptr_nr_ncbi_v => swissprot + trembl avec entete taxonomique

webblast.pl

@@ -271,8 +271,8 @@ sub HELP {
                             -quiet ........ on : do not display all the default/defined blast parameters
                                             Default off
 
-                     Environement Variables
-                     These variables can be set from the environement
+                     Environment Variables
+                     These variables can be set from the environment
            DATABASE......................[Indicates where your database file must be fetched (locally)]
            BLAST_DIRECTORY...............[Indicates where your BLAST directory is installed locally]
 
@@ -479,7 +479,7 @@ sub WEB_BLAST {
                 last;
             }
             elsif ( $response->content =~ /Status=UNKNOWN/im ){
-                print {*STDERR} "Search $rid expired\n";
+                print {*STDERR} "Search  [$rid]  expired\n";
                 $verif = 1;
                 last;
             }
@@ -557,7 +557,7 @@ sub LOCAL_BLAST
             print {*STDERR} "\nsorry invalid database for gigablast\n";exit 1;
         }
         if ( $database eq 'pdb')            { $database = 'pdbaa';}
-        if ( $database eq 'refseq_protein') { $database = 'refprot';}
+#        if ( $database eq 'refseq_protein') { $database = 'refseq_protein';}
         if ( $database eq '')               { print {*STDERR} "provide a valid database!\n"; exit;}
         open (COM,"$runblast -d $database -p blastp  -e $Eval -v $align -F F \<$query_file |");
     }