refactoring of assemble_pairs

[biopieces.git] / bp_bin / plot_phastcons_profiles

diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles
index 0fb79d133ecc977689ee70d475e72e3ceaeac943..a72c46bf93a06a8b50136381bd3dcf4df4f581f2 100755 (executable)
--- a/bp_bin/plot_phastcons_profiles
+++ b/bp_bin/plot_phastcons_profiles
@@ -33,6 +33,7 @@ use Maasha::Plot;
 use Maasha::Matrix;
 use Maasha::Filesys;
 use Maasha::UCSC;
+use Maasha::UCSC::Wiggle;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -66,14 +67,14 @@ $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 $phastcons_file  = Maasha::Config::genome_phastcons( $options->{ "genome" } );
 $phastcons_index = Maasha::Config::genome_phastcons_index( $options->{ "genome" } );
 
-$index           = Maasha::UCSC::fixedstep_index_retrieve( $phastcons_index );
+$index           = Maasha::UCSC::Wiggle::fixedstep_index_retrieve( $phastcons_index );
 $fh_phastcons    = Maasha::Filesys::file_read_open( $phastcons_file );
 
 while ( $record = Maasha::Biopieces::get_record( $in ) ) 
 {
     if ( $record->{ "CHR" } and $record->{ "CHR_BEG" } and $record->{ "CHR_END" } )
     {
-        $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" },
+        $scores = Maasha::UCSC::Wiggle::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" },
                                                                                $record->{ "CHR_BEG" },
                                                                                $record->{ "CHR_END" },
                                                                                $options->{ "flank" } );