1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691
|
#!/usr/bin/env python
"""Tests private methods of SearchPath and SearchNode classes.
"""
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import NonnegIntError
from cogent.seqsim.searchpath import SearchPath, SearchNode
__author__ = "Amanda Birmingham"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Amanda Birmingham"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Amanda Birmingham"
__email__ = "amanda.birmingham@thermofisher.com"
__status__ = "Production"
class SearchPathHelper(object):
"""Contains data and function defs used by public AND private tests"""
#all primers have certain forbidden sequences: no runs longer than 3 of
#any purines or pyrimidines
standard_forbid_seq = ['AAAA', 'GAAA', 'AGAA', 'GGAA', 'AAGA', 'GAGA', \
'AGGA', 'GGGA', 'AAAG', 'GAAG', 'AGAG', 'GGAG', \
'AAGG', 'GAGG', 'AGGG', 'GGGG', 'CCCC', 'TCCC', \
'CTCC', 'TTCC', 'CCTC', 'TCTC', 'CTTC', 'TTTC', \
'CCCT', 'TCCT', 'CTCT', 'TTCT', 'CCTT', 'TCTT', \
'CTTT', 'TTTT']
alphabets = {SearchPath.DEFAULT_KEY:"ACGT"}
#end SearchPathHelper
class SearchNodeHelper(object):
"""Contains data and function defs used by public AND private tests"""
#list of possible bases at any position
alphabet = ["A", "C", "G", "T"]
#end SearchNodeHelper
class SearchPathTests(TestCase):
"""Tests public SearchPath methods."""
#-------------------------------------------------------------------
#Tests of clearNodes
def test_clearNodes(self):
"""Should empty path stack and variable forbidden"""
#create a searchpath and add just one node
test = SearchPath(SearchPathHelper.alphabets)
test.generate(1)
#now call clear and make sure path value is "" (empty)
test.clearNodes()
self.assertEquals(test.Value, "")
#end test_clearNodes
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Tests of generate method
def tripletGenerator(self, pathobj, path_length):
"""Helper function to generate primers and catalogue triplets"""
found_triplets = {}
#make a hundred random searchpaths
for i in xrange(100):
curr_path_val = pathobj.generate(path_length)
#now find all the triplets in this path
for r in xrange(path_length-2):
curr_triplet = curr_path_val[r:r+3]
found_triplets[curr_triplet] = True
#end if
#clear out the path
pathobj.clearNodes()
#next rand sequence
return found_triplets
#end tripletGenerator
def test_generate_fullCoverage(self):
"""With no constraints, should produce all possible triplets"""
path_length = 20
test = SearchPath(SearchPathHelper.alphabets)
#make a hundred random searchpaths and see what triplets produced
found_triplets = self.tripletGenerator(test, path_length)
num_found = len(found_triplets.keys())
self.assertEquals(num_found, 64)
#end test_generate_fullCoverage
def test_generate_withForbidden(self):
"""With 2 triplet constraints, should produce all others"""
forbidden_triplet = ["ATG", "CCT"]
path_length = 20
test = SearchPath(SearchPathHelper.alphabets, forbidden_triplet)
#make a hundred random searchpaths and see what triplets produced
found_triplets = self.tripletGenerator(test, path_length)
num_found = len(found_triplets.keys())
self.assertEquals(num_found, 62)
#end test_generate_oneForbidden
def test_generate_nonePossible(self):
"""Should return null if no path can match constraints"""
alphabet = {SearchPath.DEFAULT_KEY:"AB"}
#forbid all combinations of alphabet
forbidden_seqs = ["AA", "AB", "BB", "BA"]
test = SearchPath(alphabet, forbidden_seqs)
output = test.generate(2)
self.assertEquals(output, None)
#end test_generate_nonePossible
def test_generate_multiple(self):
"""Should be able to call generate multiple times to extend path"""
test = SearchPath(SearchPathHelper.alphabets)
output1 = test.generate(2)
output2 = test.generate(3)
#make sure that the length of the path is now three
self.assertEquals(len(output2), 3)
#make sure that the new path is a superset of the old one
self.assertEquals(output1, output2[:2])
#end test_generate_multiple
def test_generate_correctAlph(self):
"""Should get correct alphabet even if node is popped then readded"""
test_alphs = {0:"A",1:"BC",2:"D",3:"E",SearchPath.DEFAULT_KEY:"X"}
forbidden_seqs = ["CD"]
test = SearchPath(test_alphs, forbidden_seqs)
#given these position alphabets and this forbidden seq,
#the only legal 3-node searchpath should be ABD. Make
#a hundred searchpaths and make sure this is the only one
#that actually shows up.
found_paths = {}
for i in xrange(100):
curr_path = test.generate(3)
found_paths[curr_path] = True
test.clearNodes()
#next
#make sure there is only one path found and that it is the right one
found_path_str = str("".join(found_paths.keys()))
self.assertEquals(len(found_paths), 1)
self.assertEquals(found_path_str, "ABD")
#end test_generate_correctAlph
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Tests of findAllowedOption
def test_findAllowedOption_currentAllowed(self):
"""Should return true when current option is allowed"""
#searchpath with no forbidden seqs, so anything should work
test = SearchPath(SearchPathHelper.alphabets)
test._add_node(SearchNode(SearchNodeHelper.alphabet))
allowed_found = test.findAllowedOption()
self.assertEquals(allowed_found, True)
#end test_findAllowedOption_currentAllowed
def test_findAllowedOption_otherAllowed(self):
"""Should return true when curr option is bad but another is good"""
node_vals = []
#create a path and put in 2 nodes; since all the forbidden seqs I
#used to init the path have 4 entries, there should be no chance that
#the path I just created has anything forbidden in it
test = self._fill_path(2, node_vals)
#add the existing path value to the forbidden list
test._fixed_forbidden["".join(node_vals)] = True
test._forbidden_lengths[2] = True
#call findAllowedOption ... should find next available good option
allowed_found = test.findAllowedOption()
self.assertEquals(allowed_found, True)
#end test_findAllowedOption_otherAllowed
def test_findAllowedOption_none(self):
"""Should return false if curr option is bad and no good exist"""
test = self._fill_path(1)
self._empty_top(test)
#get the value of the top node's only remaining option;
#add to forbidden
last_option = test._get_top().Options
test._fixed_forbidden["".join(last_option)] = True
test._forbidden_lengths[1] = True
#now make sure we get back result that no options for path remain
allowed_found = test.findAllowedOption()
self.assertEquals(allowed_found, False)
#end test_findAllowedOption_none
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Tests of removeOption
#Helper function
def _fill_path(self, num_nodes, node_vals = []):
"""create a searchpath and add searchnodes; return path"""
test = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
for i in xrange(num_nodes):
curr_node = SearchNode(SearchNodeHelper.alphabet)
node_vals.append(curr_node.Value)
test._add_node(curr_node)
#next i
return test
#end _fill_path
#Helper function
def _empty_top(self, spath):
"""remove all but one options from the top node"""
top_node = spath._get_top()
num_options = len(top_node.Options)
for i in xrange(num_options-1): top_node.removeOption()
#end _empty_top
def test_removeOption_simple(self):
"""Should correctly remove option from untapped node"""
#create a searchpath and a searchnode
test = self._fill_path(1)
orig_len_minus1 = len(test._get_top().Options) - 1
#also check that remove result is true: node still has options
has_options = test.removeOption()
self.assertEqual(has_options, True)
#get the top node and make sure that it has fewer options
top_node = test._get_top()
option_len = len(top_node.Options)
self.assertEqual(option_len, orig_len_minus1)
#end test_removeOption_simple
def test_removeOption_empty(self):
"""Should return False if removing option leads to empty stack"""
#create a searchpath with just one searchnode, then (almost) empty it
test = self._fill_path(1)
self._empty_top(test)
#now remove the last option, and make sure the stack is now empty
some_left = test.removeOption()
self.assertEquals(some_left, False)
#end test_removeOption_empty
def test_removeOption_recurse(self):
"""Should correctly remove empty node and curr option of next"""
#put two nodes in the search path and almost empty the top one
test = self._fill_path(2)
self._empty_top(test)
test.removeOption()
#make sure there's only one item left in the path
self.assertEquals(len(test._path_stack), 1)
#make sure that it has one fewer options
top_node = test._get_top()
self.assertEquals(len(top_node.Options), len(top_node.Alphabet)-1)
#end test_removeOption_recurse
#-------------------------------------------------------------------
#end SearchPathTests
class SearchNodeTests(TestCase):
"""Tests public SearchNode methods."""
#-------------------------------------------------------------------
#Tests of removeOption method
def test_removeOption_someLeft(self):
"""removeOption should cull options and return T when some left."""
#create a search node and get its current value
test = SearchNode(SearchNodeHelper.alphabet)
last_val = test.Value
some_left = test.removeOption()
#new current value must be different from old
#and return value must be true
self.assertNotEqual(test.Value, last_val)
self.assertEqual(some_left, True)
#end test_removeOption_someLeft
def test_removeOption_noneLeft(self):
"""removeOption should cull options and return F when none left."""
test = SearchNode(SearchNodeHelper.alphabet)
num_options = len(test.Options)
#removeOption num_options times: that should get 'em all
for i in xrange(num_options): some_left = test.removeOption()
#return value should be false (no options remain)
self.assertEqual(some_left, False)
#end test_removeOption_noneLeft
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Test of options property (and _get_options method)
def test_options(self):
"""Should return a copy of real options"""
test = SearchNode(SearchNodeHelper.alphabet)
optionsA = test.Options
del optionsA[0]
optionsB = test.Options
self.assertNotEqual(len(optionsA), len(optionsB))
#end test_options
#-------------------------------------------------------------------
#end SearchNodeTests
class SearchPathTests_private(TestCase):
"""Tests for private SearchPath methods."""
#No need to test __str__: just calls toString in general_tools
#No need to test _accept_option or _remove_accepted_option: they
#simply pass in the base class implementation
#No need to test _in_extra_forbidden: just returns False in base class
#implementation
#-------------------------------------------------------------------
#Helper functions
def _fill_path(self, num_nodes, node_vals = []):
"""create a searchpath and add searchnodes; return path"""
test = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
for i in xrange(num_nodes):
curr_node = SearchNode(SearchNodeHelper.alphabet)
node_vals.append(curr_node.Value)
test._add_node(curr_node)
#next i
return test
#end _fill_path
def _empty_top(self, spath):
"""remove all but one options from the top node"""
top_node = spath._get_top()
num_options = len(top_node.Options)
for i in xrange(num_options-1): top_node.removeOption()
#end _empty_top
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Tests of __init__
def test_init_noForbid(self):
"""Init should correctly set private properties w/o forbid list"""
test = SearchPath(SearchPathHelper.alphabets)
real_result = len(test._fixed_forbidden.keys())
self.assertEquals(real_result, 0)
#end test_init_noForbid
def test_init_withForbid(self):
"""Init should correctly set private properties, w/forbid list"""
user_input = SearchPathHelper.standard_forbid_seq[:]
user_input.extend(["AUG", "aaaaccuag"])
test = SearchPath(SearchPathHelper.alphabets, user_input)
user_input = [i.upper() for i in user_input]
user_input.sort()
real_result = test._fixed_forbidden.keys()
real_result.sort()
self.assertEquals(str(real_result), str(user_input))
#end test_init_withForbid
def test_init_badAlphabets(self):
"""Init should fail if alphabets param is not dictionary-like"""
self.assertRaises(ValueError, SearchPath, "blue")
#end test_init_badAlphabets
def test_init_noDefault(self):
"""Init should fail if alphabets param has no 'default' key"""
self.assertRaises(ValueError, SearchPath, {12:"A"})
#end test_init_noDefault
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Tests of value property (and _get_value method)
def test_value_empty(self):
"""Should return empty string when path is empty"""
test = SearchPath(SearchPathHelper.alphabets)
self.assertEquals(test.Value, "")
#end test_value_empty
def test_value(self):
"""Should return string of node values when nodes exist"""
node_vals = []
test = self._fill_path(3, node_vals)
self.assertEquals(test.Value, "".join(node_vals))
#end test_value
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Tests of _top_index property (and _get_top_index method)
def test_top_index(self):
"""Should return index of top node when one exists"""
test = self._fill_path(3)
top_index = test._top_index
self.assertEquals(top_index,2)
#end test_top_index
def test_top_index_None(self):
"""Should return None when stack has no entries"""
test = SearchPath(SearchPathHelper.alphabets)
top_index = test._top_index
self.assertEquals(top_index, None)
#end test_top_index_None
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Tests of _get_top method
def test_get_top(self):
"""Should return a reference to top node on stack if there is one"""
test = SearchPath(SearchPathHelper.alphabets)
test._add_node(SearchNode(SearchNodeHelper.alphabet))
topnode = SearchNode(SearchNodeHelper.alphabet)
test._add_node(topnode)
resultnode = test._get_top()
self.assertEquals(resultnode, topnode)
#end test_get_top
def test_get_top_None(self):
"""Should return None if stack is empty"""
test = SearchPath(SearchPathHelper.alphabets)
topnode = test._get_top()
self.assertEquals(topnode, None)
#end test_get_top_None
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Test of _get_forbidden_lengths
def test_get_forbidden_lengths(self):
"""get_forbidden_lengths should return dict of forbidden seq lens"""
correct_result = str([3, 4, 9])
user_input = SearchPathHelper.standard_forbid_seq[:]
user_input.extend(["AUG", "aaaaccuag"])
test = SearchPath(SearchPathHelper.alphabets, user_input)
real_dict = test._get_forbidden_lengths()
real_list = real_dict.keys()
real_list.sort()
real_result = str(real_list)
self.assertEquals(real_result, correct_result)
#end test_get_forbidden_lengths
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Tests of _add_node
def test_add_node_first(self):
"""add_node should correctly add first node and increase top index."""
test = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
test_node = SearchNode(SearchNodeHelper.alphabet)
test._add_node(test_node)
self.assertEquals(len(test._path_stack), 1)
self.assertEquals(test._top_index, 0)
#end test_add_node_first
def test_add_node_subsequent(self):
"""add_node should correctly add additional nodes and up top index."""
test = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
test_node = SearchNode(SearchNodeHelper.alphabet)
test_node2 = SearchNode(SearchNodeHelper.alphabet)
test._add_node(test_node)
test._add_node(test_node2)
self.assertEquals(len(test._path_stack), 2)
self.assertEquals(test._top_index, 1)
#end test_add_node_subsequent
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Tests of _get_nmer
def test_get_nmer(self):
"""get_nmer should return correct nmer for n <= length of stack"""
node_values = []
n = 4
test_path = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
for i in xrange(n+1):
curr_node = SearchNode(SearchNodeHelper.alphabet)
test_path._add_node(curr_node)
node_values.append(curr_node.Value)
#next
#get a nmer, and get the last n values that were put on stack;
#should be the same
real_result = test_path._get_nmer(n)
correct_result = "".join(node_values[-n:])
self.assertEquals(real_result, correct_result)
#end test_get_nmer
def test_get_nmer_tooLong(self):
"""get_nmer should return None for n > length of stack"""
test_path = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
test_node = SearchNode(SearchNodeHelper.alphabet)
test_path._add_node(test_node)
#stack is 1 long. Ask for a 2 mer
real_result = test_path._get_nmer(2)
self.assertEquals(real_result, None)
#end test_get_nmer_tooLong
def test_get_nmer_len1(self):
"""get_nmer should return correct result for nmer 1 on full stack"""
test_path = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
test_node = SearchNode(SearchNodeHelper.alphabet)
test_path._add_node(test_node)
correct_result = test_node.Value
real_result = test_path._get_nmer(1)
self.assertEquals(real_result, correct_result)
#end test_get_nmer_len1
def test_get_nmer_len0(self):
"""get_nmer should return an empty string if n is 0"""
#if n is zero, this should return "" even when stack is empty
test_path = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
real_result = test_path._get_nmer(0)
self.assertEquals(real_result, "")
#end test_get_nmer_len0
def test_get_nmer_badArg(self):
"""get_nmer should error if given a non integer-castable n"""
test_path = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
self.assertRaises(NonnegIntError, test_path._get_nmer, "blue")
#end test_get_nmer_badArg
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Tests of _check_forbidden_seqs
def test_check_forbidden_seqs_fixed(self):
"""Should return True if path includes a fixed forbidden seq"""
forbidden_seq = ["G", "U", "A"]
user_input = ["".join(forbidden_seq)]
user_input.extend(SearchPathHelper.standard_forbid_seq)
test = SearchPath(SearchPathHelper.alphabets, user_input)
test._add_node(SearchNode(SearchNodeHelper.alphabet))
#add more values, and cheat so as to make them something forbidden
for bad_val in forbidden_seq:
curr_node = SearchNode(SearchNodeHelper.alphabet)
curr_node._options[0] = bad_val #torque the node's innards
test._add_node(curr_node)
#next bad_val
real_result = test._check_forbidden_seqs()
self.assertEquals(real_result, True)
#end test_check_forbidden_seqs_fixed
def test_check_forbidden_seqs_none(self):
"""Should return False if path includes no forbidden seqs"""
#a seq that isn't in the standard fixed forbidden lib
allowed_seq = ["C", "U", "A", "T"]
test = SearchPath(SearchPathHelper.alphabets, \
SearchPathHelper.standard_forbid_seq)
test._add_node(SearchNode(SearchNodeHelper.alphabet))
#add more values, and cheat so as to make them something known
for known_val in allowed_seq:
curr_node = SearchNode(SearchNodeHelper.alphabet)
curr_node._options[0] = known_val #torque the node's innards
test._add_node(curr_node)
#next bad_val
real_result = test._check_forbidden_seqs()
self.assertEquals(real_result, False)
#end test_check_forbidden_seqs_fixed
#-------------------------------------------------------------------
#-------------------------------------------------------------------
#Tests of _get_alphabet
def test_get_alphabet_exists(self):
"""Should return alphabet for position when one exists"""
alph1 = "G"
alph2 = "ACGT"
test_alphs = {0:alph1, 2:alph1, SearchPath.DEFAULT_KEY:alph2}
test = SearchPath(test_alphs)
real_alph = test._get_alphabet(2)
self.assertEquals(str(real_alph), alph1)
#end test_get_alphabet_exists
def test_get_alphabet_default(self):
"""Should return default alphabet if none defined for position"""
#SearchPathHelper.alphabets has only a default entry
test = SearchPath(SearchPathHelper.alphabets)
real_alph = test._get_alphabet(0)
correct_alph = SearchPathHelper.alphabets[SearchPath.DEFAULT_KEY]
self.assertEquals(str(real_alph), str(correct_alph))
#end test_get_alphabet_default
def test_get_alphabet_badPosition(self):
"""Should raise error if input isn't castable to nonneg int"""
test = SearchPath(SearchPathHelper.alphabets)
self.assertRaises(NonnegIntError, test._get_alphabet, "blue")
#end test_get_alphabet_badPosition
#-------------------------------------------------------------------
#end SearchPathTests_private
class SearchNodeTests_private(TestCase):
"""Tests for private SearchNode methods."""
#No need to test __str__: just calls toString in general_tools
#No need to test _get_value and the value property: just references
#an item in an array
#No need to test _get_alphabet and alphabet property: ibid
#-------------------------------------------------------------------
#Tests of __init__
def test_init_noArg(self):
"""Init should correctly set private properties w/no arg"""
correct_result = str(SearchNodeHelper.alphabet)
test = SearchNode(SearchNodeHelper.alphabet)
options = test.Options
options.sort()
real_result = str(options)
self.assertEquals(real_result, correct_result)
#end test_init_noArg
#-------------------------------------------------------------------
#end SearchNodeTests_private
if __name__ == '__main__':
main()
|