From 25a82ef79b3c81a23e427929780f4ca044d6e2b5 Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 25 May 2010 10:07:32 +0000
Subject: [PATCH] added plot_scores

git-svn-id: http://biopieces.googlecode.com/svn/trunk@968 74ccb610-7750-0410-82ae-013aeee3265d
---
 bp_bin/plot_scores | 131 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 131 insertions(+)
 create mode 100755 bp_bin/plot_scores

diff --git a/bp_bin/plot_scores b/bp_bin/plot_scores
new file mode 100755
index 0000000..bfd9584
--- /dev/null
+++ b/bp_bin/plot_scores
@@ -0,0 +1,131 @@
+#!/usr/bin/env perl
+
+# Copyright (C) 2007-2010 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Create a lineplot from quality scores in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Maasha::Fastq;
+use Maasha::Plot;
+use Maasha::Calc;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $default, $terminals, $formats, $record, %count_hash, %sum_hash, $i, @scores, @data_list, $result, $fh, $tmp_dir );
+
+$default   = "Quality Scores";
+$terminals = "dumb,x11,aqua,post,svg";
+$formats   = "solexa,phred,decimal";
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'no_stream',  short => 'x', type => 'flag',   mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'format'  ,   short => 'f', type => 'string', mandatory => 'no',  default => "solexa", allowed => $formats,   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 => $default, allowed => undef,      disallowed => undef },
+        { long => 'xlabel',     short => 'X', type => 'string', mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+        { long => 'ylabel',     short => 'Y', type => 'string', mandatory => 'no',  default => undef,    allowed => undef,      disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( $record->{ 'SCORES' } )
+    {
+        if ( $options->{ 'format' } eq "solexa" )
+        {
+            for ( $i = 0; $i < length $record->{ 'SCORES' }; $i++ )
+            {
+                $count_hash{ $i }++;
+                $sum_hash{ $i } += Maasha::Fastq::solexa2dec( substr $record->{ "SCORES" }, $i, 1 );
+            }
+        }
+        elsif ( $options->{ 'format' } eq "phred" )
+        {
+            for ( $i = 0; $i < length $record->{ 'SCORES' }; $i++ )
+            {
+                $count_hash{ $i }++;
+                $sum_hash{ $i } += Maasha::Fastq::phred2dec( substr $record->{ "SCORES" }, $i, 1 );
+            }
+        }
+        else
+        {
+            @scores = split ";", $record->{ 'SCORES' };
+
+            for ( $i = 0; $i < @scores; $i++ )
+            {
+                $count_hash{ $i }++;
+                $sum_hash{ $i } += $scores[ $i ];
+            }
+        }
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+for ( $i = 0; $i < keys %count_hash; $i++ ) {
+    push @data_list, [ $sum_hash{ $i } / $count_hash{ $i } ];
+}
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+
+$result = Maasha::Plot::lineplot_simple( \@data_list, $options, $tmp_dir );
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
+
+print $fh "$_\n" foreach @{ $result };
+
+close $fh;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
-- 
2.39.2