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HMMER testsuite
CVS $Id: README,v 1.5 2003/04/04 00:33:11 eddy Exp $
Some tests are compiled programs. To compile them:
% make
Once they're compiled, to run the whole test suite, do:
% ./sqc 2 exercises.sqc . ../src
#####################################################################
List of compiled test drivers.
---------------------------------------------------------------------
- A test driver runs with no arguments, gives no output,
and returns EXIT_SUCCESS if the test passes.
- If the test fails, the test driver calls Die() to print a diagnostic on
stderr, and exit with EXIT_FAILURE.
- The -v option always activates rudimentary verbose output on stdout.
Current tests:
---------------
alignalign_test
Exercises P7ViterbiAlignAlignment() -- alignment of a fixed
multiple alignment to an HMM. Aligns fn3 seed alignment to
fn3 model, compares to results of aligning sequences individually;
if an excessive number of discrepancies are detected, test
fails.
Other files: fn3.seed, fn3.hmm.
evd_test
Exercises code in histogram.c, especially EVD fitting
Default generates 1000 EVD samples; fits EVD; tests that fitted
parameters are reasonably close to real ones.
masks_test
Exercises code in masks.c
Default runs XNU on a sequence and compares to a known result.
parsingviterbi_test
Exercises P7ParsingViterbi() in core_algorithms.c
Runs Fn3 model against titin using both standard Viterbi and
ParsingViterbi; compares results for identity.
tophits_test
Exercises tophits.c
Generates random scores in three tiers (good, middling, bad).
Uses RegisterHit() API; FullSort's them; tests that they
end up in the right number/order.
trace_test
Exercises traceback code in core_algorithms.c
Runs a simple HMM against synthetic sequences designed to
exercise all possible arrangements of transitions, and
does a TraceVerify() to be sure resulting trace is internally
consistent.
viterbi_exercise
Exercises P7Viterbi and P7SmallViterbi in core_algorithms.c
Configures Fn3 model into various modes; generates 100 random
seqs from each configuration; does P7Viterbi and P7SmallViterbi
alignments, TraceVerify()'s them, checks them for identity.
weeviterbi_test
Exercises P7WeeViterbi in core_algorithms.c
Runs RRM model against two subsequences of human U1A;
compares Viterbi trace to WeeViterbi trace.
#####################################################################
Other test scripts.
---------------------------------------------------------------------
test1-conversion.pl
Makes sure that hmmconvert produces identical HMMs from
byteswapped (initially different) binary HMM files.
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