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lib/Bio/DB/BigWigSet.pm  view on Meta::CPAN

	unless URI::URL->can('new');

    my $ua  = LWP::UserAgent->new;
    my $response = $ua->get($dir,Accept=>'text/html, */*;q=0.1');

    unless ($response->is_success) {
	warn "Web fetch of $dir failed: ",$response->status_line;
	return;
    }

    my $html = $response->decoded_content;
    my $base = $response->base;
    my @wigfiles = map {URI::URL->new($_=>$base)->abs} $html =~ /href="([^\"]+\.bw)"/ig;
    my @indices  = map {URI::URL->new($_=>$base)->abs} $html =~ /href="(meta[^\"]*)"/ig;
    return (\@wigfiles,\@indices);
}


=item $bws->add_bigwig($path)

Given a path to a .bw file, add the BigWig file to the set.

lib/Bio/DB/BigWigSet.pm  view on Meta::CPAN

    $base ||= dirname($file);
    my $f;

    if ($file =~ /^(ftp|http):/i) {
	my $ua = LWP::UserAgent->new;
	my $r  = $ua->get($file);
	die "Couldn't read $file: ",$r->status_line unless $r->is_success;
	eval "require IO::String; 1" 
	    or die "IO::String module is required for remote directories"
	    unless IO::String->can('new');
	$f = IO::String->new($r->decoded_content);
    }
    else {
	$f = IO::File->new($file) or die "$file: $!";
    }
    my ($current_path,%wigs);

    while (<$f>) {
	chomp;
	s/\s+$//;   # strip whitespace at ends of lines
	# strip right-column comments unless they look like colors or html fragments