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 e4c206e8707b198316965cdae4208124466602ad..dec35bfb95766397955044f3a9ee57fd77f02198 100755 (executable)
--- a/bp_bin/upload_to_ucsc
+++ b/bp_bin/upload_to_ucsc
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,6 +26,7 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Common;
 use Maasha::Biopieces;
@@ -39,7 +40,7 @@ use Maasha::UCSC::BED;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $tmp_dir, $file, $wib_file, $wig_file, $wib_dir, $fh_out, $i, $first, $format, $type, $columns, $append, $entry );
+my ( $options, $in, $out, $record, $tmp_dir, $file, $wib_file, $wig_file, $wib_dir, $fh_out, $i, $first, $format, $type, $columns, $append, $entry );
 
 $options = Maasha::Biopieces::parse_options(
     [
@@ -157,9 +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;
@@ -180,19 +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" )
 {
@@ -219,14 +220,15 @@ 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;
 
 Maasha::UCSC::ucsc_update_config( $options, $type );
 
-Maasha::Filesys::dir_remove( $tmp_dir );
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -234,20 +236,13 @@ Maasha::Filesys::dir_remove( $tmp_dir );
 
 BEGIN
 {
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
+    Maasha::Biopieces::status_set();
 }
 
 
 END
 {
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+    Maasha::Biopieces::status_log();
 }
 
 
@@ -255,4 +250,3 @@ END
 
 
 __END__
-