[Bioperl-l] Makefile; Funkiness with _rearrange issues and - on alignments

[Lincoln Stein]

Mea culpa.  I was in crisis management mode because of the GKB web site 
failing, and did not run all the regression tests before checking in.

I would be very happy to go back to the original _rearrange() before all the 
recent changes.

Lincoln

On Saturday 14 December 2002 02:19 pm, Ewan Birney wrote:
> I am in serious 1.2 debugging mode. There are actually alot of failing
> tests on my platform at the least (alpha, 5.6.1). Somethings:
>
> Makefile
> --------
>
> I have put in the suggested fix from the MakeMaker team and I believe this
> means that our Makefile.PL will work on all platforms. Could other Irix
> and Dec people check this out.
>
>
> Seq/Alphabet
>
>
> Lincoln and Hilmar - I guess you haven't been running make test across the
> entire platform when you were changing _rearrange (bad, bad).
>
>
> If you had you would have noticed that AlignIO was mysteriously failing on
> an internal sequence. after *alot* of messing around I discovered that
> Bio::PrimarySeq() called rearrange- someone thought it was a good idea to
> be able to pass in arguments like
>
>    $pseq_obj->seq( -seq => $seq_string, -alphabet => 'dna');
>
> however, most people passed arguments like:
>
>    $pseq_obj->seq($seq_string)
>
> which works fine *except* for cases like
>
>    >AKH_HAEIN/114-431
>
>    -----------------VEDAVKATIDCRGEKLSIAMMKAWFEARGY-S--VHIVDPVKQ
>
> which, with new the fixes to _rearrange triggered the
> anti-misnumbered-rearrange fix just popped in.
>
>
> After some humming and harring I decided that seq on primary_seq should
> not be this leathly complicated argument detecting thing, and removed it.
>
>
>   Does anyone *USE* the syntax
>
>    $primary_seq_object(-seq => $seq_as_string, -alphabet => 'dna');
>
> (notice that lots of people use this for new, but not for seq).
>
>
>
> Fix is committed, which fixed lots of AlignIO and BLAST test failing.
>
>
> I still have the following tests failing which I will get around to
> tomorrow if noone else beats me to it.
>
>
>
> Failed Test    Stat Wstat Total Fail  Failed  List of Failed
> ---------------------------------------------------------------------------
>---- t/BlastIndex.t   -1    11    13   11  84.62%  3-13
> t/Index.t        79 20224    12   12 100.00%  1-12
> t/PhylipDist.t                6   ??       %  ??
> 5 subtests skipped.
> Failed 3/132 test scripts, 97.73% okay. 11/5854 subtests failed, 99.81%
> okay.
>
>
>
>
>
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>.
> -----------------------------------------------------------------
>
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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================