[Bioperl-l] Bug in Bio::Restriction::Analysis

Chris Fields cjfields at illinois.edu
Thu Mar 3 17:42:41 EST 2011


Elia, Steve,

Any tests we can add for this?  I ran tests with the changes below and had several failing ones, but when only implementing the first fix ('unless (defined($cut_positions[0]))') all tests pass.  Seems to be a coordinate issue (string-based positions are 0-based, bioperl coords are 1-based).

chris

On Mar 3, 2011, at 3:45 PM, Steve Chervitz wrote:

> Good catch, Elia. Looks like an legitimate edge case. Your fix looks
> reasonable to me, but I haven't tried running it through the regression
> tests to see if it breaks anything else.
> 
> Would be good to get this fix into the upcoming release.
> 
> Cheers,
> Steve
> 
> 
> On Thu, Mar 3, 2011 at 8:50 AM, Elia Stupka <e.stupka at ucl.ac.uk> wrote:
> 
>> Hi Steve and Rob,
>> 
>> it's been sometime since I last plunged my head into the code, but today we
>> nailed a bug in Bio::Restriction::Analysis.
>> 
>> Basically if a sequence has a restriction site which is exactly at the
>> start of the sequence, it fails to produce any sites. The  culprits is this
>> line (536 of Analysis.pm)
>> 
>> unless ($cut_positions[0]) {
>> 
>> where if the position is zero, it will fail to execute the rest of the
>> code, so I changed it to:
>> 
>> unless (defined($cut_positions[0])) {
>> 
>> Also, for similar reasons a bit further down this line:
>> 
>> my $start=1; my $stop; my %seq; my %stop;
>> 
>> needs to change to:
>> my $start=0; my $stop; my %seq; my %stop;
>> 
>> I didn't commit the changes because I wanted to check if it makes sense,
>> etc.
>> 
>> The bug seems reproducible also in older, stable versions of bioperl, such
>> as 1.4 and 1.6...
>> 
>> best
>> 
>> Elia
>> 
>> 
>> 
>> ---
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>> 
> -- 
> Steve Chervitz, Ph.D.
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