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

[Rob Edwards]

It is hard to locate the exact error without more information. The  
error is caused because at some point you are trying to get a sequence  
that starts at position 2002, but the sequence is only 2001 nt long  
(hence the error that 2002 must be < 2001). I would suggest that the  
error is at some point where you are taking the 2kb fragment around the  
site. The most obvious thing to start with is what are the start/end  
coordinates that are called immediately before the error, and do they  
make sense given the length of the sequence?

Rob



On Jan 25, 2005, at 9:45 AM, Garrett Sorensen wrote:

> 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
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