[Bioperl-l] Package status for 1.5.2
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
> # Expected: "Helicobacter pylori 26695"
> # t/IO_psi.t line 60 is: ok
> $proteins->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->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
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