view release on metacpan or  search on metacpan

lib/Bio/BioStudio/GBrowse.pm  view on Meta::CPAN

sub _path_in_repository
{
  my ($chromosome) = @_;
  my $path = _dir_in_repository($chromosome);
  $path .= $chromosome->name . ".conf";
  return $path;
}

=head2 _create_chromosome_conf()

=cut

sub _create_chromosome_conf
{
  my ($chromosome) = @_;
	
  my $name = $chromosome->name();
  #Grab chromosome configuration template
  my $template_p = _gbrowse_template();
  open (my $BSCONF, '<', $template_p)
    || croak "BSERROR: Can't open configuration template $template_p : $OS_ERROR";
  my $BSref = do {local $/ = <$BSCONF>};
  close $BSCONF;

  #make edits
  #my $dbengine = $chromosome->db_engine();
  #if ($dbengine ne 'memory')
  #{
  #  my $adaptor = 'DBI::' . $dbengine;
  #  my $handlestring = '-dsn ' . _connectstring($name, $dbengine);
  #  my $userstring = '-user ' . _user($dbengine);
  #  my $passstring = '-pass ' . _pass($dbengine);
  #  $BSref =~ s{\*ENGINE\*}{$adaptor}msixg;
  #  $BSref =~ s{\*DBARG2\*}{$handlestring}msixg;
  #  $BSref =~ s{\*DBARG3\*}{$userstring}msixg;
  #  $BSref =~ s{\*DBARG4\*}{$passstring}msixg;
  #}
  #else
  #{
    my $adaptor = 'DBI::SQLite';
    my $dsn = '-dsn dbi:SQLite:database=' . $chromosome->path_to_DB();
    $BSref =~ s{\*ENGINE\*}{$adaptor}msixg;
    $BSref =~ s{\*DBARG2\*}{$dsn}msixg;
    $BSref =~ s{\*DBARG3\*}{}msixg;
    $BSref =~ s{\*DBARG4\*}{}msixg;
  #}
  
  my $seqid = $chromosome->seq_id();
  my $landmark = $seqid . q{:1..} . $chromosome->len();
	$BSref =~ s{\*LANDMARK\*}{$landmark}msixg;
  
	$BSref =~ s{\*VERSION\*}{$name}msixg;
  
	#$BSref =~ s{\*VERSIONNOTE\*}{}msixg;

  #Compute chromosome confpath, create directories if path is new
  my $conf_p = _path_in_repository($chromosome);

  #Write out chromosome configuration file
	open (my $CONF, '>', $conf_p);
  system "chmod 777 $conf_p";
	print $CONF $BSref;
	close $CONF;
  return $conf_p;
}

=head2 _add_to_GBrowse_conf()

=cut

sub _add_to_GBrowse_conf
{
  my ($chromosome) = @_;

  my $chrname = $chromosome->name();
  my $conf_p = _path_in_repository($chromosome);
  my $gbconf_p = _path_to_conf();
  
  #Read GBrowse conf file;
  open (my $CONFIN, '<', $gbconf_p)
    || croak "BSERROR: Can't open GBrowse conf $gbconf_p : $OS_ERROR";
  my $GBref = do {local $/ = <$CONFIN>};
  close $CONFIN;

  #if it doesn't have the chromosome, add a section
  if ($GBref !~ m{\[$chrname\]}msix)
  {
    open (my $CONFOUT, '>>', $gbconf_p)
      || croak "BSERROR: can't write GBrowse conf $gbconf_p : $OS_ERROR";
    print $CONFOUT "\n[$chrname]\n";
    print $CONFOUT "description     = $chrname\n";
    print $CONFOUT "path            = $conf_p\n";
    close $CONFOUT;
  }
	return 1;
}

=head2 _parse_gbrowse_colors()

=cut

sub _parse_gbrowse_colors
{
  my $bs_dir = Bio::BioStudio::ConfigData->config('conf_path') . 'gbrowse/';
  my $path = $bs_dir . 'GBrowse_colors.yaml';
  my $colorhref = {};
  return $colorhref unless (-e $path);

  my $yaml = YAML::Tiny->read($path);
  foreach my $tag (keys %{$yaml->[0]})
  {
    $colorhref->{$tag} = $yaml->[0]->{$tag};
  }
  return $colorhref;
}

=head2 get_cache_handle

=cut

sub get_cache_handle