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

  {
    remove_tree($blastdir);
    return _make_species_database($species, $repo);
  }
  
  #Recover existing BLAST database
  my $factory = Bio::Tools::Run::StandAloneBlastPlus->new(
    -db_dir  => $blastdir,
    -db_name => _BLAST_name($species),
  );
  return $factory;
}

=head2 _BLAST_name

=cut

sub _BLAST_name
{
  my ($species) = @_;
  return 'BLAST_' . $species;
}

=head2 _path_to_BLAST_database

=cut

sub _path_to_BLAST_database
{
  my ($species, $repo) = @_;
  $repo = _endslash($repo) || _repobase();
  return $repo . $species . q{/} . '_blast/';
}

=head2 _path_to_BLAST_index

=cut

sub _path_to_BLAST_index
{
  my ($species, $repo) = @_;
  my $blbase = _path_to_BLAST_database($species, $repo);
  return $blbase . '_chrindex.txt';  
}

=head2 _fetch_BLAST_index

=cut

sub _fetch_BLAST_index
{
  my ($species, $repo) = @_;
  my $indexpath = _path_to_BLAST_index($species, $repo);
  my %index = ();
  if (-e $indexpath)
  {
    open (my $BLASTINDEX, '<', $indexpath)
      || croak "BS_ERROR: Can't open BLAST index $indexpath : $OS_ERROR";
    my $indexref = do {local $/ = <$BLASTINDEX>};
    close $BLASTINDEX;
    my @indexkeys = split m{\s}, $indexref;
    %index = map {$_ => 1} @indexkeys; 
  }
  return \%index;
}

=head2 _make_BLAST_index

=cut

sub _make_BLAST_index
{
  my ($species, $repo, $chrlist) = @_;
  my $indexpath = _path_to_BLAST_index($species, $repo); 
  my @list = @{$chrlist};
  my $str = join qq{\t}, @list;
  open (my $BLASTINDEX, '>', $indexpath)
    || croak "BS_ERROR: Can't write BLAST index $indexpath : $OS_ERROR";
  print $BLASTINDEX $str;
  close $BLASTINDEX;
  return;
}

=head2 _verify_BLAST_index

=cut

sub _verify_BLAST_index
{
  my ($species, $repo) = @_;
  my %index = %{_fetch_BLAST_index($species, $repo)};
  my @chrs = @{_gather_latest($species, $repo)};
  my %latest = map {$_ => 1} @chrs;
  my $flags = 0;
  foreach my $chr (keys %latest)
  {
    $flags++ if (! exists $index{$chr});
  }
  foreach my $chr (keys %index)
  {
    $flags++ if (! exists $latest{$chr});
  }
  return $flags ? 0 : 1;
}


=head2 _make_species_database

=cut

sub _make_species_database
{
  my ($species, $repo) = @_;
  my @latest = @{_gather_latest($species, $repo)};
  my @blastdata = ();
  foreach my $chrname (@latest)
  {
    my $chr = Bio::BioStudio::Chromosome->new(-name => $chrname);
    my $seqobj = $chr->seqobj;
    my $seqlen = $seqobj->length();
    push @blastdata, $chr->seqobj;