[Bioperl-l] Problem about bioperl SeqIO

[Marc Logghe]

Hi,
Not sure, but the temporary files should be deleted as soon as the objects are destroyed.
Maybe you keep a lot of Bio::Seq::LargePrimarySeq references in scope so that for all of them the temp files are kept open ?
You *can* get to the filename but it is not intended to do so because it is a private method (_filename).

HTH,
Marc


-----Oorspronkelijk bericht-----
Van: bioperl-l-bounces at portal.open-bio.org namens claratsm at hkusua.hku.hk
Verzonden: zo 9-1-2005 17:02
Aan: bioperl-l at portal.open-bio.org
Onderwerp: [Bioperl-l] Problem about bioperl SeqIO
 
Hi,

I am a new user of bioperl and I have encountered some problems when using it
for programming. As i try to deal with a very large file, as large as a large
chromosome contigs data, so I use 
    my $seqio_mfa = Bio::SeqIO->new('-file' => $seq_file, 
                                    '-format' => 'largefasta');
However, whenever I get a subseq, it generates one temp file. And the number of
temp files generated is too large (even though most are empty) such that the
program stop with exception...something like cannot create temp file any more.
Am I able to delete the temp file during the running of my program? How can i
get the temp file name of each new sequence generated? If i can get the temp
file name, is it safe to delete the file using rmdir function?

Can anybody help me!!
Thank you


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