[Bioperl-l] Strange BioPerl/Perl problem!

[Lynn Stevens]

Hi All,

I am new to Perl and BioPerl and I have encountered a strange problem
with a script that I have written.

The script uses the System commmand to access a large DNA contig (2
million or so bases long).  I place this contig into a BioPerl seq
object and then manipulate it in various ways (using Seq->subseq) and
seq->length).  In the end I print out a much smaller subseq of the
original contig.  My script performs this function on 1000s of contigs
in a while loop ... or alternatively, I have a slightly different
script that just performs the function above once (and then I just
invoke it 1000's of times by using a shell script).

Either way, the script runs perfectly for the 1000's of sequences,
giving me the correct output (which is generally a 500 bp sequence for
each call).

However, if I start running the script more than once (several
processes going at the same time), I get lots of exceptions....of
various sorts.  They are different everytime.  This happens even when
I am running similar scripts with different names.  The only thing
that seems to make logical sense to me is that the vaiables in the
BioPerl modules are getting confused. However, I can understand why
this should occur.

Any thoughts or suggestions would be appreciated!

Lynn


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