migrated plot_chrdist

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

diff --git a/code_perl/Maasha/Plot.pm b/code_perl/Maasha/Plot.pm
index 70fa3159bd2fc2c5eb29ea5aae4094ac0ba9e784..07673c17d4cc151eacb37893aff18b735986d531 100644 (file)
--- a/code_perl/Maasha/Plot.pm
+++ b/code_perl/Maasha/Plot.pm
@@ -32,9 +32,9 @@ use strict;
 use Data::Dumper;
 use SVG;
 use IPC::Open2;
-use Time::HiRes qw( gettimeofday );
 use Maasha::Common;
-use Maasha::Calc;
+use Maasha::Filesys;
+use Maasha::Seq;
 use vars qw ( @ISA @EXPORT );
 
 use constant {
@@ -71,7 +71,7 @@ sub lineplot_simple
 
     $tmp_file = "$tmp_dir/lineplot_simple.tab";
 
-    $fh_out = Maasha::Common::write_open( $tmp_file );
+    $fh_out = Maasha::Filesys::file_write_open( $tmp_file );
 
     map { print $fh_out join( "\t", @{ $_ } ), "\n" } @{ $data };
 
@@ -337,8 +337,8 @@ sub dotplot_matches
     $forward_file  = "$tmp_dir/match_f.tab";
     $backward_file = "$tmp_dir/match_r.tab";
 
-    $fh_forward  = Maasha::Common::write_open( $forward_file );
-    $fh_backward = Maasha::Common::write_open( $backward_file );
+    $fh_forward  = Maasha::Filesys::file_write_open( $forward_file );
+    $fh_backward = Maasha::Filesys::file_write_open( $backward_file );
 
     $q_max = 0;
     $s_max = 0;
@@ -491,7 +491,7 @@ sub parse_karyo_data
 #        stalk    => "gray66",
     );
 
-    $fh = Maasha::Common::read_open( $file );
+    $fh = Maasha::Filesys::file_read_open( $file );
 
     while ( $line = <$fh> )
     {