X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bin%2Ffunction2gene;h=b6810e2be8c8ed4eab05cedd73ca50b99e3d6719;hb=d8f0d65e91cad08f2aa3c765f7523e9b54ace894;hp=c407047418332d93c80fac96b7712dae31a611e3;hpb=d8245a8bd7b77af4cdb72418346e52d8834e94a6;p=function2gene.git

diff --git a/bin/function2gene b/bin/function2gene
index c407047..b6810e2 100755
--- a/bin/function2gene
+++ b/bin/function2gene
@@ -41,7 +41,9 @@ use Storable;
 
 A file which contains a newline delinated list of keywords to search
 for. Can be specified multiple times. Lines starting with # or ; are
-ignored.
+ignored. An optional weight can be specified after the keyword, which
+is separated from the keyword by a tab. (If not specified, 1 is
+assumed.)
 
 =item B<--results>
 
@@ -158,9 +160,9 @@ $options{keywords} = [map {abs_path($_)} @{$options{keywords}}];
 
 chdir $options{results} or die "Unable to chdir to $options{results}";
 
-if (-e "do_it_all_state") {
+if (-e "function2gene_state") {
      ADVISE("Using existing state information");
-     my $state_fh = IO::File->new("do_it_all_state",'r') or die
+     my $state_fh = IO::File->new("function2gene_state",'r') or die
 	  "Unable to open state file for reading: $!";
      local $/;
      my $state_file = <$state_fh>;
@@ -190,6 +192,10 @@ if (@{$options{keywords}}) {
 	       next if /^\s*[#;]/;
 	       next unless /\w+/;
 	       chomp;
+	       s/\r$//;
+	       my ($keyword,$weight) = split /\t/, $_;
+	       $weight = 1 if not defined $weight;
+	       $state{keyword_weight}{$keyword} = $weight;
 	       if (not $old_keywords{$_}) {
 		    DEBUG("Adding new keyword '$_'");
 		    push @new_keywords, $_;
@@ -220,17 +226,40 @@ if (exists $options{restart_at} and length $options{restart_at}) {
 if (exists $options{invalidate_state}) {
      for my $invalidate_state (@{$options{invalidate_state}}) {
 	  my ($method,$database,$keyword) = split /,/, $invalidate_state;
+	  if (grep {not defined $_ } ($method,$database,$keyword) ) {
+	       print STDERR "The invalidate state option '$invalidate_state' is invalid.\n";
+	       next;
+	  }
 	  if (not exists $state{done_keywords}{$method}) {
 	       print STDERR "Method '$method' does not exist, and cannot be invalidated\n";
+	       next;
 	  }
-	  elsif (not exists $state{done_keywords}{$method}{$database}) {
+	  if (not exists $state{done_keywords}{$method}{$database}) {
 	       print STDERR "Database '$database' does not exist for method '$method', and cannot be invalidated\n";
+	       next;
+	  }
+	  if (not length $keyword) {
+	       delete $state{done_keywords}{$method}{$database};
+	       if ($method eq 'get') {
+		    delete $state{done_keywords}{parse}{$database};
+		    delete $state{done_keywords}{combine}{$database};
+	       }
+	       if ($method eq 'parse') {
+		    delete $state{done_keywords}{combine}{$database};
+	       }
+	       next;
 	  }
-	  elsif (not exists $state{done_keywords}{$method}{$database}{$keyword}) {
+	  if (not exists $state{done_keywords}{$method}{$database}{$keyword}) {
 	       print STDERR "Keyword '$keyword' does not exist for database '$database' and method '$method', and cannot be invalidated\n";
+	       next;
 	  }
-	  else {
-	       delete $state{done_keywords}{$method}{$database}{$keyword};
+	  delete $state{done_keywords}{$method}{$database}{$keyword};
+	  if ($method eq 'get') {
+	       delete $state{done_keywords}{parse}{$database}{$keyword};
+	       delete $state{done_keywords}{combine}{$database}{$keyword};
+	  }
+	  if ($method eq 'parse') {
+	       delete $state{done_keywords}{combine}{$database}{$keyword};
 	  }
      }
 }
@@ -296,7 +325,7 @@ for my $state (qw(get parse)) {
      }
      save_state(\%state);
      if ($ERRORS) {
-	  WARN("Stoping, as there are errors");
+	  WARN("Stoping, asthere are errors");
 	  exit 1;
      }
 }
@@ -310,10 +339,19 @@ if ($actions{combine}) {
 				} keys %{$state{done_keywords}{parse}{$db}}
 			   } keys %{$state{done_keywords}{parse}};
 
-     write_command_to_file('combined_results.txt',
-			   "$base_dir/combine_results",
-			   @parsed_results,
-			  );
+     # create temporary file to store keyword weights
+     my $file = IO::File->new('combined_keywords.txt','w') or
+	  die "Unable to open combined_keywords.txt for writing: $!";
+     for my $keyword (keys %{$state{keyword_weight}}) {
+	  print {$file} "$keyword\t$state{keyword_weight}{$keyword}\n";
+     }
+     system("$base_dir/combine_results",
+	    '--keywords','combined_keywords.txt',
+	    '--results','combined_results.txt',
+	    '--results-table','combined_results_table.txt',
+	    @parsed_results,
+	   ) == 0
+		or die "combine_results failed with ".($?>>8);
      for my $result (@parsed_results) {
 	  $result =~ s/^parsed_results_//;
 	  $result =~ s/\.txt$//;
@@ -321,10 +359,6 @@ if ($actions{combine}) {
 	  $state{done_keywords}{combined}{$db}{$keyword} = 1;
      }
      save_state(\%state);
-     write_command_to_file('combined_results_table.txt',
-			   "$base_dir/results_to_table",
-			   'combined_results.txt',
-			  );
      ADVISE("Finished; results in $options{results}/combined_results.txt");
 }
 else {
@@ -383,7 +417,7 @@ sub handle_action{
 
 sub save_state{
      my ($state) = @_;
-     my $state_fh = IO::File->new("do_it_all_state",'w') or die
+     my $state_fh = IO::File->new("function2gene_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: $!";