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Дата индексирования: Sun Mar 2 07:33:15 2014
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allpy: allpy/base.py annotate

allpy

annotate allpy/base.py @ 293:12a2dfa5f2a8

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Added classes UserDict and UserList in allpy.util
author Daniil Alexeyevsky <me.dendik@gmail.com>
date Thu, 16 Dec 2010 03:10:06 +0300
parents d7ad71def6c8
children cdbc9a9feafe
rev   line source
me@261 1 import sys
me@261 2 import os
me@262 3 import os.path
me@261 4 from tempfile import NamedTemporaryFile
me@262 5 import urllib2
me@261 6
me@261 7 import config
me@284 8 import fasta
me@261 9 from graph import Graph
me@262 10 from Bio.PDB.DSSP import make_dssp_dict
me@260 11 import data.codes
me@260 12
me@260 13 class MonomerType(object):
me@260 14 """Class of monomer types.
me@260 15
me@260 16 Each MonomerType object represents a known monomer type, e.g. Valine,
me@260 17 and is referenced to by each instance of monomer in a given sequence.
me@260 18
me@260 19 - `name`: full name of monomer type
me@260 20 - `code1`: one-letter code
me@260 21 - `code3`: three-letter code
me@260 22 - `is_modified`: either of True or False
me@260 23
me@260 24 class atributes:
me@260 25
me@260 26 - `by_code1`: a mapping from one-letter code to MonomerType object
me@260 27 - `by_code3`: a mapping from three-letter code to MonomerType object
me@260 28 - `by_name`: a mapping from monomer name to MonomerType object
me@260 29 - `instance_type`: class of Monomer objects to use when creating new
me@260 30 objects; this must be redefined in descendent classes
me@260 31
me@260 32 All of the class attributes MUST be redefined when subclassing.
me@260 33 """
me@260 34
me@260 35 by_code1 = {}
me@260 36 by_code3 = {}
me@260 37 by_name = {}
me@260 38 instance_type = None
me@260 39
me@260 40 def __init__(self, name="", code1="", code3="", is_modified=False):
me@260 41 self.name = name.capitalize()
me@260 42 self.code1 = code1.upper()
me@260 43 self.code3 = code3.upper()
me@260 44 self.is_modified = bool(is_modified)
me@260 45 if not is_modified:
me@260 46 self.by_code1[self.code1] = self
me@260 47 self.by_code3[code3] = self
me@260 48 self.by_name[name] = self
me@260 49 # We duplicate distinguished long names into MonomerType itself,
me@260 50 # so that we can use MonomerType.from_code3 to create the relevant
me@260 51 # type of monomer.
me@260 52 MonomerType.by_code3[code3] = self
me@260 53 MonomerType.by_name[name] = self
me@260 54
me@260 55 @classmethod
me@260 56 def _initialize(cls, type_letter, codes=data.codes.codes):
me@260 57 """Create all relevant instances of MonomerType.
me@260 58
me@260 59 `type_letter` is either of:
me@260 60
me@260 61 - 'p' for protein
me@260 62 - 'd' for DNA
me@260 63 - 'r' for RNA
me@260 64
me@260 65 `codes` is a table of monomer codes
me@260 66 """
me@260 67 for type, code1, is_modified, code3, name in codes:
me@260 68 if type == type_letter:
me@260 69 cls(name, code1, code3, is_modified)
me@260 70
me@260 71 @classmethod
me@260 72 def from_code1(cls, code1):
me@260 73 """Return monomer type by one-letter code."""
me@260 74 return cls.by_code1[code1.upper()]
me@260 75
me@260 76 @classmethod
me@260 77 def from_code3(cls, code3):
me@260 78 """Return monomer type by three-letter code."""
me@260 79 return cls.by_code3[code3.upper()]
me@260 80
me@260 81 @classmethod
me@260 82 def from_name(cls, name):
me@260 83 """Return monomer type by name."""
me@260 84 return cls.by_name[name.capitalize()]
me@260 85
me@260 86 def instance(self):
me@260 87 """Create a new monomer of given type."""
me@260 88 return self.instance_type(self)
me@260 89
me@260 90 def __eq__(self, other):
me@260 91 if hasattr(other, "type"):
me@260 92 return self is other.type
me@260 93 return self is other
me@260 94
me@260 95 class Monomer(object):
me@260 96 """Monomer object.
me@260 97
me@260 98 attributes:
me@260 99
me@260 100 - `type`: type of monomer (a MonomerType object)
me@260 101
me@282 102 class attributes:
me@282 103
me@282 104 - `monomer_type`: either MonomerType or one of it's subclasses, it is used
me@282 105 when creating new monomers. It SHOULD be redefined when subclassing
me@282 106 Monomer.
me@260 107 """
me@260 108 monomer_type = MonomerType
me@260 109
me@260 110 def __init__(self, type):
me@260 111 self.type = type
me@260 112
me@260 113 @classmethod
me@260 114 def from_code1(cls, code1):
me@260 115 return cls(cls.monomer_type.by_code1[code1.upper()])
me@260 116
me@260 117 @classmethod
me@260 118 def from_code3(cls, code3):
me@260 119 return cls(cls.monomer_type.by_code3[code3.upper()])
me@260 120
me@260 121 @classmethod
me@260 122 def from_name(cls, name):
me@260 123 return cls(cls.monomer_type.by_name[name.capitalize()])
me@260 124
me@260 125 def __eq__(self, other):
me@260 126 if hasattr(other, "type"):
me@260 127 return self.type is other.type
me@260 128 return self.type is other
bnagaev@239 129
bnagaev@239 130 class Sequence(list):
me@274 131 """Sequence of Monomers.
bnagaev@243 132
me@274 133 This behaves like list of monomer objects. In addition to standard list
me@274 134 behaviour, Sequence has the following attributes:
me@270 135
me@274 136 * name -- str with the name of the sequence
me@274 137 * description -- str with description of the sequence
me@274 138 * source -- str denoting source of the sequence
me@266 139
me@274 140 Any of them may be empty (i.e. hold empty string)
me@275 141
me@275 142 Class attributes:
me@282 143
me@275 144 * monomer_type -- type of monomers in sequence, must be redefined when
me@275 145 subclassing
me@274 146 """
me@270 147
me@275 148 monomer_type = Monomer
me@270 149
me@275 150 name = ''
me@275 151 description = ''
me@275 152 source = ''
me@275 153
me@275 154 def __init__(self, sequence=[], name=None, description=None, source=None):
me@275 155 super(Sequence, self).__init__(sequence)
me@275 156 if hasattr(sequence, 'name'):
me@275 157 vars(self).update(vars(sequence))
me@275 158 if name:
me@275 159 self.name = name
me@275 160 if description:
me@275 161 self.description = description
me@275 162 if source:
me@275 163 self.source = source
me@270 164
me@262 165 def __str__(self):
me@275 166 """Returns sequence in one-letter code."""
me@275 167 return ''.join(monomer.code1 for monomer in self)
me@270 168
me@273 169 @classmethod
me@273 170 def from_string(cls, string, name='', description=''):
me@273 171 """Create sequences from string of one-letter codes."""
me@273 172 monomer = cls.monomer_type.from_code1
me@273 173 monomers = [monomer(letter) for letter in string]
me@273 174 return cls(monomers, name, description)
me@262 175
me@284 176 @classmethod
me@284 177 def from_fasta(cls, file):
me@284 178 """Read sequence from FASTA file.
me@286 179
me@284 180 File must contain exactly one sequence.
me@284 181 """
me@284 182 sequences = fasta.parse_file(file)
me@284 183 assert len(sequences) == 1
me@287 184 name, description = sequences.keys()[0]
me@284 185 return cls(sequences[header], name, description, file.name)
me@284 186
me@287 187 class Alignment(list):
me@289 188 """Alignment. Behaves like a list of Columns."""
bnagaev@249 189
me@287 190 sequence_type = Sequence
me@289 191 """Type of sequences in alignment. SHOULD be redefined when subclassing."""
me@288 192
me@289 193 sequences = None
me@289 194 """Ordered list of sequences in alignment. Read, but DO NOT FIDDLE!"""
bnagaev@249 195
me@287 196 def __init__(self):
me@287 197 """Initialize empty alignment."""
me@287 198 super(Alignment, self).__init__()
me@287 199 self.sequences = []
me@282 200
me@287 201 def add_gapped_line(self, line, name='', description='', source=''):
me@287 202 """Add row from a line of one-letter codes and gaps."""
me@287 203 Sequence = cls.sequence_type
me@287 204 not_gap = lambda (i, char): char != "-"
me@287 205 no_gaps = line.replace("-", "")
me@287 206 sequence = Sequence(no_gaps, name, description, source)
me@287 207 for i, (j, char) in enumerate(filter(not_gap, enumerate(line))):
me@287 208 self[j][seq] = sequence[i]
me@287 209 self.sequences.append(sequence)
me@287 210
me@287 211 @classmethod
me@287 212 def from_fasta(cls, file):
me@287 213 """Create new alignment from FASTA file."""
me@287 214 self = cls()
me@287 215 for ((name, description), body) in fasta.parse_file(file):
me@287 216 self.add_gapped_line(body, name, description)
me@287 217 return self
bnagaev@249 218
me@292 219 def to_fasta(self, file):
me@292 220 """Write alignment in FASTA file as sequences with gaps."""
me@292 221 def char(monomer):
me@292 222 if monomer:
me@292 223 return monomer.code1
me@292 224 return "-"
me@292 225 for row in self.rows_as_lists():
me@292 226 seq = row.sequence
me@292 227 line = "".join(map(char, row))
me@292 228 fasta.save_file(file, line, seq.name, seq.description)
me@292 229
me@292 230 ## Unclean code follows
me@292 231
bnagaev@249 232 def length(self):
me@287 233 """Return width, ie length of each sequence with gaps."""
bnagaev@249 234 return max([len(line) for line in self.body.values()])
bnagaev@249 235
bnagaev@249 236 def height(self):
bnagaev@249 237 """ The number of sequences in alignment (it's thickness). """
bnagaev@249 238 return len(self.body)
bnagaev@249 239
bnagaev@249 240 def identity(self):
bnagaev@249 241 """ Calculate the identity of alignment positions for colouring.
bnagaev@249 242
bnagaev@249 243 For every (row, column) in alignment the percentage of the exactly
bnagaev@249 244 same residue in the same column in the alignment is calculated.
me@270 245 The data structure is just like the Alignment.body, but istead of
bnagaev@249 246 monomers it contains float percentages.
bnagaev@249 247 """
bnagaev@249 248 # Oh, God, that's awful! Absolutely not understandable.
bnagaev@249 249 # First, calculate percentages of amino acids in every column
bnagaev@249 250 contribution = 1.0 / len(self.sequences)
bnagaev@249 251 all_columns = []
bnagaev@249 252 for position in range(len(self)):
bnagaev@249 253 column_percentage = {}
bnagaev@249 254 for seq in self.body:
bnagaev@249 255 if self.body[seq][position] is not None:
bnagaev@249 256 aa = self.body[seq][position].code
bnagaev@249 257 else:
bnagaev@249 258 aa = None
bnagaev@249 259 if aa in allpy.data.amino_acids:
bnagaev@249 260 if aa in column_percentage.keys():
bnagaev@249 261 column_percentage[aa] += contribution
bnagaev@249 262 else:
bnagaev@249 263 column_percentage[aa] = contribution
bnagaev@249 264 all_columns.append(column_percentage)
bnagaev@249 265 # Second, map these percentages onto the alignment
bnagaev@249 266 self.identity_percentages = {}
bnagaev@249 267 for seq in self.sequences:
bnagaev@249 268 self.identity_percentages[seq] = []
bnagaev@249 269 for seq in self.identity_percentages:
bnagaev@249 270 line = self.identity_percentages[seq]
bnagaev@249 271 for position in range(len(self)):
bnagaev@249 272 if self.body[seq][position] is not None:
bnagaev@249 273 aa = self.body[seq][position].code
bnagaev@249 274 else:
bnagaev@249 275 aa = None
bnagaev@249 276 line.append(all_columns[position].get(aa))
bnagaev@249 277 return self.identity_percentages
bnagaev@249 278
bnagaev@249 279 @staticmethod
bnagaev@249 280 def from_sequences(*sequences):
bnagaev@249 281 """ Constructs new alignment from sequences
me@270 282
me@270 283 Add None's to right end to make equal lengthes of alignment sequences
bnagaev@249 284 """
bnagaev@249 285 alignment = Alignment()
bnagaev@249 286 alignment.sequences = sequences
bnagaev@249 287 max_length = max(len(sequence) for sequence in sequences)
bnagaev@249 288 for sequence in sequences:
bnagaev@249 289 gaps_count = max_length - len(sequence)
bnagaev@249 290 alignment.body[sequence] = sequence.monomers + [None] * gaps_count
bnagaev@249 291 return alignment
me@270 292
bnagaev@249 293 def muscle_align(self):
bnagaev@249 294 """ Simple align ths alignment using sequences (muscle)
me@270 295
bnagaev@249 296 uses old Monomers and Sequences objects
bnagaev@249 297 """
bnagaev@249 298 tmp_file = NamedTemporaryFile(delete=False)
bnagaev@249 299 self.save_fasta(tmp_file)
bnagaev@249 300 tmp_file.close()
bnagaev@249 301 os.system("muscle -in %(tmp)s -out %(tmp)s" % {'tmp': tmp_file.name})
bnagaev@249 302 sequences, body = Alignment.from_fasta(open(tmp_file.name))
bnagaev@249 303 for sequence in self.sequences:
bnagaev@249 304 try:
bnagaev@249 305 new_sequence = [i for i in sequences if sequence==i][0]
bnagaev@249 306 except:
bnagaev@249 307 raise Exception("Align: Cann't find sequence %s in muscle output" % \
bnagaev@249 308 sequence.name)
bnagaev@249 309 old_monomers = iter(sequence.monomers)
bnagaev@249 310 self.body[sequence] = []
bnagaev@249 311 for monomer in body[new_sequence]:
bnagaev@249 312 if not monomer:
bnagaev@249 313 self.body[sequence].append(monomer)
bnagaev@249 314 else:
bnagaev@249 315 old_monomer = old_monomers.next()
bnagaev@249 316 if monomer != old_monomer:
bnagaev@249 317 raise Exception("Align: alignment errors")
bnagaev@249 318 self.body[sequence].append(old_monomer)
bnagaev@249 319 os.unlink(tmp_file.name)
me@270 320
bnagaev@249 321 def column(self, sequence=None, sequences=None, original=None):
bnagaev@249 322 """ returns list of columns of alignment
me@270 323
bnagaev@249 324 sequence or sequences:
me@282 325 * if sequence is given, then column is (original_monomer, monomer)
me@282 326 * if sequences is given, then column is (original_monomer, {sequence: monomer})
me@282 327 * if both of them are given, it is an error
me@282 328
bnagaev@249 329 original (Sequence type):
me@282 330 * if given, this filters only columns represented by original sequence
bnagaev@249 331 """
bnagaev@249 332 if sequence and sequences:
bnagaev@249 333 raise Exception("Wrong usage. read help")
bnagaev@249 334 indexes = dict([(v, k) for( k, v) in enumerate(self.sequences)])
bnagaev@249 335 alignment = self.body.items()
bnagaev@249 336 alignment.sort(key=lambda i: indexes[i[0]])
bnagaev@249 337 alignment = [monomers for seq, monomers in alignment]
bnagaev@249 338 for column in zip(*alignment):
bnagaev@249 339 if not original or column[indexes[original]]:
bnagaev@249 340 if sequence:
bnagaev@249 341 yield (column[indexes[original]], column[indexes[sequence]])
bnagaev@249 342 else:
me@270 343 yield (column[indexes[original]],
bnagaev@249 344 dict([(s, column[indexes[s]]) for s in sequences]))
me@270 345
bnagaev@249 346 def secstr(self, sequence, pdb_chain, gap='-'):
bnagaev@249 347 """ Returns string representing secondary structure """
bnagaev@249 348 return ''.join([
me@270 349 (sequence.pdb_secstr[pdb_chain][m] if sequence.secstr_has(pdb_chain, m) else gap)
bnagaev@249 350 for m in self.body[sequence]])
bnagaev@249 351
bnagaev@249 352 class Block(object):
me@261 353 """ Block of alignment
me@270 354
me@261 355 Mandatory data:
me@266 356
me@261 357 * self.alignment -- alignment object, which the block belongs to
me@261 358 * self.sequences - set of sequence objects that contain monomers
me@261 359 and/or gaps, that constitute the block
me@261 360 * self.positions -- list of positions of the alignment.body that
me@261 361 are included in the block; position[i+1] is always to the right from position[i]
me@270 362
me@261 363 Don't change self.sequences -- it may be a link to other block.sequences
me@270 364
me@261 365 How to create a new block:
me@282 366
me@261 367 >>> import alignment
me@261 368 >>> import block
me@261 369 >>> proj = alignment.Alignment(open("test.fasta"))
me@261 370 >>> block1 = block.Block(proj)
me@261 371 """
me@270 372
me@261 373 def __init__(self, alignment, sequences=None, positions=None):
me@261 374 """ Builds new block from alignment
me@270 375
me@261 376 if sequences==None, all sequences are used
me@261 377 if positions==None, all positions are used
me@261 378 """
me@261 379 if sequences == None:
me@261 380 sequences = set(alignment.sequences) # copy
me@261 381 if positions == None:
me@261 382 positions = range(len(alignment))
me@261 383 self.alignment = alignment
me@261 384 self.sequences = sequences
me@261 385 self.positions = positions
me@270 386
me@261 387 def save_fasta(self, out_file, long_line=70, gap='-'):
me@270 388 """ Saves alignment to given file in fasta-format
me@270 389
me@261 390 No changes in the names, descriptions or order of the sequences
me@261 391 are made.
me@261 392 """
me@261 393 for sequence in self.sequences:
me@261 394 alignment_monomers = self.alignment.body[sequence]
me@261 395 block_monomers = [alignment_monomers[i] for i in self.positions]
me@261 396 string = ''.join([m.type.code1 if m else '-' for m in block_monomers])
me@261 397 save_fasta(out_file, string, sequence.name, sequence.description, long_line)
me@270 398
me@270 399 def geometrical_cores(self, max_delta=config.delta,
me@270 400 timeout=config.timeout, minsize=config.minsize,
me@261 401 ac_new_atoms=config.ac_new_atoms,
me@261 402 ac_count=config.ac_count):
me@261 403 """ Returns length-sorted list of blocks, representing GCs
me@270 404
me@282 405 * max_delta -- threshold of distance spreading
me@282 406 * timeout -- Bron-Kerbosh timeout (then fast O(n ln n) algorithm)
me@282 407 * minsize -- min size of each core
me@282 408 * ac_new_atoms -- min part or new atoms in new alternative core
me@282 409 current GC is compared with each of already selected GCs if
me@282 410 difference is less then ac_new_atoms, current GC is skipped
me@261 411 difference = part of new atoms in current core
me@282 412 * ac_count -- max number of cores (including main core)
me@261 413 -1 means infinity
me@282 414
me@261 415 If more than one pdb chain for some sequence provided, consider all of them
me@270 416 cost is calculated as 1 / (delta + 1)
me@282 417
me@261 418 delta in [0, +inf) => cost in (0, 1]
me@261 419 """
me@261 420 nodes = self.positions
me@261 421 lines = {}
me@261 422 for i in self.positions:
me@261 423 for j in self.positions:
me@261 424 if i < j:
me@261 425 distances = []
me@261 426 for sequence in self.sequences:
me@261 427 for chain in sequence.pdb_chains:
me@261 428 m1 = self.alignment.body[sequence][i]
me@261 429 m2 = self.alignment.body[sequence][j]
me@261 430 if m1 and m2:
me@261 431 r1 = sequence.pdb_residues[chain][m1]
me@261 432 r2 = sequence.pdb_residues[chain][m2]
me@261 433 ca1 = r1['CA']
me@261 434 ca2 = r2['CA']
me@261 435 d = ca1 - ca2 # Bio.PDB feature
me@261 436 distances.append(d)
me@261 437 if len(distances) >= 2:
me@261 438 delta = max(distances) - min(distances)
me@261 439 if delta <= max_delta:
me@261 440 lines[Graph.line(i, j)] = 1.0 / (1.0 + max_delta)
me@261 441 graph = Graph(nodes, lines)
me@261 442 cliques = graph.cliques(timeout=timeout, minsize=minsize)
me@261 443 GCs = []
me@261 444 for clique in cliques:
me@261 445 for GC in GCs:
me@261 446 if len(clique - set(GC.positions)) < ac_new_atoms * len(clique):
me@261 447 break
me@261 448 else:
me@261 449 GCs.append(Block(self.alignment, self.sequences, clique))
me@261 450 if ac_count != -1 and len(GCs) >= ac_count:
me@261 451 break
me@261 452 return GCs
me@270 453
me@261 454 def xstring(self, x='X', gap='-'):
me@261 455 """ Returns string consisting of gap chars and chars x at self.positions
me@270 456
me@261 457 Length of returning string = length of alignment
me@261 458 """
me@261 459 monomers = [False] * len(self.alignment)
me@261 460 for i in self.positions:
me@261 461 monomers[i] = True
me@261 462 return ''.join([x if m else gap for m in monomers])
me@270 463
me@261 464 def save_xstring(self, out_file, name, description='', x='X', gap='-', long_line=70):
me@261 465 """ Save xstring and name in fasta format """
me@261 466 save_fasta(out_file, self.xstring(x=x, gap=gap), name, description, long_line)
me@270 467
me@261 468 def monomers(self, sequence):
me@261 469 """ Iterates monomers of this sequence from this block """
me@261 470 alignment_sequence = self.alignment.body[sequence]
me@261 471 return (alignment_sequence[i] for i in self.positions)
me@270 472
me@261 473 def ca_atoms(self, sequence, pdb_chain):
me@261 474 """ Iterates Ca-atom of monomers of this sequence from this block """
me@261 475 return (sequence.pdb_residues[pdb_chain][monomer] for monomer in self.monomers())
me@270 476
me@261 477 def sequences_chains(self):
me@261 478 """ Iterates pairs (sequence, chain) """
me@261 479 for sequence in self.alignment.sequences:
me@261 480 if sequence in self.sequences:
me@261 481 for chain in sequence.pdb_chains:
me@261 482 yield (sequence, chain)
me@270 483
me@261 484 def superimpose(self):
me@261 485 """ Superimpose all pdb_chains in this block """
me@261 486 sequences_chains = list(self.sequences_chains())
me@261 487 if len(sequences_chains) >= 1:
me@261 488 sup = Superimposer()
me@261 489 fixed_sequence, fixed_chain = sequences_chains.pop()
me@261 490 fixed_atoms = self.ca_atoms(fixed_sequence, fixed_chain)
me@261 491 for sequence, chain in sequences_chains:
me@261 492 moving_atoms = self.ca_atoms(sequence, chain)
me@261 493 sup.set_atoms(fixed_atoms, moving_atoms)
me@261 494 # Apply rotation/translation to the moving atoms
me@261 495 sup.apply(moving_atoms)
me@270 496
me@261 497 def pdb_save(self, out_file):
me@270 498 """ Save all sequences
me@270 499
me@261 500 Returns {(sequence, chain): CHAIN}
me@261 501 CHAIN is chain letter in new file
me@261 502 """
me@261 503 tmp_file = NamedTemporaryFile(delete=False)
me@261 504 tmp_file.close()
me@270 505
me@261 506 for sequence, chain in self.sequences_chains():
me@261 507 sequence.pdb_save(tmp_file.name, chain)
me@261 508 # TODO: read from tmp_file.name
me@261 509 # change CHAIN
me@261 510 # add to out_file
me@270 511
me@261 512 os.unlink(NamedTemporaryFile)
bnagaev@239 513
me@260 514 # vim: set ts=4 sts=4 sw=4 et: