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lib/Bio/ViennaNGS/UCSC.pm  view on Meta::CPAN

sub make_assembly_hub{
  my ($fasta_path, $filesdir, $basedir, $baseURL, $big_wig_ids, $log) = @_;
  my ($basename,$dir,$ext);
  my $this_function = (caller(0))[3];
  #check arguments
  croak ("ERROR [$this_function] \$fasta_path does not exist\n") 
    unless (-e $fasta_path);
  croak ("ERROR [$this_function] \$basedir does not exist\n") 
    unless (-d $basedir);
  croak ("ERROR [$this_function]: no URL (network location for upload to UCSC) provided") 
    unless(defined $baseURL);

  unless ($baseURL =~ /\/$/) { $baseURL .= "/"; }

  my $tmp_path = dist_file('Bio-ViennaNGS', "hub.txt" );
  ($basename,$dir,$ext) = fileparse($tmp_path,qr/\..*/);
  my $template_path = dir($dir,"template-AssemblyHub");

  croak ("ERROR [$this_function] template directory not found\n") 
    unless (-d $template_path);

lib/Bio/ViennaNGS/UCSC.pm  view on Meta::CPAN

sub make_track_hub{
  my ($species, $basedir, $baseURL, $big_bed_ids, $big_wig_ids, $log) = @_;
  my ($basename,$dir,$ext);
  my $this_function = (caller(0))[3];

  #check arguments
  croak ("ERROR [$this_function] \no species provided\n")
    unless ($species);
  croak ("ERROR [$this_function] \$basedir does not exist\n")
    unless (-d $basedir);
  croak ("ERROR [$this_function]: no URL (network location for upload to UCSC) provided")
    unless(defined $baseURL);

  if (defined $log){
    open(LOG, ">>", $log) or croak "$!";
  }

  unless ($baseURL =~ /\/$/) { $baseURL .= "/"; }

  my $tmp_path = dist_file('Bio-ViennaNGS', "hub.txt" );
  ($basename,$dir,$ext) = fileparse($tmp_path,qr/\..*/);

lib/Bio/ViennaNGS/UCSC.pm  view on Meta::CPAN

Build track hubs for the UCSC genome browser.
This function takes 4 parameters:

=over

=item 1 chromosome id as used in existing ucsc assembly hub (e.g. chr1)

=item 2 path to the ouput directory (e.g. /home/user/assemblyhubs/)

=item 3 base URL where the output folder will be placed for upload to the UCSC genome browser (e.g. http://www.foo.com/folder/)

=item 4 path for the log file (/home/user/logs/assemblyhubconstructionlog)

=back

=head1 SEE ALSO

=over

=item L<Bio::ViennaNGS>