[Bioperl-l] Package status for 1.5.2

Sendu Bala bix at sendu.me.uk
Mon Sep 25 11:33:20 EDT 2006


Sendu Bala wrote:
> Sendu Bala wrote:
>
> t/IO_psi.........ok 1/21# Test 7 got: "pylori 26695" (t/IO_psi.t at line 
> 60)
> #   Expected: "Helicobacter pylori 26695"
> #  t/IO_psi.t line 60 is: ok 
> $proteins[0]->species->binomial,"Helicobacter pylori 26695";
> t/IO_psi.........NOK 7# Test 16 got: "virus 40" (t/IO_psi.t at line 81) 
> 
> #    Expected: "Simian virus 40"
> #  t/IO_psi.t line 81 is: ok $proteins[0]->species->binomial,"Simian 
> virus 40";
> t/IO_psi.........FAILED tests 7, 16 
>
> So this is 'just' another taxonomy issue. I'll look into it.

I've committed a fix but it involves a slight behaviour change - now it 
acts how you might have expected Bio::Species to behave on funky virus 
and bacteria names from other classes like SeqIO: the binomial of 
'Helicobacter pylori 26695' is 'Helicobacter pylori' and the binomial of 
'Simian virus 40' is 'Simian virus'. I changed the tests to ask for 
binomial('FULL') instead, which is what you might have done in the old 
days to get the full name. (Nowadays you would ask for the 
scientific_name()).


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