refactoring of assemble_pairs

[biopieces.git] / bp_bin / upload_to_ucsc

diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc
index aac49282267a919c50d2fb82380fc6bfa1241352..dec35bfb95766397955044f3a9ee57fd77f02198 100755 (executable)
--- a/bp_bin/upload_to_ucsc
+++ b/bp_bin/upload_to_ucsc
@@ -158,9 +158,9 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
         close $fh_out;
 
         if ( $format eq "BED" ) {
-            Maasha::UCSC::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
+            Maasha::UCSC::BED::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
         } elsif ( $format eq "PSL" ) {
-            Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append ); 
+            Maasha::UCSC::BED::psl_upload_to_ucsc( $file, $options, $append ); 
         }
 
         unlink $file;
@@ -181,19 +181,19 @@ if ( $format eq "BED" )
 {
     $type = "bed $columns";
 
-    Maasha::UCSC::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
+    Maasha::UCSC::BED::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
 }
 elsif ( $format eq "BED_SS" )
 {
     $type = "type bed 6 +";
 
-    Maasha::UCSC::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
+    Maasha::UCSC::BED::bed_upload_to_ucsc( $tmp_dir, $file, $options, $append );
 }
 elsif ( $format eq "PSL" )
 {
     $type = "psl";
 
-    Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append ); 
+    Maasha::UCSC::PSL::psl_upload_to_ucsc( $file, $options, $append ); 
 }
 elsif ( $format eq "WIGGLE" )
 {
@@ -220,7 +220,7 @@ elsif ( $format eq "WIGGLE" )
 
     $type = "wig 0";
 
-    Maasha::UCSC::wiggle_upload_to_ucsc( $tmp_dir, $wib_dir, $file, $options );
+    Maasha::UCSC::Wiggle::wiggle_upload_to_ucsc( $tmp_dir, $wib_dir, $file, $options );
 }
 
 unlink $file;