[Bioperl-l] Restriction::Analysis strange error - please help

[Garrett Sorensen]

Hello,  I'm new to the mailing list.  Thanks in advance for any help.

I'm really stumped by the following error when running restriction
analysis on large numbers of seq objects.  This only occurs sometimes
when dealing with large numbers of sequences.


------------- EXCEPTION  -------------
MSG: Bad start,end parameters. Start [2002] has to be less than end [2001]
STACK Bio::PrimarySeq::subseq
/home/garrett/Perl/lib/perl5/site_perl/5.8.5/Bio/PrimarySeq.pm:362
STACK Bio::Seq::subseq
/home/garrett/Perl/lib/perl5/site_perl/5.8.5/Bio/Seq.pm:636
STACK Bio::Restriction::Analysis::fragment_maps
/home/garrett/Perl/lib/perl5/site_perl/5.8.5/Bio/Restriction/Analysis.pm:552
STACK toplevel Restriction_analyser_multi_CpG_a.pl:182


Incase it helps here is what my program is doing:
-Reads in multiple fasta sequences (~7kb average size) on at a time
and creates a SeqIO object for each.
-Restriction sites for a particular enzyme are determined for each
SeqIO object and then a fragment 2kb in size is created around that
site.
-A new Seq object is created using the above fragment using
"$upStreamSeqobj = Bio::Seq->new (-seq => $upStreamSeq);"
-This new Seq object is fed into Restriction Analysis to generate
fragments for another enzyme.

Thanks so much for any help, best regards,
Garrett