X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fplot_phastcons_profiles;h=a72c46bf93a06a8b50136381bd3dcf4df4f581f2;hb=48bea5c28b89dc5586d0bddb338ccd6ba23aa1f9;hp=52489f5c5e668539c1ab491f19bade47951e8702;hpb=c11bd52c815bb8ad844ef837d41c9b5aa0bc2bdb;p=biopieces.git

diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles
index 52489f5..a72c46b 100755
--- a/bp_bin/plot_phastcons_profiles
+++ b/bp_bin/plot_phastcons_profiles
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
 
 # Copyright (C) 2007-2009 Martin A. Hansen.
 
@@ -26,18 +26,20 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
+use warnings;
 use strict;
 use Maasha::Biopieces;
 use Maasha::Plot;
 use Maasha::Matrix;
 use Maasha::Filesys;
 use Maasha::UCSC;
+use Maasha::UCSC::Wiggle;
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $default, $terminals, $phastcons_file, $phastcons_index,
+my ( $options, $in, $out, $default, $terminals, $phastcons_file, $phastcons_index,
      $index, $fh_phastcons, $record, $scores, $AoA, $plot, $fh, $tmp_dir );
 
 $default   = "PhastCons Profiles";
@@ -45,16 +47,17 @@ $terminals = "dumb,x11,aqua,post,svg";
 
 $options = Maasha::Biopieces::parse_options(
     [
-        { long => 'no_stream', short => 'x', type => 'flag',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
-        { long => 'data_out',  short => 'o', type => 'file',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
-        { long => 'genome',    short => 'g', type => 'genome', mandatory => 'yes', default => undef,    allowed => undef,      disallowed => undef },
-        { long => 'mean',      short => 'm', type => 'flag',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
-        { long => 'median',    short => 'M', type => 'flag',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
-        { long => 'flank',     short => 'f', type => 'uint',   mandatory => 'no',  default => 0,        allowed => undef,      disallowed => undef },
-        { long => 'terminal',  short => 't', type => 'string', mandatory => 'no',  default => 'dumb',   allowed => $terminals, disallowed => undef },
-        { long => 'title',     short => 'T', type => 'string', mandatory => 'no',  default => $default, allowed => undef,      disallowed => undef },
-        { long => 'xlabel',    short => 'X', type => 'string', mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
-        { long => 'ylabel',    short => 'Y', type => 'string', mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'no_stream',  short => 'x', type => 'flag',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'data_out',   short => 'o', type => 'file',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'genome',     short => 'g', type => 'genome', mandatory => 'yes', default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'mean',       short => 'm', type => 'flag',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'median',     short => 'M', type => 'flag',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'flank',      short => 'f', type => 'uint',   mandatory => 'no',  default => 0,        allowed => undef,      disallowed => undef },
+        { long => 'terminal',   short => 't', type => 'string', mandatory => 'no',  default => 'dumb',   allowed => $terminals, disallowed => undef },
+        { long => 'title',      short => 'T', type => 'string', mandatory => 'no',  default => $default, allowed => undef,      disallowed => undef },
+        { long => 'xlabel',     short => 'X', type => 'string', mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'ylabel',     short => 'Y', type => 'string', mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'logscale_y', short => 'L', type => 'flag',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
     ]   
 );
 
@@ -64,14 +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" } );
@@ -99,7 +102,8 @@ print $fh "$_\n" foreach @{ $plot };
 
 close $fh;
 
-Maasha::Filesys::dir_remove( $tmp_dir );
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
@@ -107,20 +111,13 @@ 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();
 }
 
 
@@ -128,4 +125,3 @@ END
 
 
 __END__
-