[Bioperl-l] StandAloneFasta::version

Nathan S. Haigh n.haigh at sheffield.ac.uk
Tue Nov 7 02:05:40 EST 2006


Chris Fields wrote:
> Nathan,
>
> Weren't the problems with the reported StandAloneFasta.pm test fails 
> due to differences in the returned order of the Hits/HSPs in the FASTA 
> reports from the different versions?  The test results you posted on 
> the wiki (where I commented on this) seem to indicate that:
>
> not ok 11
> # Test 11 got: "0" (t/StandAloneFasta.t at line 75)
> #    Expected: "994"
> #  t/StandAloneFasta.t line 75 is: ok $hsp->num_identical, 994;
> not ok 12
> # Test 12 got: "1977" (t/StandAloneFasta.t at line 76)
> #    Expected: "994"
> #  t/StandAloneFasta.t line 76 is: ok $hsp->length, 994;
> ok 13
> not ok 14
> # Test 14 got: "0" (t/StandAloneFasta.t at line 88)
> #    Expected: "994"
> #  t/StandAloneFasta.t line 88 is: ok $hsp->num_identical, 994;
> not ok 15
> # Test 15 got: "1977" (t/StandAloneFasta.t at line 89)
> #    Expected: "994"
> #  t/StandAloneFasta.t line 89 is: ok $hsp->length, 994;
>
> It looks like a value is returned for the tests, so parsing isn't 
> broken.  They just aren't returned in the order specified, so the 
> tests are faulty, not the parsing.  The tests could be fixed by using 
> id/score key/value pairs in a hash or something similar.  We probably 
> shouldn't limit to a specific version unless parsing is actually broken.
>
> Chris
>
Chris,

I agree, I was going to update the tests later this morning :-P  Any 
thoughts about version() or should I just leave it be for now?

Cheers
Nath


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