[Bioperl-l] Problem about bioperl SeqIO

claratsm at hkusua.hku.hk claratsm at hkusua.hku.hk
Sun Jan 9 11:02:36 EST 2005


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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