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

Chris Fields cjfields at illinois.edu
Thu Mar 3 17:57:57 EST 2011


Forgot to add the summary, just for completeness. lots of errors like this that are halting tests:

------------- EXCEPTION -------------
MSG: Bad start parameter (0). Start must be positive.
STACK Bio::PrimarySeq::subseq /Users/cjfields/bioperl/bioperl-live/blib/lib/Bio/PrimarySeq.pm:400
STACK Bio::Restriction::Analysis::fragment_maps Bio/Restriction/Analysis.pm:556
STACK toplevel t/Restriction/Analysis-refac.t:143
-------------------------------------

Test Summary Report
-------------------
t/Restriction/Analysis-refac.t (Wstat: 65280 Tests: 26 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 91 tests but ran 26.
t/Restriction/Analysis.t      (Wstat: 65280 Tests: 118 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 177 tests but ran 118.
t/Restriction/Gel.t           (Wstat: 65280 Tests: 3 Failed: 0)
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 9 tests but ran 3.
Files=4, Tests=165, 29 wallclock secs ( 0.05 usr  0.03 sys +  3.44 cusr  0.21 csys =  3.73 CPU)
Result: FAIL
Failed 3/4 test programs. 0/165 subtests failed.

-c

On Mar 3, 2011, at 4:42 PM, Chris Fields wrote:

> 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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>>> Senior Lecturer, Bioinformatics
>>> 
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>>> University College London
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>>> London
>>> UK
>>> 
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>>> 
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>>> 
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>>> 
>>> 
>>> 
>>> 
>> -- 
>> Steve Chervitz, Ph.D.
>> Omicia Inc. |  Senior Computational Biologist
>> 2200 Powell Street, Ste 525, Emeryville CA 94608
>> T 510-595-0800 | F 510-588-4523 | M 510-390-3613 | schervitz at omicia.com
>> 
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> 
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