migrated count_records

git-svn-id: http://biopieces.googlecode.com/svn/trunk@412 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/count_records b/bp_bin/count_records
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..5ccc1e6a91532c38de7e6b31ccb2fdcbc67a34a1 100755 (executable)
--- a/bp_bin/count_records
+++ b/bp_bin/count_records
@@ -1,6 +1,103 @@
-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Count the number of records in the stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use warnings;
 use strict;
+use Maasha::Fasta;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_out, $count, $result, $line );
+
+$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 },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$data_out = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
+
+$count = 0;
+
+if ( $options->{ "no_stream" } )
+{
+    while ( $line = <$in> )
+    {
+        chomp $line;
+
+        $count++ if $line eq "---";
+    }
+}
+else
+{
+    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+    {
+        Maasha::Biopieces::put_record( $record, $out );
+
+        $count++;
+    }
+}
+
+$result = { "RECORDS_COUNT" => $count };
+
+Maasha::Biopieces::put_record( $result, $data_out );
+
+close $data_out;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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 );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::BioRun;
+__END__

diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm
index bb5437f6274d9659ca14041fc05bb7e1f5793120..a43ce9c5b6affbbb649a1ab3fe45272712ef743c 100644 (file)
--- a/code_perl/Maasha/BioRun.pm
+++ b/code_perl/Maasha/BioRun.pm
@@ -165,7 +165,6 @@ sub run_script
     elsif ( $script eq "merge_records" )            { script_merge_records(             $in, $out, $options ) }
     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 "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 ) }
@@ -590,13 +589,6 @@ sub get_options
             eval|e=s
         );
     }
-    elsif ( $script eq "count_records" )
-    {
-        @options = qw(
-            no_stream|x
-            data_out|o=s
-        );
-    }
     elsif ( $script eq "sort_records" )
     {
         @options = qw(
@@ -3430,52 +3422,6 @@ sub script_flip_tab
 }
 
 
-sub script_count_records
-{
-    # Martin A. Hansen, August 2007.
-
-    # Count records in stream.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $record, $count, $result, $fh, $line );
-
-    $count = 0;
-
-    if ( $options->{ "no_stream" } )
-    {
-        while ( $line = <$in> )
-        {
-            chomp $line;
-
-            $count++ if $line eq "---";
-        }
-    }
-    else
-    {
-        while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-        {
-            Maasha::Biopieces::put_record( $record, $out );
-
-            $count++;
-        }
-    }
-
-    $result = { "RECORDS_COUNT" => $count };
-
-    $fh = write_stream( $options->{ "data_out" } );
-
-    Maasha::Biopieces::put_record( $result, $fh );
-
-    close $fh;
-}
-
-
 sub script_sort_records
 {
     # Martin A. Hansen, August 2007.