GBrowse

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bin/gbrowse_netinstall.pl  view on Meta::CPAN

  print STDERR "Adding needed PPM repositories. This may take a while....\n";
  for my $name (keys %REPOSITORIES) {
     next if $repository{$name};
     system("ppm rep add $name $REPOSITORIES{$name}");
  }
}

sub find_bioperl_ppm {
  print STDERR "Finding most recent bioperl...";
  open S,"ppm search bioperl |" or die "Couldn't open ppm for listing: $!";
  local $/ = ''; # paragraph mode
  my ($blessed_one,$blessed_version);
  my $best = 0;
  while (<S>) {
    chomp;
    my ($number)     = /^(\d+): bioperl/m;
    my ($version)    = /^\s+Version: (.+)/m;
    my ($repository) = /^\s+Repo: (.+)/m;
    my $multiplier = 10000000;
    my $magnitude  = 0;
    # this dumb thing converts 1.5.1 into a real number

bin/gbrowse_netinstall2.pl  view on Meta::CPAN

  print STDERR "Adding needed PPM repositories. This may take a while....\n";
  for my $name (keys %REPOSITORIES) {
     next if $repository{$name};
     system("ppm rep add $name $REPOSITORIES{$name}");
  }
}

sub find_bioperl_ppm {
  print STDERR "Finding most recent bioperl...";
  open S,"ppm search bioperl |" or die "Couldn't open ppm for listing: $!";
  local $/ = ''; # paragraph mode
  my ($blessed_one,$blessed_version);
  my $best = 0;
  while (<S>) {
    chomp;
    my ($number)     = /^(\d+): bioperl/m;
    my ($version)    = /^\s+Version: (.+)/m;
    my ($repository) = /^\s+Repo: (.+)/m;
    my $multiplier = 10000000;
    my $magnitude  = 0;
    # this dumb thing converts 1.5.1 into a real number

bin/scan_gbrowse.pl  view on Meta::CPAN

    if (is_error($response)) {
	die "Could not scan $url. Status code was $response";
    }
    open my $fh,'<',$dest    or die "Could not open $dest: $!";
    open my $out,'>',$cache  or die "Could not open $cache for writing: $!";

    my ($hostname)    = $url  =~ /^\w+:\/\/([^\/]+)/;
    (my $colon_escape = $url) =~ s/:/\\:/g;

    # paragraph mode to read stanzas
    local $/ = '';
    while (<$fh>) {
	my ($label,$rest)    = /\[([^\]]+)\]\s+(.+)/s;
	my $remote           = "$url?gbgff=1;s=1;t=$label;segment=\$segment";
	chomp($rest);
	print $out <<END;
[${hostname}_${source}_${label}]
remote feature = $remote
category       = Tracks from $colon_escape
$rest

cgi-bin/das  view on Meta::CPAN

    };
    return $result;
}

sub hash_sofile {
    my $self = shift;
    my ($so_file,$so_hash) = @_;
    my %hash;
    tie %hash,'DB_File',$so_hash,Fcntl->O_CREAT|Fcntl->O_RDWR,0666,$DB_File::DB_HASH or return;
    open my $f,$so_file or return;
    local $/ = '';  # paragraph mode
    while (<$f>) {
	next unless /\[Term\]/;
	my ($id)     = /^id: +(SO:\d+)/m;
	my ($name)   = /^name: (.+)/m;
	my @synonyms = /^synonym: "(.+)"/mg;
	$hash{lc $_} = $id foreach ($name,@synonyms);
    }
}

sub types {