[Bioperl-l] progress on Bio::Search::Tiling

Mark A. Jensen maj at fortinbras.us
Wed May 27 00:00:38 EDT 2009


Hi All-

Have now looked at all 1093 tests in blast.t. Specifically, I
refactored the portions of t/SearchIO/blast.t that involved the
underlying use of SearchUtils::tile_hsps() to use Tiling::MapTiling
objects instead. The refactored blast.t is called blast-MapTiling.t
and is deposited in bioperl-dev/trunk/t/SearchIO. Other tests are
unchanged from blast.t.

With the current bioperl-dev revision of MapTiling (r15712), I get
6/1095 "failures", which you may judge below. The results indicate to
me that the algorithm is working, and that the translated dna
coordinate transformations (which kick in based on study of the
algorithm name) are correct, at least in this limited set.

Comments *highly* appreciated-- many thanks for any time you spend
considering this.

cheers, 
Mark

...
ok 347
not ok 348
#   Failed test at blast-MapTiling.t line 504.
#          got: '0.3639'
#     expected: '0.3640'
not ok 349
#   Failed test at blast-MapTiling.t line 505.
#          got: '0.3656'
#     expected: '0.3660'
not ok 350
#   Failed test at blast-MapTiling.t line 506.
#          got: '0.5373'
#     expected: '0.5370'
ok 351
...
ok 388
not ok 389 - tricky.wublast(1)
#   Failed test 'tricky.wublast(1)'
#   at blast-MapTiling.t line 571.
#     '0.222'
#         >
#     '0.9'
# Not sure why frac_identical should be > 0.9, when no reported 'Identities' value is greater than 24% /maj
ok 390 - tricky.wublast(2)
ok 391 - tricky.wublast(3)
ok 392 - tricky.wublast(4)
ok 393
not ok 394
#   Failed test at blast-MapTiling.t line 588.
#          got: '0.999'
#     expected: '1.000'
not ok 395
#   Failed test at blast-MapTiling.t line 588.
#          got: '0.940'
#     expected: '0.943'
ok 396
...
ok 1094
ok 1095
# Looks like you failed 6 tests of 1095.



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