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lib/Bio/Grid/Run/SGE/Util.pm  view on Meta::CPAN

  for my $dir (@dirs) {
    push @expanded_dirs, bsd_glob( $dir, GLOB_TILDE | GLOB_ERR );
    confess 'glob error' if (GLOB_ERROR);
  }

  return unless (@expanded_dirs);

  @expanded_dirs = map { File::Spec->rel2abs($_) } @expanded_dirs;

  return wantarray ? @expanded_dirs : ( shift @expanded_dirs );
}

sub glob_list {
  my $input_files = shift;

  my @abs_input_files;
  for my $glob_pattern (@$input_files) {
    my @files = my_glob($glob_pattern);
    next unless ( @files > 0 );
    for my $f (@files) {
      confess "Couldn't find/access $f" unless ( -f $f || -d $f );
    }
    push @abs_input_files, @files;
  }
  confess "INDEX: no input files found" unless ( @abs_input_files > 0 );

  return \@abs_input_files;
}

sub my_glob {
  my (@dirs) = @_;

  return unless defined wantarray;    # don't bother doing more
  my @expanded_dirs;
  for my $dir (@dirs) {
    push @expanded_dirs, bsd_glob( $dir, GLOB_TILDE | GLOB_ERR );
    confess 'glob error' if (GLOB_ERROR);
  }

  cluck "no results in glob: " . join( ", ", @dirs ) unless (@expanded_dirs);

  @expanded_dirs = map { File::Spec->rel2abs($_) } @expanded_dirs;

  return wantarray ? @expanded_dirs : ( shift @expanded_dirs );
}

sub expand_path {
  my @expanded = expand_path_rel(@_);
  @expanded = map { File::Spec->rel2abs($_) } @expanded;
  return wantarray ? @expanded : ( shift @expanded );
}

sub expand_path_rel {
  my @files = @_;
  my @expanded;
  for my $file (@files) {
    confess "trying to expand empty path" unless($file);
    $file =~ s{ ^ ~ ( [^/]* ) }
            { $1
                ? (getpwnam($1))[7]
                : ( $ENV{HOME} || $ENV{LOGDIR} || (getpwuid($>))[7] )
            }ex;
    push @expanded, $file;
  }

  return wantarray ? @expanded : ( shift @expanded );
}


sub my_mkdir {
  my ($path) = @_;

  eval { mkpath($path) };
  if ($@) {
    confess "Couldn't create $path: $@";
  }
}

sub delete_by_regex {
  my ( $dir, $file_regex, $simulate ) = @_;

  $dir = my_glob($dir);

  opendir( my $dh, $dir ) || die "can't opendir >$dir< $!";
  for ( readdir($dh) ) {
    if (/$file_regex/) {
      my $file = File::Spec->catfile( $dir, $_ );
      if ($simulate) {
        print STDERR $file;
      } else {
        unlink $file;
      }
    }
  }
  closedir $dh;
  return;
}

sub concat_files {
  my $c = shift;

  my $dir = expand_path( $c->{result_dir} );

  my $file_regex = qr/\Q$c->{job_name}\E #job name
                        \.j$c->{job_id} #the job id
                        \.[0-9]+ #the sge task id
                        \.c[\-0-9]+(?:\.[\w\-.#]+)? # combination idx
                        (?:\..*)? #suffix
                        $/x;

  my @to_be_unlinked;
  open my $concat_fh, '>', catfile( $dir, "$c->{job_name}.j$c->{job_id}.result.concat" )
    or confess "Can't open filehandle: $!";

  my @paths = path($dir)->children($file_regex);
  for my $abs_f (@paths) {
    open my $fh, '<', $abs_f or confess "Can't open filehandle for $abs_f: $!";
    while ( my $line = <$fh> ) { print $concat_fh $line; }
    $fh->close;
    push @to_be_unlinked, $abs_f;
  }