added --verbose run option for blast_seq

[biopieces.git] / code_perl / Maasha / Biopieces.pm

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index ce308a3ebcba15cd00ea1c9ef68bfb098e88e0e3..072846c1783f29aafe88befbec10dcdbe357e888 100644 (file)
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -3473,7 +3473,41 @@ sub script_blast_seq
         }
     }
 
-    Maasha::Common::run( "blastall", "-p $options->{ 'program' } -e $options->{ 'e_val' } -a $options->{ 'cpus' } -m 8 -i $tmp_in -d $options->{ 'database' } -F $options->{ 'filter' } -o $tmp_out > /dev/null 2>&1", 1 );
+    if ( $options->{ 'verbose' } )
+    {
+        Maasha::Common::run(
+            "blastall",
+            join( " ",
+                "-p $options->{ 'program' }",
+                "-e $options->{ 'e_val' }",
+                "-a $options->{ 'cpus' }",
+                "-m 8",
+                "-i $tmp_in",
+                "-d $options->{ 'database' }",
+                "-F $options->{ 'filter' }",
+                "-o $tmp_out",
+            ),
+            1
+        );
+    }
+    else
+    {
+        Maasha::Common::run(
+            "blastall",
+            join( " ",
+                "-p $options->{ 'program' }",
+                "-e $options->{ 'e_val' }",
+                "-a $options->{ 'cpus' }",
+                "-m 8",
+                "-i $tmp_in",
+                "-d $options->{ 'database' }",
+                "-F $options->{ 'filter' }",
+                "-o $tmp_out",
+                "> /dev/null 2>&1"
+            ),
+            1
+        );
+    }
 
     unlink $tmp_in;