[Bioperl-l] Bio::Restriction::Analysis cut site problem in 1.5.2

Steven Brown sdbrown at annular.org
Wed Feb 7 18:41:13 EST 2007


The module seems to have trouble handling the cut-site specifiers  
that surround the sequence that the enzyme is specific for.  The error:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Bad end parameter (22). End must be less than the total length  
of sequence (total=6)
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/lib/perl5/site_perl/5.8.6/ 
Bio/Root/Root.pm:328
STACK: Bio::PrimarySeq::subseq /usr/local/lib/perl5/site_perl/5.8.6/ 
Bio/PrimarySeq.pm:371
STACK: Bio::Restriction::Analysis::_enzyme_sites /usr/local/lib/perl5/ 
site_perl/5.8.6/Bio/Restriction/Analysis.pm:884
STACK: Bio::Restriction::Analysis::_cuts /usr/local/lib/perl5/ 
site_perl/5.8.6/Bio/Restriction/Analysis.pm:785
STACK: Bio::Restriction::Analysis::cut /usr/local/lib/perl5/site_perl/ 
5.8.6/Bio/Restriction/Analysis.pm:369
STACK: Bio::Restriction::Analysis::cutters /usr/local/lib/perl5/ 
site_perl/5.8.6/Bio/Restriction/Analysis.pm:678
---snip (my script line)---
-----------------------------------------------------------

The offending enzyme:

---snip---
<1>AcuI
<2>Eco57I,Bsp6II,BspD6II,BspKT5I,Eco112I,Eco125I,FsfI
<3>CTGAAG(16/14)
---snip---

If I get rid of the (16/14) the error disappears and the right  
sequence site is matched.  It seems like maybe a decision was made  
not analyze enzymes with remote cut positions, or the code wouldn't  
throw the error...?  Any information on this would be helpful.

Thanks,
Steve


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