From: Don Armstrong <don@donarmstrong.com>
Date: Fri, 26 Oct 2007 20:26:45 +0000 (+0000)
Subject:  * Rename do_it_all; document function2gene more clearly
X-Git-Url: https://git.donarmstrong.com/?p=function2gene.git;a=commitdiff_plain;h=3557eb364c40602a2f2d3f4c2a68edd6ee00b632

 * Rename do_it_all; document function2gene more clearly


git-svn-id: file:///srv/svn/function2gene/trunk@13 a0738b58-4706-0410-8799-fb830574a030
---

diff --git a/bin/do_it_all b/bin/do_it_all
deleted file mode 100755
index 9a681ec..0000000
--- a/bin/do_it_all
+++ /dev/null
@@ -1,378 +0,0 @@
-#! /usr/bin/perl
-# do_it_all, is part of the gene search suite and is released
-# under the terms of the GPL version 2, or any later version, at your
-# option. See the file README and COPYING for more information.
-# Copyright 2007 by Don Armstrong <don@donarmstrong.com>.
-
-
-use threads;
-use warnings;
-use strict;
-
-use Getopt::Long;
-use Pod::Usage;
-
-use Storable;
-
-=head1 NAME
-
-  do_it_all - Call out to each of the search modules to search for
-  each of the terms
-
-=head1 SYNOPSIS
-
- do_it_all --keywords keywords.txt --results gene_search_results
-
- Options:
-  --keywords newline delineated list of keywords to search for
-  --results directory to store results in
-  --database databases to search
-  --restart-at mode to start searching at
-  --debug, -d debugging level (Default 0)
-  --help, -h display this help
-  --man, -m display manual
-
-=head1 OPTIONS
-
-=over
-
-=item B<--keywords>
-
-A file which contains a newline delinated list of keywords to search
-for. Can be specified multiple times. Lines starting with # or ; are
-ignored.
-
-=item B<--results>
-
-Directory in which to store results; also stores the current state of
-the system
-
-=item B<--database>
-
-Databases to search, can be specified multiple times. [Defaults to
-NCBI, GeneCards and Harvester, the only currently supported
-databases.]
-
-=item B<--restart-at>
-
-If you need to restart the process at a particular state (which has
-already been completed) specify this option.
-
-=item B<--debug, -d>
-
-Debug verbosity. (Default 0)
-
-=item B<--help, -h>
-
-Display brief useage information.
-
-=item B<--man, -m>
-
-Display this manual.
-
-=back
-
-=head1 EXAMPLES
-
-
-=cut
-
-
-use vars qw($DEBUG);
-use Cwd qw(abs_path);
-use IO::File;
-use Storable qw(thaw freeze);
-use File::Basename qw(basename dirname);
-use Thread::Queue;
-
-my %options = (databases       => [],
-	       keywords        => [],
-	       debug           => 0,
-	       help            => 0,
-	       man             => 0,
-	       results         => '',
-	       );
-
-GetOptions(\%options,'keywords=s@','databases=s@',
-	   'restart_at|restart-at=s','results=s',
-	   'debug|d+','help|h|?','man|m');
-
-pod2usage() if $options{help};
-pod2usage({verbose=>2}) if $options{man};
-
-my $base_dir = dirname(abs_path($0));
-
-my $ERRORS='';
-
-$ERRORS.="restart-at must be one of get, parse or combine\n" if
-     exists $options{restart_at} and $options{restart_at} !~ /^(?:get|parse|combine)$/;
-
-$ERRORS.="unknown database(s)" if
-     @{$options{databases}} and
-     grep {$_ !~ /^(?:ncbi|genecard|harvester)$/i} @{$options{databases}};
-
-if (not length $options{results}) {
-     $ERRORS.="results directory not specified";
-}
-elsif (not -d $options{results} or not -w $options{results}) {
-     $ERRORS.="results directory $options{results} does not exist or is not writeable";
-}
-
-pod2usage($ERRORS) if length $ERRORS;
-
-if (not @{$options{databases}}) {
-     $options{databases} = [qw(ncbi genecard harvester)]
-}
-
-$DEBUG = $options{debug};
-
-# There are three states for our engine
-# Getting results
-# Parsing them
-# Combining results
-
-# first, check to see if the state in the result directory exists
-
-my %state;
-
-$options{keywords} = [map {abs_path($_)} @{$options{keywords}}];
-
-chdir $options{results} or die "Unable to chdir to $options{results}";
-
-if (-e "do_it_all_state") {
-     ADVISE("Using existing state information");
-     my $state_fh = IO::File->new("do_it_all_state",'r') or die
-	  "Unable to open state file for reading: $!";
-     local $/;
-     my $state_file = <$state_fh>;
-     %state = %{thaw($state_file)} or die "Unable to thaw state file";
-}
-else {
-     ADVISE("Starting new run");
-     %state = (keywords => [],
-	       databases => [map {lc($_)} @{$options{databases}}],
-	       done_keywords => {
-				 get => {},
-				 parse => {},
-				 combine => {},
-				},
-	      );
-}
-
-my @new_keywords;
-if (@{$options{keywords}}) {
-     # uniqify keywords
-     my %old_keywords;
-     @old_keywords{@{$state{keywords}}} = (1) x @{$state{keywords}};
-     for my $keyword_file (@{$options{keywords}}) {
-	  my $keyword_fh = IO::File->new($keyword_file,'r') or die
-	       "Unable to open $keyword_file for reading: $!";
-	  while (<$keyword_fh>) {
-	       next if /^\s*[#;]/;
-	       next unless /\w+/;
-	       chomp;
-	       if (not $old_keywords{$_}) {
-		    DEBUG("Adding new keyword '$_'");
-		    push @new_keywords, $_;
-	       }
-	       else {
-		    DEBUG("Not adding duplicate keyword '$_'");
-	       }
-	  }
-     }
-     push @{$state{keywords}},@new_keywords;
-}
-
-if (exists $options{restart_at} and length $options{restart_at}) {
-     if (lc($options{restart_at}) eq 'get') {
-	  delete $state{done_keywords}{get};
-	  delete $state{done_keywords}{parse};
-	  delete $state{done_keywords}{combine};
-     }
-     elsif (lc($options{restart_at}) eq 'parse') {
-	  delete $state{done_keywords}{parse};
-	  delete $state{done_keywords}{combine};
-     }
-     elsif (lc($options{restart_at}) eq 'combine') {
-	  delete $state{done_keywords}{combine};
-     }
-}
-
-# now we need to figure out what has to happen
-# for each keyword, we check to see if we've got results, parsed
-# results, and combined it. If not, we queue up those actions.
-
-my %actions = (combine => 0,
-	       get     => {},
-	       parse   => {},
-	      );
-
-if (not @{$state{keywords}}) {
-     ADVISE("There are no keywords specified");
-}
-
-for my $keyword (@{$state{keywords}}) {
-     for my $database (@{$state{databases}}) {
-	  if (not exists $state{done_keywords}{get}{$database}{$keyword}) {
-	       push @{$actions{get}{$database}}, $keyword;
-	       delete $state{done_keywords}{parse}{$database}{$keyword} if
-		    exists $state{done_keywords}{parse}{$database}{$keyword};
-	       delete $state{done_keywords}{combine}{$database}{$keyword} if
-		    exists $state{done_keywords}{combine}{$database}{$keyword};
-	  }
-	  if (not exists $state{done_keywords}{parse}{$database}{$keyword}) {
-	       push @{$actions{parse}{$database}},$keyword;
-	       delete $state{done_keywords}{combine}{$database}{$keyword} if
-		    exists $state{done_keywords}{combine}{$database}{$keyword};
-	  }
-	  if (not exists $state{done_keywords}{combine}{$database}{$keyword}) {
-	      $actions{combine} = 1;
-	  }
-     }
-}
-
-
-for my $state (qw(get parse)) {
-     my %databases;
-     for my $database (keys %{$actions{$state}}) {
-	  next unless @{$actions{$state}{$database}};
-	  $databases{$database}{queue} = Thread::Queue->new
-	       or die "Unable to create new thread queue";
-	  $databases{$database}{thread} = threads->create(\&handle_action,$state,$database,$databases{$database}{queue})
-	       or die "Unable to create new thread";
-	  $databases{$database}{queue}->enqueue(@{$actions{$state}{$database}});
-	  $databases{$database}{queue}->enqueue(undef);
-     }
-     my $ERRORS=0;
-     for my $database (keys %databases) {
-	  my ($actioned_keywords,$failed_keywords) = @{$databases{$database}{thread}->join||[]};
-	  if (not defined $failed_keywords) {
-	       ADVISE("Something bad happened during '$state' of '$database'");
-	       $ERRORS = 1;
-	  }
-	  elsif (@{$failed_keywords}) {
-	       ADVISE("These keywords failed during '$state' of '$database':",@{$failed_keywords});
-	       $ERRORS=1;
-	  }
-	  @{$state{done_keywords}{$state}{$database}}{@{$actioned_keywords}} = (1) x @{$actioned_keywords};
-	  delete @{$state{done_keywords}{$state}{$database}}{@{$failed_keywords}};
-     }
-     save_state(\%state);
-     if ($ERRORS) {
-	  WARN("Stoping, as there are errors");
-	  exit 1;
-     }
-}
-
-if ($actions{combine}) {
-     save_state(\%state);
-     # deal with combining results
-     my @parsed_results = map { my $db = $_;
-				map {
-				     "parsed_results_${db}_${_}.txt"
-				} keys %{$state{done_keywords}{parse}{$db}}
-			   } keys %{$state{done_keywords}{parse}};
-
-     write_command_to_file('combined_results.txt',
-			   "$base_dir/combine_results",
-			   @parsed_results,
-			  );
-     for my $result (@parsed_results) {
-	  s/^parsed_results_//;
-	  s/\.txt$//;
-	  my ($db,$keyword) = split /_/, $_, 2;
-	  $state{done_keywords}{combined}{$db}{$keyword} = 1;
-     }
-     save_state(\%state);
-     ADVISE("Finished; results in $options{results}/combined_results");
-}
-else {
-     ADVISE('Nothing to do. [Perhaps you wanted --restart-at?]');
-}
-
-sub handle_action{
-     my ($state,$database,$queue) = @_;
-     my $keyword;
-     my $actioned_keywords = [];
-     my $failed_keywords = [];
-     DEBUG("Beginning to handle actions for state '$state' database '$database'");
-     while ($keyword = $queue->dequeue) {
-	  DEBUG("Handling state '$state' database '$database' keyword '$keyword'");
-	  # handle the action, baybee
-	  if ($state eq 'get') {
-	       my $command_fh;
-	       eval {
-		    open($command_fh,'|-',
-			 "$base_dir/get_${database}_results",
-			) or die "unable to execute '$base_dir/get_${database}_results'";
-		    print {$command_fh} "$keyword\n" or die "unable to print $keyword to 'get_${database}_results'";
-		    close($command_fh) or die "Unable to close filehandle";
-		    if ($? != 0) {
-			 die "get_${database}_results with keyword $keyword failed with error code ".($?>>8);
-		    }
-	       };
-	       if ($@) {
-		    WARN($@);
-		    push @{$failed_keywords}, $keyword;
-		    next;
-	       }
-	  }
-	  elsif ($state eq 'parse') {
-	       eval {
-		    write_command_to_file("parsed_results_${database}_${keyword}.txt",
-					  "$base_dir/parse_${database}_results",
-					  '--keywords',
-					  $keyword,
-					 );
-	       };
-	       if ($@) {
-		    WARN("parse_${database}_results failed with $@");
-		    push @{$failed_keywords}, $keyword;
-		    next;
-	       }
-	  }
-	  else {
-	       die "I don't know how to handle state $state";
-	  }
-	  ADVISE("$state results from '$database' for '$keyword'");
-	  push @{$actioned_keywords},$keyword;
-     }
-     return [$actioned_keywords,$failed_keywords];
-}
-
-sub save_state{
-     my ($state) = @_;
-     my $state_fh = IO::File->new("do_it_all_state",'w') or die
-	  "Unable to open state file for writing: $!";
-     print {$state_fh} freeze($state) or die "Unable to freeze state file";
-     close $state_fh or die "Unable to close state file: $!";
-}
-
-sub write_command_to_file{
-     my ($file,@command) = @_;
-     my $fh = IO::File->new($file,'w') or
-	  die "Unable to open $file for writing: $!";
-     my $command_fh;
-     open($command_fh,'-|',
-	  @command,
-	 ) or die "Unable to execute $command[0] $!";
-     print {$fh} <$command_fh>;
-     close $fh;
-     close $command_fh or die "$command[0] failed with ".($?>>8);
-}
-
-
-sub ADVISE{
-     print STDOUT map {($_,qq(\n))} @_;
-}
-
-sub DEBUG{
-     print STDERR map {($_,qq(\n))} @_;
-}
-
-
-sub WARN {
-     print STDERR map {($_,qq(\n))} @_;
-}
-
-__END__
diff --git a/bin/function2gene b/bin/function2gene
new file mode 100755
index 0000000..922deac
--- /dev/null
+++ b/bin/function2gene
@@ -0,0 +1,381 @@
+#! /usr/bin/perl
+# function2gene, is part of the function2gene suite and is released
+# under the terms of the GPL version 2, or any later version, at your
+# option. See the file README and COPYING for more information.
+# Copyright 2007 by Don Armstrong <don@donarmstrong.com>.
+
+
+use threads;
+use warnings;
+use strict;
+
+use Getopt::Long;
+use Pod::Usage;
+
+use Storable;
+
+=head1 NAME
+
+  function2gene - Call out to each of the search modules to search for
+  each of the terms
+
+=head1 SYNOPSIS
+
+ function2gene --keywords keywords.txt --results gene_search_results
+
+ Options:
+  --keywords newline delineated list of keywords to search for
+  --results directory to store results in
+  --database databases to search
+  --restart-at mode to start searching at
+  --debug, -d debugging level (Default 0)
+  --help, -h display this help
+  --man, -m display manual
+
+=head1 OPTIONS
+
+=over
+
+=item B<--keywords>
+
+A file which contains a newline delinated list of keywords to search
+for. Can be specified multiple times. Lines starting with # or ; are
+ignored.
+
+=item B<--results>
+
+Directory in which to store results; also stores the current state of
+the system
+
+=item B<--database>
+
+Databases to search, can be specified multiple times. [Defaults to
+NCBI, GeneCards and Harvester, the only currently supported
+databases.]
+
+=item B<--restart-at>
+
+If you need to restart the process at a particular state (which has
+already been completed) specify this option.
+
+=item B<--debug, -d>
+
+Debug verbosity. (Default 0)
+
+=item B<--help, -h>
+
+Display brief useage information.
+
+=item B<--man, -m>
+
+Display this manual.
+
+=back
+
+=head1 EXAMPLES
+
+   # Search all databases for transferrin
+   echo 'transferrin' > keywords.txt
+   function2gene --keywords keywords.txt --results keyword_results
+
+=cut
+
+
+use vars qw($DEBUG);
+use Cwd qw(abs_path);
+use IO::File;
+use Storable qw(thaw freeze);
+use File::Basename qw(basename dirname);
+use Thread::Queue;
+
+my %options = (databases       => [],
+	       keywords        => [],
+	       debug           => 0,
+	       help            => 0,
+	       man             => 0,
+	       results         => '',
+	       );
+
+GetOptions(\%options,'keywords=s@','databases=s@',
+	   'restart_at|restart-at=s','results=s',
+	   'debug|d+','help|h|?','man|m');
+
+pod2usage() if $options{help};
+pod2usage({verbose=>2}) if $options{man};
+
+my $base_dir = dirname(abs_path($0));
+
+my $ERRORS='';
+
+$ERRORS.="restart-at must be one of get, parse or combine\n" if
+     exists $options{restart_at} and $options{restart_at} !~ /^(?:get|parse|combine)$/;
+
+$ERRORS.="unknown database(s)" if
+     @{$options{databases}} and
+     grep {$_ !~ /^(?:ncbi|genecard|harvester)$/i} @{$options{databases}};
+
+if (not length $options{results}) {
+     $ERRORS.="results directory not specified";
+}
+elsif (not -d $options{results} or not -w $options{results}) {
+     $ERRORS.="results directory $options{results} does not exist or is not writeable";
+}
+
+pod2usage($ERRORS) if length $ERRORS;
+
+if (not @{$options{databases}}) {
+     $options{databases} = [qw(ncbi genecard harvester)]
+}
+
+$DEBUG = $options{debug};
+
+# There are three states for our engine
+# Getting results
+# Parsing them
+# Combining results
+
+# first, check to see if the state in the result directory exists
+
+my %state;
+
+$options{keywords} = [map {abs_path($_)} @{$options{keywords}}];
+
+chdir $options{results} or die "Unable to chdir to $options{results}";
+
+if (-e "do_it_all_state") {
+     ADVISE("Using existing state information");
+     my $state_fh = IO::File->new("do_it_all_state",'r') or die
+	  "Unable to open state file for reading: $!";
+     local $/;
+     my $state_file = <$state_fh>;
+     %state = %{thaw($state_file)} or die "Unable to thaw state file";
+}
+else {
+     ADVISE("Starting new run");
+     %state = (keywords => [],
+	       databases => [map {lc($_)} @{$options{databases}}],
+	       done_keywords => {
+				 get => {},
+				 parse => {},
+				 combine => {},
+				},
+	      );
+}
+
+my @new_keywords;
+if (@{$options{keywords}}) {
+     # uniqify keywords
+     my %old_keywords;
+     @old_keywords{@{$state{keywords}}} = (1) x @{$state{keywords}};
+     for my $keyword_file (@{$options{keywords}}) {
+	  my $keyword_fh = IO::File->new($keyword_file,'r') or die
+	       "Unable to open $keyword_file for reading: $!";
+	  while (<$keyword_fh>) {
+	       next if /^\s*[#;]/;
+	       next unless /\w+/;
+	       chomp;
+	       if (not $old_keywords{$_}) {
+		    DEBUG("Adding new keyword '$_'");
+		    push @new_keywords, $_;
+	       }
+	       else {
+		    DEBUG("Not adding duplicate keyword '$_'");
+	       }
+	  }
+     }
+     push @{$state{keywords}},@new_keywords;
+}
+
+if (exists $options{restart_at} and length $options{restart_at}) {
+     if (lc($options{restart_at}) eq 'get') {
+	  delete $state{done_keywords}{get};
+	  delete $state{done_keywords}{parse};
+	  delete $state{done_keywords}{combine};
+     }
+     elsif (lc($options{restart_at}) eq 'parse') {
+	  delete $state{done_keywords}{parse};
+	  delete $state{done_keywords}{combine};
+     }
+     elsif (lc($options{restart_at}) eq 'combine') {
+	  delete $state{done_keywords}{combine};
+     }
+}
+
+# now we need to figure out what has to happen
+# for each keyword, we check to see if we've got results, parsed
+# results, and combined it. If not, we queue up those actions.
+
+my %actions = (combine => 0,
+	       get     => {},
+	       parse   => {},
+	      );
+
+if (not @{$state{keywords}}) {
+     ADVISE("There are no keywords specified");
+}
+
+for my $keyword (@{$state{keywords}}) {
+     for my $database (@{$state{databases}}) {
+	  if (not exists $state{done_keywords}{get}{$database}{$keyword}) {
+	       push @{$actions{get}{$database}}, $keyword;
+	       delete $state{done_keywords}{parse}{$database}{$keyword} if
+		    exists $state{done_keywords}{parse}{$database}{$keyword};
+	       delete $state{done_keywords}{combine}{$database}{$keyword} if
+		    exists $state{done_keywords}{combine}{$database}{$keyword};
+	  }
+	  if (not exists $state{done_keywords}{parse}{$database}{$keyword}) {
+	       push @{$actions{parse}{$database}},$keyword;
+	       delete $state{done_keywords}{combine}{$database}{$keyword} if
+		    exists $state{done_keywords}{combine}{$database}{$keyword};
+	  }
+	  if (not exists $state{done_keywords}{combine}{$database}{$keyword}) {
+	      $actions{combine} = 1;
+	  }
+     }
+}
+
+
+for my $state (qw(get parse)) {
+     my %databases;
+     for my $database (keys %{$actions{$state}}) {
+	  next unless @{$actions{$state}{$database}};
+	  $databases{$database}{queue} = Thread::Queue->new
+	       or die "Unable to create new thread queue";
+	  $databases{$database}{thread} = threads->create(\&handle_action,$state,$database,$databases{$database}{queue})
+	       or die "Unable to create new thread";
+	  $databases{$database}{queue}->enqueue(@{$actions{$state}{$database}});
+	  $databases{$database}{queue}->enqueue(undef);
+     }
+     my $ERRORS=0;
+     for my $database (keys %databases) {
+	  my ($actioned_keywords,$failed_keywords) = @{$databases{$database}{thread}->join||[]};
+	  if (not defined $failed_keywords) {
+	       ADVISE("Something bad happened during '$state' of '$database'");
+	       $ERRORS = 1;
+	  }
+	  elsif (@{$failed_keywords}) {
+	       ADVISE("These keywords failed during '$state' of '$database':",@{$failed_keywords});
+	       $ERRORS=1;
+	  }
+	  @{$state{done_keywords}{$state}{$database}}{@{$actioned_keywords}} = (1) x @{$actioned_keywords};
+	  delete @{$state{done_keywords}{$state}{$database}}{@{$failed_keywords}};
+     }
+     save_state(\%state);
+     if ($ERRORS) {
+	  WARN("Stoping, as there are errors");
+	  exit 1;
+     }
+}
+
+if ($actions{combine}) {
+     save_state(\%state);
+     # deal with combining results
+     my @parsed_results = map { my $db = $_;
+				map {
+				     "parsed_results_${db}_${_}.txt"
+				} keys %{$state{done_keywords}{parse}{$db}}
+			   } keys %{$state{done_keywords}{parse}};
+
+     write_command_to_file('combined_results.txt',
+			   "$base_dir/combine_results",
+			   @parsed_results,
+			  );
+     for my $result (@parsed_results) {
+	  s/^parsed_results_//;
+	  s/\.txt$//;
+	  my ($db,$keyword) = split /_/, $_, 2;
+	  $state{done_keywords}{combined}{$db}{$keyword} = 1;
+     }
+     save_state(\%state);
+     ADVISE("Finished; results in $options{results}/combined_results");
+}
+else {
+     ADVISE('Nothing to do. [Perhaps you wanted --restart-at?]');
+}
+
+sub handle_action{
+     my ($state,$database,$queue) = @_;
+     my $keyword;
+     my $actioned_keywords = [];
+     my $failed_keywords = [];
+     DEBUG("Beginning to handle actions for state '$state' database '$database'");
+     while ($keyword = $queue->dequeue) {
+	  DEBUG("Handling state '$state' database '$database' keyword '$keyword'");
+	  # handle the action, baybee
+	  if ($state eq 'get') {
+	       my $command_fh;
+	       eval {
+		    open($command_fh,'|-',
+			 "$base_dir/get_${database}_results",
+			) or die "unable to execute '$base_dir/get_${database}_results'";
+		    print {$command_fh} "$keyword\n" or die "unable to print $keyword to 'get_${database}_results'";
+		    close($command_fh) or die "Unable to close filehandle";
+		    if ($? != 0) {
+			 die "get_${database}_results with keyword $keyword failed with error code ".($?>>8);
+		    }
+	       };
+	       if ($@) {
+		    WARN($@);
+		    push @{$failed_keywords}, $keyword;
+		    next;
+	       }
+	  }
+	  elsif ($state eq 'parse') {
+	       eval {
+		    write_command_to_file("parsed_results_${database}_${keyword}.txt",
+					  "$base_dir/parse_${database}_results",
+					  '--keywords',
+					  $keyword,
+					 );
+	       };
+	       if ($@) {
+		    WARN("parse_${database}_results failed with $@");
+		    push @{$failed_keywords}, $keyword;
+		    next;
+	       }
+	  }
+	  else {
+	       die "I don't know how to handle state $state";
+	  }
+	  ADVISE("$state results from '$database' for '$keyword'");
+	  push @{$actioned_keywords},$keyword;
+     }
+     return [$actioned_keywords,$failed_keywords];
+}
+
+sub save_state{
+     my ($state) = @_;
+     my $state_fh = IO::File->new("do_it_all_state",'w') or die
+	  "Unable to open state file for writing: $!";
+     print {$state_fh} freeze($state) or die "Unable to freeze state file";
+     close $state_fh or die "Unable to close state file: $!";
+}
+
+sub write_command_to_file{
+     my ($file,@command) = @_;
+     my $fh = IO::File->new($file,'w') or
+	  die "Unable to open $file for writing: $!";
+     my $command_fh;
+     open($command_fh,'-|',
+	  @command,
+	 ) or die "Unable to execute $command[0] $!";
+     print {$fh} <$command_fh>;
+     close $fh;
+     close $command_fh or die "$command[0] failed with ".($?>>8);
+}
+
+
+sub ADVISE{
+     print STDOUT map {($_,qq(\n))} @_;
+}
+
+sub DEBUG{
+     print STDERR map {($_,qq(\n))} @_;
+}
+
+
+sub WARN {
+     print STDERR map {($_,qq(\n))} @_;
+}
+
+__END__