added -o option and tests to analyze_vals

[biopieces.git] / bp_bin / analyze_vals

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
index d1d9ede3af31a59045be0d51fe0f21fe57a46efe..726c91c53c62f5c22560b77260f45d094340b018 100755 (executable)
--- a/bp_bin/analyze_vals
+++ b/bp_bin/analyze_vals
@@ -36,12 +36,13 @@ use Data::Dumper;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $options, $in, $out, $record, $analysis, $key, $len, %skip_hash,
+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 },
     ]   
@@ -50,6 +51,9 @@ $options = Maasha::Biopieces::parse_options(
 $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" } };
 
@@ -122,13 +126,15 @@ foreach $key ( sort keys %{ $analysis } )
     $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";
+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 );