X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fanalyze_vals;h=e7e8249a8faf73c53bce080d333e56a73a2b7aa1;hb=9e506c77bf020025b9788beac9ece546e0dd93ee;hp=d1d9ede3af31a59045be0d51fe0f21fe57a46efe;hpb=ee3bad350dd7f0b98ef97086e0ed78c343020e4e;p=biopieces.git

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
index d1d9ede..e7e8249 100755
--- a/bp_bin/analyze_vals
+++ b/bp_bin/analyze_vals
@@ -1,6 +1,6 @@
-#!/usr/bin/env perl
+#!/usr/bin/env ruby
 
-# Copyright (C) 2007-2009 Martin A. Hansen.
+# Copyright (C) 2007-2013 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
@@ -18,135 +18,95 @@
 
 # http://www.gnu.org/copyleft/gpl.html
 
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Determine type, count, min, max, sum and mean for values in stream.
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+# This program is part of the Biopieces framework (www.biopieces.org).
 
-use warnings;
-use strict;
-use Maasha::Biopieces;
-use Maasha::Calc;
-use Data::Dumper;
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+# Determine basic stats for records in the stream.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-
-my ( $options, $in, $out, $record, $analysis, $key, $len, %skip_hash,
-     %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 => '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" } );
-
-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" }++;
+require 'maasha/biopieces'
+
+casts = []
+casts << {long: 'keys',    short: 'k', type: 'list', mandatory: false, default: nil, allowed: nil, disallowed: nil}
+casts << {long: 'no_keys', short: 'K', type: 'list', mandatory: false, default: nil, allowed: nil, disallowed: nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+stats = Hash.new { |h, k| h[k] = {} }
+
+def to_number(value)
+  begin num = Integer(value)
+    return num
+  rescue
+    begin num = Float(value)
+      return num
+    rescue
+    end
+  end
+end
+
+def min(value1, value2)
+  return value2 unless value1
+  [value1, value2].min
+end
+
+def max(value1, value2)
+  return value2 unless value1
+  [value1, value2].max
+end
+
+keys    = options[:keys].map { |k| k.to_sym }                                  if options[:keys]
+no_keys = options[:no_keys].each_with_object({}) { |i, h| h[i.to_sym] = true } if options[:no_keys]
+get_keys = nil
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each do |record|
+    unless get_keys
+      get_keys = keys || record.keys
+      get_keys.reject! { |k| no_keys[k] } if no_keys
+    end
+
+    get_keys.each do |key|
+      key = key.to_sym
+      value = record[key]
+
+      stats[key][:sum]   ||= 0
+      stats[key][:count] ||= 0
+
+      if num = to_number(value)
+        stats[key][:min]   = min(stats[key][:min], num)
+        stats[key][:max]   = max(stats[key][:max], num)
+        stats[key][:type]  = :numeric
+        stats[key][:sum]  += num
+      else
+        stats[key][:min]   = min(stats[key][:min], value.length)
+        stats[key][:max]   = max(stats[key][:max], value.length)
+        stats[key][:type]  = :alphabetic
+        stats[key][:sum]  += value.length
+      end
+
+      stats[key][:count] += 1
+    end
+  end
+
+  stats.each do |key, value|
+    stat_record = {
+      :KEY   => key,
+      :TYPE  => value[:type].to_s.capitalize,
+      :COUNT => value[:count],
+      :MIN   => value[:min].is_a?(Float) ? "%0.2f" % value[:min] : value[:min],
+      :MAX   => value[:max].is_a?(Float) ? "%0.2f" % value[:max] : value[:max],
+      :SUM   => value[:sum].is_a?(Float) ? "%0.2f" % value[:sum] : value[:sum],
+      :MEAN  => "%0.2f" % (value[:sum] / value[:count].to_f)
     }
 
-    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->{ $key }->{ "MEAN" };
-}
-
-print "$keys\n";
-print "$types\n";
-print "$counts\n";
-print "$mins\n";
-print "$maxs\n";
-print "$sums\n";
-print "$means\n";
-
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-BEGIN
-{
-    Maasha::Biopieces::status_set();
-}
-
-
-END
-{
-    Maasha::Biopieces::status_log();
-}
+    output.puts stat_record
+  end
+end
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<