Bio.SearchIO._model.query

20 21 """Class representing search results from a single query. 22 23 QueryResult is the container object that stores all search hits from a 24 single search query. It is the top-level object returned by SearchIO's two 25 main functions, `read` and `parse`. Depending on the search results and 26 search output format, a QueryResult object will contain zero or more Hit 27 objects (see Hit). 28 29 You can take a quick look at a QueryResult's contents and attributes by 30 invoking `print` on it: 31 32 >>> from Bio import SearchIO 33 >>> qresult = SearchIO.parse('Blast/mirna.xml', 'blast-xml').next() 34 >>> print qresult 35 Program: blastn (2.2.27+) 36 Query: 33211 (61) 37 mir_1 38 Target: refseq_rna 39 Hits: ---- ----- ---------------------------------------------------------- 40 # # HSP ID + description 41 ---- ----- ---------------------------------------------------------- 42 0 1 gi|262205317|ref|NR_030195.1| Homo sapiens microRNA 52... 43 1 1 gi|301171311|ref|NR_035856.1| Pan troglodytes microRNA... 44 2 1 gi|270133242|ref|NR_032573.1| Macaca mulatta microRNA ... 45 3 2 gi|301171322|ref|NR_035857.1| Pan troglodytes microRNA... 46 4 1 gi|301171267|ref|NR_035851.1| Pan troglodytes microRNA... 47 5 2 gi|262205330|ref|NR_030198.1| Homo sapiens microRNA 52... 48 6 1 gi|262205302|ref|NR_030191.1| Homo sapiens microRNA 51... 49 7 1 gi|301171259|ref|NR_035850.1| Pan troglodytes microRNA... 50 8 1 gi|262205451|ref|NR_030222.1| Homo sapiens microRNA 51... 51 9 2 gi|301171447|ref|NR_035871.1| Pan troglodytes microRNA... 52 10 1 gi|301171276|ref|NR_035852.1| Pan troglodytes microRNA... 53 11 1 gi|262205290|ref|NR_030188.1| Homo sapiens microRNA 51... 54 ... 55 56 If you just want to know how many hits a QueryResult has, you can invoke 57 `len` on it. Alternatively, you can simply type its name in the interpreter: 58 59 >>> len(qresult) 60 100 61 >>> qresult 62 QueryResult(id='33211', 100 hits) 63 64 QueryResult behaves like a hybrid of Python's built-in list and dictionary. 65 You can retrieve its items (Hit objects) using the integer index of the 66 item, just like regular Python lists: 67 68 >>> first_hit = qresult[0] 69 >>> first_hit 70 Hit(id='gi|262205317|ref|NR_030195.1|', query_id='33211', 1 hsps) 71 72 You can slice QueryResult objects as well. Slicing will return a new 73 QueryResult object containing only the sliced hits: 74 75 >>> sliced_qresult = qresult[:3] # slice the first three hits 76 >>> len(qresult) 77 100 78 >>> len(sliced_qresult) 79 3 80 >>> print sliced_qresult 81 Program: blastn (2.2.27+) 82 Query: 33211 (61) 83 mir_1 84 Target: refseq_rna 85 Hits: ---- ----- ---------------------------------------------------------- 86 # # HSP ID + description 87 ---- ----- ---------------------------------------------------------- 88 0 1 gi|262205317|ref|NR_030195.1| Homo sapiens microRNA 52... 89 1 1 gi|301171311|ref|NR_035856.1| Pan troglodytes microRNA... 90 2 1 gi|270133242|ref|NR_032573.1| Macaca mulatta microRNA ... 91 92 Like Python dictionaries, you can also retrieve hits using the hit's ID. 93 This is useful for retrieving hits that you know should exist in a given 94 search: 95 96 >>> hit = qresult['gi|262205317|ref|NR_030195.1|'] 97 >>> hit 98 Hit(id='gi|262205317|ref|NR_030195.1|', query_id='33211', 1 hsps) 99 100 You can also replace a Hit in QueryResult with another Hit using either the 101 integer index or hit key string. Note that the replacing object must be a 102 Hit that has the same `query_id` property as the QueryResult object. 103 104 If you're not sure whether a QueryResult contains a particular hit, you can 105 use the hit ID to check for membership first: 106 107 >>> 'gi|262205317|ref|NR_030195.1|' in qresult 108 True 109 >>> 'gi|262380031|ref|NR_023426.1|' in qresult 110 False 111 112 Or, if you just want to know the rank / position of a given hit, you can 113 use the hit ID as an argument for the `index` method. Note that the values 114 returned will be zero-based. So zero (0) means the hit is the first in the 115 QueryResult, three (3) means the hit is the fourth item, and so on. If the 116 hit does not exist in the QueryResult, a `ValueError` will be raised. 117 118 >>> qresult.index('gi|262205317|ref|NR_030195.1|') 119 0 120 >>> qresult.index('gi|262205330|ref|NR_030198.1|') 121 5 122 >>> qresult.index('gi|262380031|ref|NR_023426.1|') 123 Traceback (most recent call last): 124 ... 125 ValueError: ... 126 127 To ease working with a large number of hits, QueryResult has several 128 `filter` and `map` methods, analogous to Python's built-in functions with 129 the same names. There are `filter` and `map` methods available for 130 operations over both Hit objects or HSP objects. As an example, here we are 131 using the `hit_map` method to rename all hit IDs within a QueryResult: 132 133 >>> def renamer(hit): 134 ... hit.id = hit.id.split('|')[3] 135 ... return hit 136 >>> mapped_qresult = qresult.hit_map(renamer) 137 >>> print mapped_qresult 138 Program: blastn (2.2.27+) 139 Query: 33211 (61) 140 mir_1 141 Target: refseq_rna 142 Hits: ---- ----- ---------------------------------------------------------- 143 # # HSP ID + description 144 ---- ----- ---------------------------------------------------------- 145 0 1 NR_030195.1 Homo sapiens microRNA 520b (MIR520B), micr... 146 1 1 NR_035856.1 Pan troglodytes microRNA mir-520b (MIR520B... 147 2 1 NR_032573.1 Macaca mulatta microRNA mir-519a (MIR519A)... 148 ... 149 150 The principle for other `map` and `filter` methods are similar: they accept 151 a function, applies it, and returns a new QueryResult object. 152 153 There are also other methods useful for working with list-like objects: 154 `append`, `pop`, and `sort`. More details and examples are available in 155 their respective documentations. 156 157 Finally, just like Python lists and dictionaries, QueryResult objects are 158 iterable. Iteration over QueryResults will yield Hit objects: 159 160 >>> for hit in qresult[:4]: # iterate over the first four items 161 ... hit 162 ... 163 Hit(id='gi|262205317|ref|NR_030195.1|', query_id='33211', 1 hsps) 164 Hit(id='gi|301171311|ref|NR_035856.1|', query_id='33211', 1 hsps) 165 Hit(id='gi|270133242|ref|NR_032573.1|', query_id='33211', 1 hsps) 166 Hit(id='gi|301171322|ref|NR_035857.1|', query_id='33211', 2 hsps) 167 168 If you need access to all the hits in a QueryResult object, you can get 169 them in a list using the `hits` property. Similarly, access to all hit IDs is 170 available through the `hit_keys` property. 171 172 >>> qresult.hits 173 [Hit(id='gi|262205317|ref|NR_030195.1|', query_id='33211', 1 hsps), ...] 174 >>> qresult.hit_keys 175 ['gi|262205317|ref|NR_030195.1|', 'gi|301171311|ref|NR_035856.1|', ...] 176 177 """ 178 179 # attributes we don't want to transfer when creating a new QueryResult class 180 # from this one 181 _NON_STICKY_ATTRS = ('_items',) 182

183 - def __init__(self, id='<unknown id>', hits=[], 184 hit_key_function=lambda hit: hit.id):

185 """Initializes a QueryResult object. 186 187 Arguments: 188 id -- String of query sequence ID. 189 hits -- Iterator returning Hit objects. 190 hit_key_function -- Function to define hit keys, defaults to a function 191 that return Hit object IDs. 192 193 """ 194 if id is None: 195 raise ValueError("Query ID string is required for QueryResult " 196 "creation") 197 198 self._id = id 199 self._hit_key_function = hit_key_function 200 self._items = OrderedDict() 201 self._description = '<unknown description>' 202 self.program = '<unknown program>' 203 self.target = '<unknown target>' 204 self.version = '<unknown version>' 205 206 # validate Hit objects and fill up self._items 207 for hit in hits: 208 # validation is handled by __setitem__ 209 self.append(hit)

210 211 # handle Python 2 OrderedDict behavior 212 if hasattr(OrderedDict, 'iteritems'): 213

214 - def __iter__(self):

215 return iter(self.iterhits())

216 217 @property

218 - def hits(self):

219 """Hit objects contained in the QueryResult.""" 220 return self._items.values()

221 222 @property

223 - def hit_keys(self):

224 """Hit IDs of the Hit objects contained in the QueryResult.""" 225 return self._items.keys()

226 227 @property

228 - def items(self):

229 """List of tuples of Hit IDs and Hit objects.""" 230 return self._items.items()

231

232 - def iterhits(self):

233 """Returns an iterator over the Hit objects.""" 234 for hit in self._items.itervalues(): 235 yield hit

236

237 - def iterhit_keys(self):

238 """Returns an iterator over the ID of the Hit objects.""" 239 for hit_id in self._items.iterkeys(): 240 yield hit_id

241

242 - def iteritems(self):

243 """Returns an iterator yielding tuples of Hit ID and Hit objects.""" 244 for item in self._items.iteritems(): 245 yield item

246 247 else: 248

249 - def __iter__(self):

250 return iter(self.hits)

251 252 @property

253 - def hits(self):

254 """Hit objects contained in the QueryResult.""" 255 return list(self._items.values())

256 257 @property

258 - def hit_keys(self):

259 """Hit IDs of the Hit objects contained in the QueryResult.""" 260 return list(self._items.keys())

261 262 @property

263 - def items(self):

264 """List of tuples of Hit IDs and Hit objects.""" 265 return list(self._items.items())

266

267 - def iterhits(self):

268 """Returns an iterator over the Hit objects.""" 269 for hit in self._items.values(): 270 yield hit

271

272 - def iterhit_keys(self):

273 """Returns an iterator over the ID of the Hit objects.""" 274 for hit_id in self._items.keys(): 275 yield hit_id

276

277 - def iteritems(self):

278 """Returns an iterator yielding tuples of Hit ID and Hit objects.""" 279 for item in self._items.items(): 280 yield item

281

282 - def __contains__(self, hit_key):

283 if isinstance(hit_key, Hit): 284 return self._hit_key_function(hit_key) in self._items 285 return hit_key in self._items

286

287 - def __len__(self):

288 return len(self._items)

289

290 - def __nonzero__(self):

291 return bool(self._items)

292

293 - def __repr__(self):

294 return "QueryResult(id=%r, %r hits)" % (self.id, len(self))

295

296 - def __str__(self):

297 lines = [] 298 299 # set program and version line 300 lines.append('Program: %s (%s)' % (self.program, self.version)) 301 302 # set query id line 303 qid_line = ' Query: %s' % self.id 304 if hasattr(self, 'seq_len'): 305 qid_line += ' (%i)' % self.seq_len 306 if self.description: 307 qid_line += trim_str('\n %s' % self.description, 80, '...') 308 lines.append(qid_line) 309 310 # set target line 311 lines.append(' Target: %s' % self.target) 312 313 # set hit lines 314 if not self.hits: 315 lines.append(' Hits: 0') 316 else: 317 lines.append(' Hits: %s %s %s' % ('-'*4, '-'*5, '-'*58)) 318 pattern = '%13s %5s %56s' 319 lines.append(pattern % ('#', '# HSP', 320 'ID + description'.ljust(58))) 321 lines.append(pattern % ('-'*4, '-'*5, '-'*58)) 322 for idx, hit in enumerate(self.hits): 323 if idx < 30: 324 hid_line = '%s %s' % (hit.id, hit.description) 325 if len(hid_line) > 58: 326 hid_line = hid_line[:55] + '...' 327 lines.append(pattern % (idx, str(len(hit)), 328 hid_line.ljust(58))) 329 elif idx > len(self.hits) - 4: 330 hid_line = '%s %s' % (hit.id, hit.description) 331 if len(hid_line) > 58: 332 hid_line = hid_line[:55] + '...' 333 lines.append(pattern % (idx, str(len(hit)), 334 hid_line.ljust(58))) 335 elif idx == 30: 336 lines.append('%14s' % '~~~') 337 338 return '\n'.join(lines)

339

340 - def __getitem__(self, hit_key):

341 # retrieval using slice objects returns another QueryResult object 342 if isinstance(hit_key, slice): 343 # should we return just a list of Hits instead of a full blown 344 # QueryResult object if it's a slice? 345 hits = list(self.hits)[hit_key] 346 obj = self.__class__(self.id, hits, self._hit_key_function) 347 self._transfer_attrs(obj) 348 return obj 349 350 # if key is an int, then retrieve the Hit at the int index 351 elif isinstance(hit_key, int): 352 return list(self._items.values())[hit_key] 353 354 # if key is a string, then do a regular dictionary retrieval 355 return self._items[hit_key]

356

357 - def __setitem__(self, hit_key, hit):

358 # only accept string keys 359 if not isinstance(hit_key, basestring): 360 raise TypeError("QueryResult object keys must be a string.") 361 # hit must be a Hit object 362 if not isinstance(hit, Hit): 363 raise TypeError("QueryResult objects can only contain Hit objects.") 364 # and it must have the same query ID as this object's ID 365 if hit.query_id != self.id: 366 raise ValueError("Expected Hit with query ID '%s', found '%s' " 367 "instead." % (self.id, hit.query_id)) 368 369 self._items[hit_key] = hit

370

371 - def __delitem__(self, hit_key):

372 # if hit_key an integer or slice, get the corresponding key first 373 # and put it into a list 374 if isinstance(hit_key, int): 375 hit_keys = [list(self.hit_keys)[hit_key]] 376 # the same, if it's a slice 377 elif isinstance(hit_key, slice): 378 hit_keys = list(self.hit_keys)[hit_key] 379 # otherwise put it in a list 380 else: 381 hit_keys = [hit_key] 382 383 for key in hit_keys: 384 del self._items[key] 385 return

386 387 ## properties ## 388 id = partialcascade('_id', 'query_id', """QueryResult ID string""") 389 description = partialcascade('_description', 'query_description', 390 """QueryResult description""") 391 392 @property

393 - def hsps(self):

394 """HSP objects contained in the QueryResult.""" 395 return [hsp for hsp in chain(*self.hits)]

396 397 @property

398 - def fragments(self):

399 """HSPFragment objects contained in the QueryResult.""" 400 return [frag for frag in chain(*self.hsps)]

401 402 ## public methods ##

403 - def absorb(self, hit):

404 """Adds a Hit object to the end of QueryResult. If the QueryResult 405 already has a Hit with the same ID, append the new Hit's HSPs into 406 the existing Hit. 407 408 Arguments: 409 hit -- Hit object to absorb. 410 411 This method is used for file formats that may output the same Hit in 412 separate places, such as BLAT or Exonerate. In both formats, Hit 413 with different strands are put in different places. However, SearchIO 414 considers them to be the same as a Hit object should be all database 415 entries with the same ID, regardless of strand orientation. 416 417 """ 418 try: 419 self.append(hit) 420 except ValueError: 421 assert hit.id in self 422 for hsp in hit: 423 self[hit.id].append(hsp)

424

425 - def append(self, hit):

426 """Adds a Hit object to the end of QueryResult. 427 428 Parameters 429 hit -- Hit object to append. 430 431 Any Hit object appended must have the same `query_id` property as the 432 QueryResult's `id` property. If the hit key already exists, a 433 `ValueError` will be raised. 434 435 """ 436 # if a custom hit_key_function is supplied, use it to define th hit key 437 if self._hit_key_function is not None: 438 hit_key = self._hit_key_function(hit) 439 else: 440 hit_key = hit.id 441 442 if hit_key not in self: 443 self[hit_key] = hit 444 else: 445 raise ValueError("Hit '%s' already present in this QueryResult." % 446 hit_key)

447

448 - def hit_filter(self, func=None):

449 """Creates a new QueryResult object whose Hit objects pass the filter 450 function. 451 452 Arguments: 453 func -- Callback function that accepts a Hit object as its parameter, 454 does a boolean check, and returns True or False 455 456 Here is an example of using `hit_filter` to select Hits whose 457 description begins with the string 'Homo sapiens', case sensitive: 458 459 >>> from Bio import SearchIO 460 >>> qresult = SearchIO.parse('Blast/mirna.xml', 'blast-xml').next() 461 >>> def desc_filter(hit): 462 ... return hit.description.startswith('Homo sapiens') 463 ... 464 >>> len(qresult) 465 100 466 >>> filtered = qresult.hit_filter(desc_filter) 467 >>> len(filtered) 468 39 469 >>> print filtered[:4] 470 Program: blastn (2.2.27+) 471 Query: 33211 (61) 472 mir_1 473 Target: refseq_rna 474 Hits: ---- ----- ---------------------------------------------------------- 475 # # HSP ID + description 476 ---- ----- ---------------------------------------------------------- 477 0 1 gi|262205317|ref|NR_030195.1| Homo sapiens microRNA 52... 478 1 2 gi|262205330|ref|NR_030198.1| Homo sapiens microRNA 52... 479 2 1 gi|262205302|ref|NR_030191.1| Homo sapiens microRNA 51... 480 3 1 gi|262205451|ref|NR_030222.1| Homo sapiens microRNA 51... 481 482 Note that instance attributes (other than the hits) from the unfiltered 483 QueryResult are retained in the filtered object. 484 485 >>> qresult.program == filtered.program 486 True 487 >>> qresult.target == filtered.target 488 True 489 490 """ 491 hits = filter(func, self.hits) 492 obj = self.__class__(self.id, hits, self._hit_key_function) 493 self._transfer_attrs(obj) 494 return obj

495

496 - def hit_map(self, func=None):

497 """Creates a new QueryResult object, mapping the given function to its 498 Hits. 499 500 Arguments: 501 func -- Callback function that accepts a Hit object as its parameter and 502 also returns a Hit object. 503 504 Here is an example of using `hit_map` with a function that discards all 505 HSPs in a Hit except for the first one: 506 507 >>> from Bio import SearchIO 508 >>> qresult = SearchIO.parse('Blast/mirna.xml', 'blast-xml').next() 509 >>> print qresult[:8] 510 Program: blastn (2.2.27+) 511 Query: 33211 (61) 512 mir_1 513 Target: refseq_rna 514 Hits: ---- ----- ---------------------------------------------------------- 515 # # HSP ID + description 516 ---- ----- ---------------------------------------------------------- 517 0 1 gi|262205317|ref|NR_030195.1| Homo sapiens microRNA 52... 518 1 1 gi|301171311|ref|NR_035856.1| Pan troglodytes microRNA... 519 2 1 gi|270133242|ref|NR_032573.1| Macaca mulatta microRNA ... 520 3 2 gi|301171322|ref|NR_035857.1| Pan troglodytes microRNA... 521 4 1 gi|301171267|ref|NR_035851.1| Pan troglodytes microRNA... 522 5 2 gi|262205330|ref|NR_030198.1| Homo sapiens microRNA 52... 523 6 1 gi|262205302|ref|NR_030191.1| Homo sapiens microRNA 51... 524 7 1 gi|301171259|ref|NR_035850.1| Pan troglodytes microRNA... 525 526 >>> top_hsp = lambda hit: hit[:1] 527 >>> mapped_qresult = qresult.hit_map(top_hsp) 528 >>> print mapped_qresult[:8] 529 Program: blastn (2.2.27+) 530 Query: 33211 (61) 531 mir_1 532 Target: refseq_rna 533 Hits: ---- ----- ---------------------------------------------------------- 534 # # HSP ID + description 535 ---- ----- ---------------------------------------------------------- 536 0 1 gi|262205317|ref|NR_030195.1| Homo sapiens microRNA 52... 537 1 1 gi|301171311|ref|NR_035856.1| Pan troglodytes microRNA... 538 2 1 gi|270133242|ref|NR_032573.1| Macaca mulatta microRNA ... 539 3 1 gi|301171322|ref|NR_035857.1| Pan troglodytes microRNA... 540 4 1 gi|301171267|ref|NR_035851.1| Pan troglodytes microRNA... 541 5 1 gi|262205330|ref|NR_030198.1| Homo sapiens microRNA 52... 542 6 1 gi|262205302|ref|NR_030191.1| Homo sapiens microRNA 51... 543 7 1 gi|301171259|ref|NR_035850.1| Pan troglodytes microRNA... 544 545 """ 546 hits = [deepcopy(hit) for hit in self.hits] 547 if func is not None: 548 hits = map(func, hits) 549 obj = self.__class__(self.id, hits, self._hit_key_function) 550 self._transfer_attrs(obj) 551 return obj

552

553 - def hsp_filter(self, func=None):

554 """Creates a new QueryResult object whose HSP objects pass the filter 555 function. 556 557 `hsp_filter` is the same as `hit_filter`, except that it filters 558 directly on each HSP object in every Hit. If a the filtering removes 559 all HSP object in a given Hit, the entire Hit will be discarded. This 560 will result in the QueryResult having less Hit after filtering. 561 562 """ 563 hits = filter(None, (hit.filter(func) for hit in self.hits)) 564 obj = self.__class__(self.id, hits, self._hit_key_function) 565 self._transfer_attrs(obj) 566 return obj

567

568 - def hsp_map(self, func=None):

569 """Creates a new QueryResult object, mapping the given function to its 570 HSPs. 571 572 `hsp_map` is the same as `hit_map`, except that it applies the given 573 function to all HSP objects in every Hit, instead of the Hit objects. 574 575 """ 576 hits = filter(None, (hit.map(func) for hit in list(self.hits)[:])) 577 obj = self.__class__(self.id, hits, self._hit_key_function) 578 self._transfer_attrs(obj) 579 return obj

580 581 # marker for default self.pop() return value 582 # this method is adapted from Python's built in OrderedDict.pop 583 # implementation 584 __marker = object() 585

586 - def pop(self, hit_key=-1, default=__marker):

587 """Removes the specified hit key and return the Hit object. 588 589 Arguments: 590 hit_key -- Integer index or string of hit key that points to a Hit 591 object. 592 default -- Value that will be returned if the Hit object with the 593 specified index or hit key is not found. 594 595 By default, `pop` will remove and return the last Hit object in the 596 QueryResult object. To remove specific Hit objects, you can use its 597 integer index or hit key. 598 599 >>> from Bio import SearchIO 600 >>> qresult = SearchIO.parse('Blast/mirna.xml', 'blast-xml').next() 601 >>> len(qresult) 602 100 603 >>> for hit in qresult[:5]: 604 ... print hit.id 605 ... 606 gi|262205317|ref|NR_030195.1| 607 gi|301171311|ref|NR_035856.1| 608 gi|270133242|ref|NR_032573.1| 609 gi|301171322|ref|NR_035857.1| 610 gi|301171267|ref|NR_035851.1| 611 612 # remove the last hit 613 >>> qresult.pop() 614 Hit(id='gi|397513516|ref|XM_003827011.1|', query_id='33211', 1 hsps) 615 616 # remove the first hit 617 >>> qresult.pop(0) 618 Hit(id='gi|262205317|ref|NR_030195.1|', query_id='33211', 1 hsps) 619 620 # remove hit with the given ID 621 >>> qresult.pop('gi|301171322|ref|NR_035857.1|') 622 Hit(id='gi|301171322|ref|NR_035857.1|', query_id='33211', 2 hsps) 623 624 """ 625 # if key is an integer (index) 626 # get the ID for the Hit object at that index 627 if isinstance(hit_key, int): 628 # raise the appropriate error if there is no hit 629 if not self: 630 raise IndexError("pop from empty list") 631 hit_key = list(self.hit_keys)[hit_key] 632 633 try: 634 return self._items.pop(hit_key) 635 except KeyError: 636 # if key doesn't exist and no default is set, raise a KeyError 637 if default is self.__marker: 638 raise KeyError(hit_key) 639 # if key doesn't exist but a default is set, return the default value 640 return default

641

642 - def index(self, hit_key):

643 """Returns the index of a given hit key, zero-based. 644 645 Arguments: 646 hit_key -- Hit ID string to look up. 647 648 This method is useful for finding out the integer index (usually 649 correlated with search rank) of a given hit key. 650 651 >>> from Bio import SearchIO 652 >>> qresult = SearchIO.parse('Blast/mirna.xml', 'blast-xml').next() 653 >>> qresult.index('gi|301171259|ref|NR_035850.1|') 654 7 655 656 """ 657 if isinstance(hit_key, Hit): 658 return list(self.hit_keys).index(hit_key.id) 659 return list(self.hit_keys).index(hit_key)

660

661 - def sort(self, key=None, reverse=False, in_place=True):

662 # no cmp argument to make sort more Python 3-like 663 """Sorts the Hit objects. 664 665 Arguments: 666 key -- Function used to sort the Hit objects. 667 reverse -- Boolean, whether to reverse the sorting or not. 668 in_place -- Boolean, whether to perform sorting in place (in the same 669 object) or not (creating a new object). 670 671 `sort` defaults to sorting in-place, to mimick Python's `list.sort` 672 method. If you set the `in_place` argument to False, it will treat 673 return a new, sorted QueryResult object and keep the initial one 674 unsorted. 675 676 """ 677 if key is None: 678 # if reverse is True, reverse the hits 679 if reverse: 680 sorted_hits = list(self.hits)[::-1] 681 # otherwise (default options) make a copy of the hits 682 else: 683 sorted_hits = list(self.hits)[:] 684 else: 685 sorted_hits = sorted(self.hits, key=key, reverse=reverse) 686 687 # if sorting is in-place, don't create a new QueryResult object 688 if in_place: 689 new_hits = OrderedDict() 690 for hit in sorted_hits: 691 new_hits[self._hit_key_function(hit)] = hit 692 self._items = new_hits 693 # otherwise, return a new sorted QueryResult object 694 else: 695 obj = self.__class__(self.id, sorted_hits, self._hit_key_function) 696 self._transfer_attrs(obj) 697 return obj

Source Code for Module Bio.SearchIO._model.query