[Bioperl-l] Root::IO tempfile error

[Marc Logghe]

Hi Charles,
You have to pass the UNLINK argument, saying you don't want to delete the file as soon as the filehandle is closed. By default it is 1.
This should work:
my ($tfh,$tempfile) = $io->tempfile(-DIR => TEMPOUTDIR, -UNLINK => 0);

HTH,
Marc

> -----Original Message-----
> From: Charles Hauser [mailto:chauser at duke.edu]
> Sent: woensdag 3 maart 2004 1:13
> To: BioPerl-List
> Subject: [Bioperl-l] Root::IO tempfile error
> 
> 
> 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
>  
> 
> 
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