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

{
  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

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

sub parse_fonts
{
  my $bs_dir = _path_to_conf();
  opendir(my $FDIR, $bs_dir);
  my @fonts = grep {$_ =~ m{\.otf\z}msix} readdir($FDIR);
  closedir $FDIR;
  my %fonthsh;
  foreach my $font (@fonts)
  {
    my $path = $bs_dir . $font;
    my ($name, $ext) = split m{\.}, $font;
    $fonthsh{$name} = $path;
  }
  return \%fonthsh;
}

=head2 _path_to_colors

=cut

sub _path_to_colors

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

=cut

sub fetch_comments
{
  my ($self) = @_;
  my $path = $self->path_to_GFF;
  open (my $FILE, '<', $path) || $self->throw("Can't find $path: $OS_ERROR\n");
  my $ref = do {local $/ = <$FILE>};
  close $FILE;
  my @lines = split m{\n}, $ref;
  my @precomments = grep {$_ =~ m{^\# [^\#.]+ }msx} @lines;
  my @comments = map {$_ . "\n"} @precomments;
  return \@comments;
}

=head2 fetch_features

=cut

sub fetch_features