update search program with options for do_it_all; implement calls to subsideary scripts

[function2gene.git] / bin / parse_ncbi_results

diff --git a/bin/parse_ncbi_results b/bin/parse_ncbi_results
index 51d339db66e38bb02918c5d0c3ce94f760558b30..1e2b8d4f4dd72989d809d4e7a546b6eb1b501d66 100755 (executable)
--- a/bin/parse_ncbi_results
+++ b/bin/parse_ncbi_results
@@ -77,9 +77,12 @@ my %options = (debug    => 0,
               man      => 0,
               dir      => '.',
               keyword  => undef,
+              keywords => 0,
              );
 
-GetOptions(\%options,'keyword|k=s','debug|d+','help|h|?','man|m');
+GetOptions(\%options,'keyword|k=s','debug|d+','help|h|?','man|m',
+          'keywords'
+         );
 
 
 pod2usage() if $options{help};
@@ -179,10 +182,16 @@ $parser->setHandlers('Start' => \&tag_start,
                     'Char'  => \&tag_content
                    );
 
+print STDOUT join(",", map {qq("$_");} qw(Name RefSeq Location Alias Function Description Keyword DBName Filename)),qq(\n);
 for (@ARGV) {
      $file_name = $_;
-     ($keyword) = $options{keyword} || $file_name =~ m#(?:^|/)([^\/]+?)[\s-]+AND[\s\-].+_results.xml$#;
-     print STDOUT join(",", map {qq("$_");} qw(Name RefSeq Location Alias Function Description Keyword DBName Filename)),qq(\n);
+     if ($options{keywords}) {
+         $keyword = $_;
+         $file_name = "ncbi_${keyword}_results.xml";
+     }
+     else {
+         ($keyword) = $options{keyword} || $file_name =~ m#(?:^|/)([^\/]+?)[\s-]+AND[\s\-].+_results.xml$#;
+     }
      my $file = new IO::File $file_name, 'r' or die "Unable to open file $file_name $!";
 
      $parser->parse($file);