[Bioperl-l] t/SeqIO.t -- improvements?
MEC at stowers-institute.org
Thu Sep 7 14:16:18 EDT 2006
Jey, et al,
I like this idea and have wondered the same in the past.
I have sometimes done exactly what Jay is suggesting: I code a script,
validate its output independently, and then save the 'validated' output
as reference for future tests. For instance, I wrote a script TFBSscan
(basically a wrapper around TFBS modules) whose test.t looks like this:
use Test::More tests => 6;
#./TFBSscan --notag_db --DBmatrix JASPAR=PFM:ID:MA0026,MA0100,MA0002
./t/testseqs.fasta > ./t/t1.out &
# I manaully validated ./t/t1.out, so, now lets it the basis for a test:
$diff = `TFBSscan --notag_db --DBmatrix
JASPAR=PFM:ID:MA0026,MA0100,MA0002 ./t/testseqs.fasta | diff ./t/t1.out
ok (! $diff, 'JASPAR') or diag("here's the unexpected difference
I figured that there are some useful abstractions one could put on top
of this, perhaps in another Test:: module, but I've not seen it.
I'm curious in general as to others' approaches to this both in BioPerl
project and elsewhere.
>From: bioperl-l-bounces at lists.open-bio.org
>[mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Jay Hannah
>Sent: Thursday, September 07, 2006 12:37 PM
>Subject: [Bioperl-l] t/SeqIO.t -- improvements?
>So if I understand t/SeqIO.t correctly it reads (for example)
>and if nothing explodes the test passes.
>Wouldn't it be better if:
>(1) fasta.out was generated to contain *all* sequences, not
>just the first.
>(2) a test was added to verify that fasta.out exactly matches
>test.fasta (diff is blank).
>Or have I misunderstood something?
>Are patches welcome? Shall I submit the patch to this mailing
>list or elsewhere? Should I worry about Windows compatibility?
>Bioperl-l mailing list
>Bioperl-l at lists.open-bio.org
More information about the Bioperl-l