[Bioperl-l] Restriction Enzyme cuts on Circular plasmids

[Rob Edwards]

The following is a quick patch for Bio/Restriction/Analysis.pm so that 
it handles circular sequences correctly if there is another cut site in 
the region that has been linearized. At the moment it won't handle a 
single cut site at that point (e.g. pBR322 has a single EcoRI site at 
the point it is circularized). I am not sure how to deal with this and 
need to think about it (the fragments are right but the cut sites are 
not).

Can someone submit it for me?

I have submitted a Bugzilla report as #1548

120c120,121
< for further analysis. However, this will change the start of the
---
 > for further analysis. This fragment will also be checked for cuts
 > by the enzyme(s). However, this will change the start of the
737c738,749
<                 unshift (@re_frags, $last.$first);
---
 >               my $newfrag=$last.$first;
 >               my @cuts = split /($beforeseq)($afterseq)/i, $newfrag;
 >               my @newfrags;
 >               if ($#cuts) {
 >                # there is another cut
 >                for (my $i=0; $i<=$#cuts; $i+=2) {push (@newfrags, 
$cuts[$i].$cuts[$i+1])}
 >               }
 >               else {
 >                # there isn't another cut
 >                push (@newfrags, $newfrag);
 >               }
 >               push @re_frags, @newfrags;


Thanks

Rob