adding bzip2 support in ruby

[biopieces.git] / bp_bin / random_records

diff --git a/bp_bin/random_records b/bp_bin/random_records
index 4cd1d4413a253b7338666f848168a0f9929fba03..b700dc19a22ef646d32d262ecb255533a5f29218 100755 (executable)
--- a/bp_bin/random_records
+++ b/bp_bin/random_records
@@ -1,6 +1,123 @@
 #!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Select a number of random records from the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
-
 use Maasha::Biopieces;
+use Maasha::Filesys;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $tmp_dir, $tmp_file, $fh_out, $fh_in, $count, $i, %rand_hash, $rand, $max );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => 10, allowed => undef, disallowed => 0 },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$tmp_dir  = Maasha::Biopieces::get_tmpdir();
+$tmp_file = "$tmp_dir/random_records.tmp";
+
+$fh_out = Maasha::Filesys::file_write_open( $tmp_file );
+
+$count = 0;
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    Maasha::Biopieces::put_record( $record, $fh_out );
+
+    $count++;
+}
+
+close $fh_out;
+
+$max = 0;
+$i   = 0;
+
+Maasha::Common::error( qq(Requested random records > records in stream) ) if $options->{ "num" } > $count;
+
+while ( $i < $options->{ "num" } )
+{
+    $rand = int( rand( $count ) );
+
+    if ( not exists $rand_hash{ $rand } )
+    {
+        $rand_hash{ $rand } = 1;
+
+        $max = $rand if $rand > $max;
+
+        $i++;
+    }
+}
+
+$fh_in = Maasha::Filesys::file_read_open( $tmp_file );
+
+$count = 0;
+
+while ( $record = Maasha::Biopieces::get_record( $fh_in ) ) 
+{
+    Maasha::Biopieces::put_record( $record, $out ) if exists $rand_hash{ $count };
+
+    last if $count == $max;
+
+    $count++;
+}
+
+close $fh_in;
+
+unlink $tmp_file;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__