[Bioperl-l] Root::IO tempfile error

[Charles Hauser]

All,

I'm working on a web blast script and it appears that Bio::SeqIO is not
writing the temp file for the input sequence.
(I'm using CVS version of bioperl updated this am)

If I output $tempfile, Bio::Root::IO appears to be creating it:

	/scratch/B3ltaJkxr4

but if I look in /scratch nada, and if I let the script execute blast
and attempt to open the results($tempfile.bls.txt) I get the server
error below.

ideas?

thanks Charles


relevant snippet of code:

    use constant TEMPOUTDIR  => '/scratch';

    my $io = new Bio::Root::IO;
    my ($tfh,$tempfile) = $io->tempfile(-DIR => TEMPOUTDIR);
    my $out = new Bio::SeqIO(-fh => $tfh, -format => 'fasta');
    $out->write_seq($seq);
    $out->close();

    [snip set up blast params  ]

    my $blastexe = "$prog -i $tempfile -o $tempfile.bls.txt -d ".BLASTDIR."/$db E=$evalue $options";
    `$blastexe`;

    my $parser = new Bio::SearchIO(-file   => "$tempfile.bls.txt",
				   -format => 'blast');




------------- EXCEPTION  -------------
MSG: Could not open /scratch/B3ltaJkxr4.bls.txt: No such file or directory
STACK Bio::Root::IO::_initialize_io /usr/local/src/bioperl/core/Bio/Root/IO.pm:273
STACK Bio::Root::IO::new /usr/local/src/bioperl/core/Bio/Root/IO.pm:213
STACK Bio::SearchIO::new /usr/local/src/bioperl/core/Bio/SearchIO.pm:135
STACK Bio::SearchIO::new /usr/local/src/bioperl/core/Bio/SearchIO.pm:167
STACK toplevel /var/www/cgi-bin/BLAST/foo.pl:217