clearning up kmer_stats and kmer_freq

[biopieces.git] / bp_bin / blast_seq

diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq
index be2b8163cd99bdc6e2f9f7f8da14d4f4bda37a0f..ccca6d42838da08b69ce4d65719d399098f35994 100755 (executable)
--- a/bp_bin/blast_seq
+++ b/bp_bin/blast_seq
@@ -174,10 +174,10 @@ sub guess_database_type
     # a .phr file exists.
 
     # Returns string;
-    if ( -f $options->{ 'database' } . ".phr" ) {
-        return "protein";
+    if ( -f $options->{ 'database' } . ".phr" or -f $options->{ 'database' } . ".pal" ) {
+        return "PROTEIN";
     } else {
-        return "nucleotide";
+        return "NUCLEOTIDE";
     }
 }
 
@@ -197,13 +197,13 @@ sub guess_program
 
     my ( $program );
 
-    if ( $q_type      ne "protein" and $s_type ne "protein" ) {
+    if ( $q_type      ne "PROTEIN" and $s_type ne "PROTEIN" ) {
         $program = "blastn";
-    } elsif ( $q_type eq "protein" and $s_type eq "protein" ) {
+    } elsif ( $q_type eq "PROTEIN" and $s_type eq "PROTEIN" ) {
         $program = "blastp";
-    } elsif ( $q_type ne "protein" and $s_type eq "protein" ) {
+    } elsif ( $q_type ne "PROTEIN" and $s_type eq "PROTEIN" ) {
         $program = "blastx";
-    } elsif ( $q_type eq "protein" and $s_type ne "protein" ) {
+    } elsif ( $q_type eq "PROTEIN" and $s_type ne "PROTEIN" ) {
         $program = "tblastn";
     }