diff --git a/misc-scripts/import/import_bed_simple_feature.pl b/misc-scripts/import/import_bed_simple_feature.pl index 383f20e49e88c04da5ba65b390eeeb03a237eb6a..9ff21a62a1e01e7d665fa3f07a44ddc22cec1860 100644 --- a/misc-scripts/import/import_bed_simple_feature.pl +++ b/misc-scripts/import/import_bed_simple_feature.pl @@ -18,21 +18,22 @@ use File::Fetch; my ($url,$db_name,$db_host,$db_user,$db_pass,$db_port,$db_version,$help,$species,$group); my ($logic_name, $description, $display_label); +my ($directory); $species = "human"; $group = 'core'; GetOptions ("url|file=s" => \$url, - "db_name|name|database=s" => \$db_name, - "db_host|host=s" => \$db_host, - "db_user|user|username=s" => \$db_user, - "db_pass|pass|password=s" => \$db_pass, - "db_port|port=s" => \$db_port, - "db_version|version=s" => \$db_version, + "db_name|dbname|database=s" => \$db_name, + "db_host|dbhost|host=s" => \$db_host, + "db_user|dbuser|user|username=s" => \$db_user, + "db_pass|dbpass|pass|password=s" => \$db_pass, + "db_port|dbport|port=s" => \$db_port, "species=s" => \$species, 'group=s' => \$group, 'logic_name=s' => \$logic_name, 'description=s' => \$description, 'display_label=s' => \$display_label, + 'directory=s' => \$directory, "h!" => \$help, "help!" => \$help, ); @@ -48,8 +49,7 @@ my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new( -host => $db_host, -user => $db_user, -pass => $db_pass, - -port => $db_port, - -db_version => $db_version, + -port => $db_port ); run(); @@ -67,7 +67,8 @@ sub get_file { } else { my $file_fetch = File::Fetch->new(uri=>$url); - $file = $file_fetch->fetch() or die "Unable to get data from given URL. ".$file_fetch->error; + my @args = ($directory) ? ('to', $directory) : (); + $file = $file_fetch->fetch(@args) or die "Unable to get data from given URL. ".$file_fetch->error; } return $file; } @@ -151,21 +152,42 @@ Description: Import data from a BED file into the simple_feature table. Only supports 6 column BED files (location, name and score). +Synopsis: + + perl import_bed_simple_feature.pl -url [PATH} -db_name NAME + Options: -url Supply the URL to download from or file path + -directory Location to download to; defaults to current directory -logic_name Analysis logic name import data against + -db_name The DB to add these features to + -database + -dbname + -db_host Hostname for the DB - -db_user - -db_pass - -db_port - -db_version + -host + -dbhost + + -db_user Username for the DB + -user + -username + -dbuser + + -db_pass Password for the DB + -pass + -password + -dbpass + + -db_port Port for the DB + -dbport + -port + -species Name of the species; defaults to human -group Name of the DB group; defaults to core -description Analysis description; only needed if analysis is not already in the DB -display_label Analysis display label for the website; only needed if analysis is not already in the DB - -help "; } \ No newline at end of file