Bio-BioStudio

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Build.PL  view on Meta::CPAN

    'gbrowse_plugins/BS_RepeatSmasher.pm',
  ];
  require GBrowse::ConfigData;
  my $plugin_path = GBrowse::ConfigData->config('conf') . q{/} . 'plugins/';
  $BSB->config_data(gbrowse_plugin_path => $plugin_path);
  $BSB->add_build_element('gbrowse_plugins');
  $BSB->install_path(gbrowse_plugins => $plugin_path);
  print "\tWill install gbrowse plugins in $plugin_path\n";
  print "\tWill run with gbrowse installation in $gba\n";
  $BSB->process_gbrowse_files($plugins);
  chmod 0777, GBrowse::ConfigData->config('conf') . q{/} . 'GBrowse.conf';
}

$BSB->config_data(SGE_support => $sge);
if ( $BSB->config_data('SGE_support') )
{
  print "\tWill enable qsub\n";
}

#Optionally configure BLAST+ if Standalonetools is installed
$BSB->config_data(blast_support => $bl);

install_util/BioStudioInstall.pm  view on Meta::CPAN

use strict;
use warnings;

sub ACTION_install
{
  my $self = shift;
  $self->SUPER::ACTION_install;
  my $confpath = $self->config_data('conf_path');
  $confpath = $self->_endslash($confpath);
  my $command = "chmod -R 777 $confpath*";
  print $command, "\n";
  system $command;
  print "\n";
}

sub process_conf_files
{
  my $BSB = shift;
  my $files = shift;
  return unless $files;

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

  
	$BSref =~ s{\*VERSION\*}{$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

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

sub _prepare_repository
{
  my ($repo, $species, $chrnum) = @_;
  $repo = _endslash($repo) || _repobase();
  return unless ($species);
  my $spath = $repo . $species . q{/};
  my $cpath = undef;
  if (! -e $spath)
  {
    mkdir $spath;
    chmod 0777, $spath;
  }
  if ($chrnum)
  {
    $cpath = $spath . $chrnum . q{/};
    if (! -e $cpath)
    {
      mkdir $cpath;
      chmod 0777, $cpath;
    }
  }
  return $chrnum  ? $cpath  : $spath;
}

=head2 _endslash

=cut

sub _endslash

lib/Bio/BioStudio/RestrictionEnzyme/Seek.pm  view on Meta::CPAN

      push @reals, $out;
    }
    else
    {
      print "Failed on $out\n";
    }
  }
  my $loadpath = $tmp_path . $key . q{_} . $redbname . '.load';
  my $catcmd = "cat @reals > $loadpath";
  safeopen($catcmd);
  chmod 0777, $loadpath;
  my $REDB = Bio::BioStudio::RestrictionEnzyme::Store->new
  (
    -name => $redbname,
    -enzyme_definitions => $RES,
    -create => 1,
    -file => $loadpath
  );
  $REDB->dumpfile($loadpath);
  $REDB->load();
  push @CLEANUP, @OUTS, @{$morefiles};

lib/Bio/BioStudio/RestrictionEnzyme/Seek.pm  view on Meta::CPAN

  my @regs = grep {$_->class ne 'IIB'} values %{$RES};
  my @bees = grep {$_->class eq 'IIB'} values %{$RES};

  ## Create and populate the prefix tree of restriction enzyme recognition sites
  my $tree = $chr->GD->build_prefix_tree(-input => \@regs, -peptide => 1);

  my $tmp_path = Bio::BioStudio::ConfigData->config('tmp_path');
  my $filename = $tmp_path . $redbname . '.out';
  #my @feats = sort {$b->end - $b->start <=> $a->end - $a->start} @{$featlist};
  my @feats = sort {$a->end - $a->start <=> $b->end - $b->start} @{$featlist};
  chmod 0777, $filename;
  open my $OUT, '>', $filename;
  foreach my $feat (@feats)
  {
    my $id = $feat->display_name;
    #print "Checking $id\n";
    my $results;
    my $besults;
    if ($feat->primary_tag eq 'CDS')
    {
      $besults = find_IIBs_in_CDS($chr, \@bees, $feat);