refactoring of assemble_pairs

[biopieces.git] / bp_bin / analyze_vals

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
index 4cd1d4413a253b7338666f848168a0f9929fba03..726c91c53c62f5c22560b77260f45d094340b018 100755 (executable)
--- a/bp_bin/analyze_vals
+++ b/bp_bin/analyze_vals
@@ -1,6 +1,161 @@
 #!/usr/bin/env perl
 
+# Copyright (C) 2007-2009 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Determine type, count, min, max, sum and mean for values in stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
-
 use Maasha::Biopieces;
+use Maasha::Calc;
+use Data::Dumper;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $analysis, $key, $len, %skip_hash, $data_out,
+     %key_hash, $skip, $keys, $types, $counts, $mins, $maxs, $sums, $means );
+
+$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 => 'keys',      short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'no_keys',   short => 'K', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$data_out = Maasha::Biopieces::write_stream( $options->{ "data_out" }, $options->{ "compress" } );
+$data_out ||= \*STDOUT;
+
+map { $skip_hash{ $_ } = 1 } @{ $options->{ "no_keys" } };
+map { $key_hash{ $_ } = 1; $skip = 1 } @{ $options->{ "keys" } };
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    foreach $key ( keys %{ $record } )
+    {
+        next if $skip and not exists $key_hash{ $key };
+        next if $skip_hash{ $key };
+
+        if ( Maasha::Calc::is_a_number( $record->{ $key } ) )
+        {
+            if ( not exists $analysis->{ $key } )
+            {
+                $analysis->{ $key }->{ "MIN" } = $record->{ $key };
+                $analysis->{ $key }->{ "MAX" } = $record->{ $key };
+            }
+
+            $analysis->{ $key }->{ "MAX" } = Maasha::Calc::max( $analysis->{ $key }->{ "MAX" }, $record->{ $key } );
+            $analysis->{ $key }->{ "MIN" } = Maasha::Calc::min( $analysis->{ $key }->{ "MIN" }, $record->{ $key } );
+
+            $analysis->{ $key }->{ "TYPE" } = "num";
+            $analysis->{ $key }->{ "SUM" } += $record->{ $key };
+        }
+        else
+        {
+            $len = length $record->{ $key };
+
+            if ( not exists $analysis->{ $key } )
+            {
+                $analysis->{ $key }->{ "MIN" } = $len;
+                $analysis->{ $key }->{ "MAX" } = $len;
+            }
+
+            $analysis->{ $key }->{ "MAX" } = Maasha::Calc::max( $analysis->{ $key }->{ "MAX" }, $len );
+            $analysis->{ $key }->{ "MIN" } = Maasha::Calc::min( $analysis->{ $key }->{ "MIN" }, $len );
+
+            $analysis->{ $key }->{ "TYPE" } = "alph";
+            $analysis->{ $key }->{ "SUM" } += $len;
+        }
+
+        $analysis->{ $key }->{ "COUNT" }++;
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+foreach $key ( keys %{ $analysis } )
+{
+    $analysis->{ $key }->{ "MEAN" } = sprintf "%.2f", $analysis->{ $key }->{ "SUM" } / $analysis->{ $key }->{ "COUNT" };
+    $analysis->{ $key }->{ "SUM" }  = sprintf "%.2f", $analysis->{ $key }->{ "SUM" };
+}
+
+$keys   = "KEY  ";
+$types  = "TYPE ";
+$counts = "COUNT";
+$mins   = "MIN  ";
+$maxs   = "MAX  ";
+$sums   = "SUM  ";
+$means  = "MEAN ";
+
+foreach $key ( sort keys %{ $analysis } )
+{
+    $keys   .= sprintf "% 15s", $key;
+    $types  .= sprintf "% 15s", $analysis->{ $key }->{ "TYPE" };
+    $counts .= sprintf "% 15s", $analysis->{ $key }->{ "COUNT" };
+    $mins   .= sprintf "% 15s", $analysis->{ $key }->{ "MIN" };
+    $maxs   .= sprintf "% 15s", $analysis->{ $key }->{ "MAX" };
+    $sums   .= sprintf "% 15s", $analysis->{ $key }->{ "SUM" };
+    $means  .= sprintf "% 15s", $analysis->{ $key }->{ "MEAN" };
+}
+
+print $data_out "$keys\n";
+print $data_out "$types\n";
+print $data_out "$counts\n";
+print $data_out "$mins\n";
+print $data_out "$maxs\n";
+print $data_out "$sums\n";
+print $data_out "$means\n";
+
+close $data_out;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__