Option output_file|o added to store the GFF output stream in a specific file.

misc-scripts/alternative_splicing/Fetch_gff.pl

@@ -30,7 +30,7 @@
 
 =head1 SYNOPSIS
 
-  Fetch_gff.pl -dbhost host -dbuser ensro -dbname homo_sapiens_core_57_37b
+  Fetch_gff.pl -dbhost host -dbuser ensro -dbname homo_sapiens_core_58_37c -output_file homo_sapiens_core_58_37c_variants.gff
 
 =head1 DESCRIPTION
 
@@ -39,7 +39,7 @@ from an Ensembl core database.
 
 here is an example commandline
 
-  ./Fetch_gff.pl -dbhost host -dbuser user -dbname my_db -dbpass ****
+  ./Fetch_gff.pl -dbhost host -dbuser user -dbname my_db -dbpass **** -output_file transcript_variants.gff
 
 =head1 OPTIONS
 
@@ -48,6 +48,7 @@ here is an example commandline
     -dbuser         what username to connect as (dbuser= in locator)
     -dbpass         what password to use (dbpass= in locator)
     -chr            which chromosome (optional)
+		-output_file|-o where the GFF output is written (optional, STDOUT by default) 
     -help           displays this documentation with PERLDOC
 
 =cut
@@ -71,6 +72,7 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
 		my $dbuser      = '';
 		my $dbpass      = '';
 		my $chr         = undef;
+		my $output_file = undef;
 		my $help;
 		my @coord_system;
 
@@ -79,22 +81,36 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
 								'dbport:n'        => \$port,
 								'dbname:s'        => \$dbname,
 								'dbuser:s'        => \$dbuser,
-							'chr:s'      => \$chr,
 								'dbpass:s'        => \$dbpass,
+								'chr:s'           => \$chr,
+								'output_file|o=s' => \$output_file,
 								'h|help'          => \$help,
 								) or ($help = 1);
 
-  if(!$host || !$dbuser || !$dbname || !$dbpass){
+		if(!$host || !$dbuser || !$dbname){
 				print STDERR "Can't get any information without database details\n";
-    print STDERR "-dbhost $host -dbuser $dbuser -dbname $dbname ".
-      " -dbpass $dbpass\n";
+				print STDERR "-dbhost '$host' -dbuser '$dbuser' -dbname '$dbname' ".
+						" -dbpass '$dbpass'\n";
 				$help = 1;
-}
+		}
 
 		if ($help) {
 				exec('perldoc', $0);
 		}
 
+		
+		my $output_stream;
+
+		if (defined($output_file)) {
+
+				open ($output_stream, ">$output_file") || throw "Can't open '$output_file' file for writing\n";
+
+		} else {
+
+				$output_stream = \*STDOUT;
+				print STDERR "Will write GFF stream to the standard output.\n"; 
+		}
+
 		my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new
 				(-dbname => $dbname,
 				 -host   => $host,
@@ -149,10 +165,9 @@ use Bio::EnsEMBL::Utils::Exception qw(throw warning);
 								my $slice = $exon->slice->seq_region_name();
 								$exon_std =~ s/-1/-/ ;
 								$exon_std =~ s/1/+/ ;
-							print "$chr\tEnsembl\texon\t$exon_start\t$exon_end\t.\t$exon_std\t.\tgene_id \"$gene_id\"; transcript_id \"$transcr_id\"; exon_id \"$exon_id\"\n" ;
+								print $output_stream "$chr\tEnsembl\texon\t$exon_start\t$exon_end\t.\t$exon_std\t.\tgene_id \"$gene_id\"; transcript_id \"$transcr_id\"; exon_id \"$exon_id\"\n" ;
 						}
 				}
-			
 		}
 		
 		exit 0;