migrated sum_vals

git-svn-id: http://biopieces.googlecode.com/svn/trunk@436 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..2a69acda842780d6041bb7dd1b734cc2e3458945 100755 (executable)
--- a/bp_bin/sum_vals
+++ b/bp_bin/sum_vals
@@ -1,6 +1,96 @@
-#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Calculate the total sums for the values of given keys.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use warnings;
 use strict;
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $key, %sum_hash, $fh );
+
+$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 => 'yes', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    foreach $key ( @{ $options->{ "keys" } } )
+    {
+        if ( $record->{ $key } ) {
+            $sum_hash{ $key } += $record->{ $key };
+        }
+    }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
+}
+
+$fh = Maasha::Biopieces::write_stream( $options->{ "data_out" } );
+
+foreach $key ( @{ $options->{ "keys" } } ) {
+    Maasha::Biopieces::put_record( { $key . "_SUM" => $sum_hash{ $key } || 0 } , $fh );
+}
+
+close $fh;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+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 33884c4002a3e061138a46b3452fc578e5e0968c..8ad923964d17b37898232e0ae6869b2091f98803 100644 (file)
--- a/code_perl/Maasha/BioRun.pm
+++ b/code_perl/Maasha/BioRun.pm
@@ -157,7 +157,6 @@ sub run_script
     elsif ( $script eq "plot_matches" )             { script_plot_matches(              $in, $out, $options ) }
     elsif ( $script eq "plot_seqlogo" )             { script_plot_seqlogo(              $in, $out, $options ) }
     elsif ( $script eq "plot_phastcons_profiles" )  { script_plot_phastcons_profiles(   $in, $out, $options ) }
-    elsif ( $script eq "sum_vals" )                 { script_sum_vals(                  $in, $out, $options ) }
     elsif ( $script eq "upload_to_ucsc" )           { script_upload_to_ucsc(            $in, $out, $options ) }
 
     close $in if defined $in;
@@ -530,14 +529,6 @@ sub get_options
             direction|d=s
         );
     }
-    elsif ( $script eq "sum_vals" )
-    {
-        @options = qw(
-            no_stream|x
-            data_out|o=s
-            keys|k=s
-        );
-    }
     elsif ( $script eq "upload_to_ucsc" )
     {
         @options = qw(
@@ -663,7 +654,7 @@ sub get_options
     Maasha::Common::error( qq(both --in_file and --genome specified) )  if $script eq "soap_seq" and $options{ "genome" } and $options{ "in_file" };
     Maasha::Common::error( qq(no --genome specified) )                  if $script =~ /get_genome_align|get_genome_phastcons|plot_phastcons_profiles|plot_karyogram/ and not $options{ "genome" };
     Maasha::Common::error( qq(no --key specified) )                     if $script =~ /plot_lendist|plot_histogram/ and not $options{ "key" };
-    Maasha::Common::error( qq(no --keys speficied) )                    if $script =~ /sort_records|sum_vals/ and not $options{ "keys" };
+    Maasha::Common::error( qq(no --keys speficied) )                    if $script =~ /sort_records/ and not $options{ "keys" };
 
     if ( $script eq "upload_to_ucsc" )
     {
@@ -2683,43 +2674,6 @@ sub script_plot_matches
 }
 
 
-sub script_sum_vals
-{
-    # Martin A. Hansen, August 2007.
-
-    # Calculates the sums for values of given keys.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $record, $key, %sum_hash, $fh );
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) 
-    {
-        foreach $key ( @{ $options->{ "keys" } } )
-        {
-            if ( $record->{ $key } ) {
-                $sum_hash{ $key } += $record->{ $key };
-            }
-        }
-
-        Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
-    }
-
-    $fh = write_stream( $options->{ "data_out" } );
-
-    foreach $key ( @{ $options->{ "keys" } } ) {
-        Maasha::Biopieces::put_record( { $key . "_SUM" => $sum_hash{ $key } || 0 } , $fh );
-    }
-
-    close $fh;
-}
-
-
 sub script_upload_to_ucsc
 {
     # Martin A. Hansen, August 2007.