[Bioperl-l] Root::IO tempfile error

Charles Hauser chauser at duke.edu
Tue Mar 2 19:13:06 EST 2004


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:


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.


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');

    [snip set up blast params  ]

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

    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

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