MfAnnotGeneCommandSet.pir

#
# This class represents the content of a configuration
# file used by mfannot; that file stores a list of external
# programs (with their arguments) that are used to add
# further annotations; the output of the programs are
# expected to be a series of XML documents of type
# AnnotPairCollection.
#

- PerlClass PirObject::MfAnnotGeneCommandSet
- InheritsFrom  PirObject
- FieldsTable

# Field name            Struct          Type            Comments
#---------------------- --------------- --------------- -----------------------
debug                   single          string          any perl true/false
genename                single          string          genename
percontig               single          string          0 or 1, not yet implemented
filerank                single          int4
commandset              hash            <MfAnnotGeneCommands>  keys = "pre", "post", or 0 .. n

- EndFieldsTable
- Methods

our $DEBUG = 0; # class global; debug can also be turned on for each object, see above
our $RCS_VERSION='$Id: MfAnnotGeneCommandSet.pir,v 1.4 2009/05/08 15:30:59 nbeck Exp $';
our ($VERSION) = ($RCS_VERSION =~ m#,v ([\w\.]+)#);

sub set_debug {
  my $self = shift;
  $self->debug(@_);
}

sub debug {
  my $self = shift;
  return $self->AUTO_debug() unless @_;
  my $commandset = $self->get_commandset();
  foreach my $genecom (values %$commandset) {
    $genecom->set_debug(@_);
  }
  $self->AUTO_debug(@_);
}

sub Execute {
  my $self          = shift;
  my $cwd           = shift || ""; # cwd of bashcommands
  my $tmpdir        = shift || ""; # where we can create temp files
  my $substitutions = shift || {};  # hash VAR => val to substitute in place of the string %VAR% in bashcommands

  die "Error: no valid CWD supplied for Execute()... got '$cwd'.\n"       unless $cwd && -d $cwd;
  die "Error: no valid TMPDIR supplied for Execute()... got '$tmpdir'.\n" unless $tmpdir && -d $tmpdir;

  my $debug        = $self->get_debug() || $DEBUG;
  $self->set_debug($debug); # propagate to each MfAnnotGeneCommands under us
  my $genename     = $self->get_genename() || "unk";

  my $commandset  = $self->get_commandset();
  my @commandkeys = sort { $a <=> $b } grep(/^\d+$/,keys %$commandset);

  my $outfilename  = $substitutions->{"OUTFILE"} || "";
  my $foundoutfile = 0;
  my ($outcapt,$errcapt) = ("(none)","(none)");
  foreach my $commandkey ( "pre", @commandkeys, "post" ) {
    my $genecom = $commandset->{$commandkey} || next; # ignore missing optional blocks
    next if $foundoutfile && $commandkey =~ m#^\d+$#;
    my $commandlabel = $commandkey eq "pre"
               ? "A-Pre"
               : $commandkey eq "post"
               ? "C-Post"
               : "B-$commandkey";
    ($outcapt,$errcapt) = $genecom->Execute($cwd,$tmpdir,$substitutions,$commandlabel);
    $foundoutfile = 1 if (-f $outfilename && -s _ > 0);
  }
  
  ($outcapt,$errcapt);
}