migrated random_records

git-svn-id: http://biopieces.googlecode.com/svn/trunk@398 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/random_records b/bp_bin/random_records
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..f45f942028a7e730067999550747a05068c8733d 100755 (executable)
--- a/bp_bin/random_records
+++ b/bp_bin/random_records
@@ -1,6 +1,128 @@
-#!/usr/bin/env perl
+#!/usr/bin/env perl -w
+
+# 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 ( $run_time_beg, $run_time_end, $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::Filesys::dir_remove( $tmp_dir );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    $run_time_beg = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::log_biopiece();
+}
+
+
+END
+{
+    Maasha::Biopieces::close_stream( $in );
+    Maasha::Biopieces::close_stream( $out );
+
+    $run_time_end = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
 
-use Maasha::BioRun;

diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm
index 53c09c7bef87d662264e35b6bedef88858dfeb38..4863090db82fe3962cc8fe1af93018c7c3fb884b 100644 (file)
--- a/code_perl/Maasha/BioRun.pm
+++ b/code_perl/Maasha/BioRun.pm
@@ -172,7 +172,6 @@ sub run_script
     elsif ( $script eq "compute" )                  { script_compute(                   $in, $out, $options ) }
     elsif ( $script eq "flip_tab" )                 { script_flip_tab(                  $in, $out, $options ) }
     elsif ( $script eq "count_records" )            { script_count_records(             $in, $out, $options ) }
-    elsif ( $script eq "random_records" )           { script_random_records(            $in, $out, $options ) }
     elsif ( $script eq "sort_records" )             { script_sort_records(              $in, $out, $options ) }
     elsif ( $script eq "count_vals" )               { script_count_vals(                $in, $out, $options ) }
     elsif ( $script eq "plot_histogram" )           { script_plot_histogram(            $in, $out, $options ) }
@@ -642,12 +641,6 @@ sub get_options
             data_out|o=s
         );
     }
-    elsif ( $script eq "random_records" )
-    {
-        @options = qw(
-            num|n=s
-        );
-    }
     elsif ( $script eq "sort_records" )
     {
         @options = qw(
@@ -3870,76 +3863,6 @@ sub script_count_records
 }
 
 
-sub script_random_records
-{
-    # Martin A. Hansen, August 2007.
-
-    # Pick a number or random records from stream.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $record, $tmp_file, $fh_out, $fh_in, $count, $i, %rand_hash, $rand, $max );
-
-    $options->{ "num" } ||= 10;
-
-    $tmp_file = "$BP_TMP/random_records.tmp";
-
-    $fh_out = Maasha::Common::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::Common::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;
-}
-
-
 sub script_sort_records
 {
     # Martin A. Hansen, August 2007.