fixed s/Common/Filesys/ renaming in UCSC.pm

git-svn-id: http://biopieces.googlecode.com/svn/trunk@984 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_perl/Maasha/UCSC.pm b/code_perl/Maasha/UCSC.pm
index 5c188fd1ffbaa800cf5dd42cb8238297b4c0728d..26645133da231e76138f07ecf724df6a14470f2d 100644 (file)
--- a/code_perl/Maasha/UCSC.pm
+++ b/code_perl/Maasha/UCSC.pm
@@ -214,7 +214,7 @@ sub bed_get_entries
 
     my ( $fh, $entry, @list );
 
-    $fh = Maasha::Common::read_open( $path );
+    $fh = Maasha::Filesys::file_read_open( $path );
 
     while ( $entry = bed_get_entry( $fh ) ) {
         push @list, $entry;
@@ -438,7 +438,7 @@ sub bed_sort
          $cols,        # Number of columns in BED file
        ) = @_;
 
-    &Maasha::Common::run( "bed_sort", "--sort $sort_mode --cols $cols $bed_file" );
+    Maasha::Common::run( "bed_sort", "--sort $sort_mode --cols $cols $bed_file" );
 }
 
 
@@ -461,13 +461,13 @@ sub bed_split_to_files
 
     foreach $bed_file ( @{ $bed_files } )
     {
-        $fh_in = Maasha::Common::read_open( $bed_file );
+        $fh_in = Maasha::Filesys::file_read_open( $bed_file );
 
         while ( $entry = bed_entry_get_array( $fh_in, $cols ) )
         {
             $key = $entry->[ CHR ];
 
-            $fh_hash{ $key } = Maasha::Common::write_open( "$tmp_dir/$key.temp" ) if not exists $fh_hash{ $key };
+            $fh_hash{ $key } = Maasha::Filesys::file_write_open( "$tmp_dir/$key.temp" ) if not exists $fh_hash{ $key };
             
             bed_entry_put_array( $entry, $fh_hash{ $key } );
         }
@@ -650,7 +650,7 @@ sub bed_upload_to_ucsc
 
         $sql_file = "$tmp_dir/upload_RNA_SS.sql";
 
-        $fh_out   = Maasha::Common::write_open( $sql_file );
+        $fh_out   = Maasha::Filesys::file_write_open( $sql_file );
 
         print $fh_out qq(
 CREATE TABLE $table (
@@ -913,7 +913,7 @@ sub fixedstep_index_create
 
     my ( $fh, $pos, $index_beg, $index_len, $entry, $locator, $chr, $step, $beg, $end, $len, %index, $i );
 
-    $fh = Maasha::Common::read_open( $path );
+    $fh = Maasha::Filesys::file_read_open( $path );
 
     $pos = 0;
 
@@ -972,7 +972,7 @@ sub fixedstep_index_store
 
     # returns nothing
 
-    Maasha::Common::file_store( $path, $index );
+    Maasha::Filesys::file_store( $path, $index );
 }
 
 
@@ -989,7 +989,7 @@ sub fixedstep_index_retrieve
 
     my $index;
 
-    $index = Maasha::Common::file_retrieve( $path );
+    $index = Maasha::Filesys::file_retrieve( $path );
 
     return wantarray ? %{ $index } : $index;
 }
@@ -1052,7 +1052,7 @@ sub fixedstep_index_lookup
         
             if ( $beg <= $index->{ $chr }->[ $index_beg ]->[ FS_CHR_END ] and $end >= $index->{ $chr }->[ $index_beg ]->[ FS_CHR_BEG ] )
             {
-                @vals = split "\n", Maasha::Common::file_read(
+                @vals = split "\n", Maasha::Filesys::file_read(
                     $fh,
                     $index->{ $chr }->[ $index_beg ]->[ FS_INDEX_BEG ] + 6 * ( $beg - $index->{ $chr }->[ $index_beg ]->[ FS_CHR_BEG ] ),
                     6 * ( $end - $beg + 1 ),
@@ -1076,7 +1076,7 @@ sub fixedstep_index_lookup
 
             if ( $beg <= $index->{ $chr }->[ $index_beg ]->[ FS_CHR_END ] )
             {
-                @vals = split "\n", Maasha::Common::file_read(
+                @vals = split "\n", Maasha::Filesys::file_read(
                     $fh,
                     $index->{ $chr }->[ $index_beg ]->[ FS_INDEX_BEG ] + 6 * ( $beg - $index->{ $chr }->[ $index_beg ]->[ FS_CHR_BEG ] ),
                     6 * ( $index->{ $chr }->[ $index_beg ]->[ FS_CHR_END ] - $beg + 1 ),
@@ -1091,7 +1091,7 @@ sub fixedstep_index_lookup
 
             if ( $end <= $index->{ $chr }->[ $index_end ]->[ FS_CHR_END ] )
             {
-                @vals = split "\n", Maasha::Common::file_read(
+                @vals = split "\n", Maasha::Filesys::file_read(
                     $fh,
                     $index->{ $chr }->[ $index_end ]->[ FS_INDEX_BEG ],
                     6 * ( $end - $index->{ $chr }->[ $index_end ]->[ FS_CHR_BEG ] + 1 ),
@@ -1104,7 +1104,7 @@ sub fixedstep_index_lookup
 
             for ( $i = $index_beg + 1; $i <= $index_end - 1; $i++ )
             {
-                @vals = split "\n", Maasha::Common::file_read(
+                @vals = split "\n", Maasha::Filesys::file_read(
                     $fh,
                     $index->{ $chr }->[ $i ]->[ FS_INDEX_BEG ],
                     6 * ( $index->{ $chr }->[ $i ]->[ FS_CHR_END ] - $index->{ $chr }->[ $i ]->[ FS_CHR_BEG ] + 1 ),
@@ -1484,7 +1484,7 @@ sub maf_parse
 
     my ( $fh, $line, @fields, @align );
 
-    $fh = Maasha::Common::read_open( $path );
+    $fh = Maasha::Filesys::file_read_open( $path );
 
     while ( $line = <$fh> )
     {
@@ -1588,7 +1588,7 @@ sub ucsc_get_user
 
     return if not -f $file;
 
-    $fh = Maasha::Common::read_open( $file );
+    $fh = Maasha::Filesys::file_read_open( $file );
 
     while ( $line = <$fh> )
     {
@@ -1623,7 +1623,7 @@ sub ucsc_get_password
 
     return if not -f $file;
 
-    $fh = Maasha::Common::read_open( $file );
+    $fh = Maasha::Filesys::file_read_open( $file );
 
     while ( $line = <$fh> )
     {