-#!/usr/bin/env perl -w
+#!/usr/bin/env perl
# Copyright (C) 2007-2009 Martin A. Hansen.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+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";
$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 },
]
);
$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" } );
close $fh;
-Maasha::Filesys::dir_remove( $tmp_dir );
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
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();
}
__END__
-