allpy: allpy/base.py annotate

allpy

annotate allpy/base.py @ 289:d7ad71def6c8

Experimenting with styles of docstrings in allpy.base.Alignment (to be recognized by Sphinx)

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Thu, 16 Dec 2010 01:25:54 +0300
parents	9c68d8eab8f5
children	751048390c45

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
bnagaev@249	219 def length(self):
me@287	220 """Return width, ie length of each sequence with gaps."""
bnagaev@249	221 return max([len(line) for line in self.body.values()])
bnagaev@249	222
bnagaev@249	223 def height(self):
bnagaev@249	224 """ The number of sequences in alignment (it's thickness). """
bnagaev@249	225 return len(self.body)
bnagaev@249	226
bnagaev@249	227 def identity(self):
bnagaev@249	228 """ Calculate the identity of alignment positions for colouring.
bnagaev@249	229
bnagaev@249	230 For every (row, column) in alignment the percentage of the exactly
bnagaev@249	231 same residue in the same column in the alignment is calculated.
me@270	232 The data structure is just like the Alignment.body, but istead of
bnagaev@249	233 monomers it contains float percentages.
bnagaev@249	234 """
bnagaev@249	235 # Oh, God, that's awful! Absolutely not understandable.
bnagaev@249	236 # First, calculate percentages of amino acids in every column
bnagaev@249	237 contribution = 1.0 / len(self.sequences)
bnagaev@249	238 all_columns = []
bnagaev@249	239 for position in range(len(self)):
bnagaev@249	240 column_percentage = {}
bnagaev@249	241 for seq in self.body:
bnagaev@249	242 if self.body[seq][position] is not None:
bnagaev@249	243 aa = self.body[seq][position].code
bnagaev@249	244 else:
bnagaev@249	245 aa = None
bnagaev@249	246 if aa in allpy.data.amino_acids:
bnagaev@249	247 if aa in column_percentage.keys():
bnagaev@249	248 column_percentage[aa] += contribution
bnagaev@249	249 else:
bnagaev@249	250 column_percentage[aa] = contribution
bnagaev@249	251 all_columns.append(column_percentage)
bnagaev@249	252 # Second, map these percentages onto the alignment
bnagaev@249	253 self.identity_percentages = {}
bnagaev@249	254 for seq in self.sequences:
bnagaev@249	255 self.identity_percentages[seq] = []
bnagaev@249	256 for seq in self.identity_percentages:
bnagaev@249	257 line = self.identity_percentages[seq]
bnagaev@249	258 for position in range(len(self)):
bnagaev@249	259 if self.body[seq][position] is not None:
bnagaev@249	260 aa = self.body[seq][position].code
bnagaev@249	261 else:
bnagaev@249	262 aa = None
bnagaev@249	263 line.append(all_columns[position].get(aa))
bnagaev@249	264 return self.identity_percentages
bnagaev@249	265
bnagaev@249	266 @staticmethod
bnagaev@249	267 def from_sequences(*sequences):
bnagaev@249	268 """ Constructs new alignment from sequences
me@270	269
me@270	270 Add None's to right end to make equal lengthes of alignment sequences
bnagaev@249	271 """
bnagaev@249	272 alignment = Alignment()
bnagaev@249	273 alignment.sequences = sequences
bnagaev@249	274 max_length = max(len(sequence) for sequence in sequences)
bnagaev@249	275 for sequence in sequences:
bnagaev@249	276 gaps_count = max_length - len(sequence)
bnagaev@249	277 alignment.body[sequence] = sequence.monomers + [None] * gaps_count
bnagaev@249	278 return alignment
me@270	279
bnagaev@249	280 def save_fasta(self, out_file, long_line=70, gap='-'):
bnagaev@249	281 """ Saves alignment to given file
me@270	282
bnagaev@249	283 Splits long lines to substrings of length=long_line
me@270	284 To prevent this, set long_line=None
bnagaev@249	285 """
bnagaev@249	286 block.Block(self).save_fasta(out_file, long_line=long_line, gap=gap)
me@270	287
bnagaev@249	288 def muscle_align(self):
bnagaev@249	289 """ Simple align ths alignment using sequences (muscle)
me@270	290
bnagaev@249	291 uses old Monomers and Sequences objects
bnagaev@249	292 """
bnagaev@249	293 tmp_file = NamedTemporaryFile(delete=False)
bnagaev@249	294 self.save_fasta(tmp_file)
bnagaev@249	295 tmp_file.close()
bnagaev@249	296 os.system("muscle -in %(tmp)s -out %(tmp)s" % {'tmp': tmp_file.name})
bnagaev@249	297 sequences, body = Alignment.from_fasta(open(tmp_file.name))
bnagaev@249	298 for sequence in self.sequences:
bnagaev@249	299 try:
bnagaev@249	300 new_sequence = [i for i in sequences if sequence==i][0]
bnagaev@249	301 except:
bnagaev@249	302 raise Exception("Align: Cann't find sequence %s in muscle output" % \
bnagaev@249	303 sequence.name)
bnagaev@249	304 old_monomers = iter(sequence.monomers)
bnagaev@249	305 self.body[sequence] = []
bnagaev@249	306 for monomer in body[new_sequence]:
bnagaev@249	307 if not monomer:
bnagaev@249	308 self.body[sequence].append(monomer)
bnagaev@249	309 else:
bnagaev@249	310 old_monomer = old_monomers.next()
bnagaev@249	311 if monomer != old_monomer:
bnagaev@249	312 raise Exception("Align: alignment errors")
bnagaev@249	313 self.body[sequence].append(old_monomer)
bnagaev@249	314 os.unlink(tmp_file.name)
me@270	315
bnagaev@249	316 def column(self, sequence=None, sequences=None, original=None):
bnagaev@249	317 """ returns list of columns of alignment
me@270	318
bnagaev@249	319 sequence or sequences:
me@282	320 * if sequence is given, then column is (original_monomer, monomer)
me@282	321 * if sequences is given, then column is (original_monomer, {sequence: monomer})
me@282	322 * if both of them are given, it is an error
me@282	323
bnagaev@249	324 original (Sequence type):
me@282	325 * if given, this filters only columns represented by original sequence
bnagaev@249	326 """
bnagaev@249	327 if sequence and sequences:
bnagaev@249	328 raise Exception("Wrong usage. read help")
bnagaev@249	329 indexes = dict([(v, k) for( k, v) in enumerate(self.sequences)])
bnagaev@249	330 alignment = self.body.items()
bnagaev@249	331 alignment.sort(key=lambda i: indexes[i[0]])
bnagaev@249	332 alignment = [monomers for seq, monomers in alignment]
bnagaev@249	333 for column in zip(*alignment):
bnagaev@249	334 if not original or column[indexes[original]]:
bnagaev@249	335 if sequence:
bnagaev@249	336 yield (column[indexes[original]], column[indexes[sequence]])
bnagaev@249	337 else:
me@270	338 yield (column[indexes[original]],
bnagaev@249	339 dict([(s, column[indexes[s]]) for s in sequences]))
me@270	340
bnagaev@249	341 def secstr(self, sequence, pdb_chain, gap='-'):
bnagaev@249	342 """ Returns string representing secondary structure """
bnagaev@249	343 return ''.join([
me@270	344 (sequence.pdb_secstr[pdb_chain][m] if sequence.secstr_has(pdb_chain, m) else gap)
bnagaev@249	345 for m in self.body[sequence]])
bnagaev@249	346
bnagaev@249	347 class Block(object):
me@261	348 """ Block of alignment
me@270	349
me@261	350 Mandatory data:
me@266	351
me@261	352 * self.alignment -- alignment object, which the block belongs to
me@261	353 * self.sequences - set of sequence objects that contain monomers
me@261	354 and/or gaps, that constitute the block
me@261	355 * self.positions -- list of positions of the alignment.body that
me@261	356 are included in the block; position[i+1] is always to the right from position[i]
me@270	357
me@261	358 Don't change self.sequences -- it may be a link to other block.sequences
me@270	359
me@261	360 How to create a new block:
me@282	361
me@261	362 >>> import alignment
me@261	363 >>> import block
me@261	364 >>> proj = alignment.Alignment(open("test.fasta"))
me@261	365 >>> block1 = block.Block(proj)
me@261	366 """
me@270	367
me@261	368 def __init__(self, alignment, sequences=None, positions=None):
me@261	369 """ Builds new block from alignment
me@270	370
me@261	371 if sequences==None, all sequences are used
me@261	372 if positions==None, all positions are used
me@261	373 """
me@261	374 if sequences == None:
me@261	375 sequences = set(alignment.sequences) # copy
me@261	376 if positions == None:
me@261	377 positions = range(len(alignment))
me@261	378 self.alignment = alignment
me@261	379 self.sequences = sequences
me@261	380 self.positions = positions
me@270	381
me@261	382 def save_fasta(self, out_file, long_line=70, gap='-'):
me@270	383 """ Saves alignment to given file in fasta-format
me@270	384
me@261	385 No changes in the names, descriptions or order of the sequences
me@261	386 are made.
me@261	387 """
me@261	388 for sequence in self.sequences:
me@261	389 alignment_monomers = self.alignment.body[sequence]
me@261	390 block_monomers = [alignment_monomers[i] for i in self.positions]
me@261	391 string = ''.join([m.type.code1 if m else '-' for m in block_monomers])
me@261	392 save_fasta(out_file, string, sequence.name, sequence.description, long_line)
me@270	393
me@270	394 def geometrical_cores(self, max_delta=config.delta,
me@270	395 timeout=config.timeout, minsize=config.minsize,
me@261	396 ac_new_atoms=config.ac_new_atoms,
me@261	397 ac_count=config.ac_count):
me@261	398 """ Returns length-sorted list of blocks, representing GCs
me@270	399
me@282	400 * max_delta -- threshold of distance spreading
me@282	401 * timeout -- Bron-Kerbosh timeout (then fast O(n ln n) algorithm)
me@282	402 * minsize -- min size of each core
me@282	403 * ac_new_atoms -- min part or new atoms in new alternative core
me@282	404 current GC is compared with each of already selected GCs if
me@282	405 difference is less then ac_new_atoms, current GC is skipped
me@261	406 difference = part of new atoms in current core
me@282	407 * ac_count -- max number of cores (including main core)
me@261	408 -1 means infinity
me@282	409
me@261	410 If more than one pdb chain for some sequence provided, consider all of them
me@270	411 cost is calculated as 1 / (delta + 1)
me@282	412
me@261	413 delta in [0, +inf) => cost in (0, 1]
me@261	414 """
me@261	415 nodes = self.positions
me@261	416 lines = {}
me@261	417 for i in self.positions:
me@261	418 for j in self.positions:
me@261	419 if i < j:
me@261	420 distances = []
me@261	421 for sequence in self.sequences:
me@261	422 for chain in sequence.pdb_chains:
me@261	423 m1 = self.alignment.body[sequence][i]
me@261	424 m2 = self.alignment.body[sequence][j]
me@261	425 if m1 and m2:
me@261	426 r1 = sequence.pdb_residues[chain][m1]
me@261	427 r2 = sequence.pdb_residues[chain][m2]
me@261	428 ca1 = r1['CA']
me@261	429 ca2 = r2['CA']
me@261	430 d = ca1 - ca2 # Bio.PDB feature
me@261	431 distances.append(d)
me@261	432 if len(distances) >= 2:
me@261	433 delta = max(distances) - min(distances)
me@261	434 if delta <= max_delta:
me@261	435 lines[Graph.line(i, j)] = 1.0 / (1.0 + max_delta)
me@261	436 graph = Graph(nodes, lines)
me@261	437 cliques = graph.cliques(timeout=timeout, minsize=minsize)
me@261	438 GCs = []
me@261	439 for clique in cliques:
me@261	440 for GC in GCs:
me@261	441 if len(clique - set(GC.positions)) < ac_new_atoms * len(clique):
me@261	442 break
me@261	443 else:
me@261	444 GCs.append(Block(self.alignment, self.sequences, clique))
me@261	445 if ac_count != -1 and len(GCs) >= ac_count:
me@261	446 break
me@261	447 return GCs
me@270	448
me@261	449 def xstring(self, x='X', gap='-'):
me@261	450 """ Returns string consisting of gap chars and chars x at self.positions
me@270	451
me@261	452 Length of returning string = length of alignment
me@261	453 """
me@261	454 monomers = [False] * len(self.alignment)
me@261	455 for i in self.positions:
me@261	456 monomers[i] = True
me@261	457 return ''.join([x if m else gap for m in monomers])
me@270	458
me@261	459 def save_xstring(self, out_file, name, description='', x='X', gap='-', long_line=70):
me@261	460 """ Save xstring and name in fasta format """
me@261	461 save_fasta(out_file, self.xstring(x=x, gap=gap), name, description, long_line)
me@270	462
me@261	463 def monomers(self, sequence):
me@261	464 """ Iterates monomers of this sequence from this block """
me@261	465 alignment_sequence = self.alignment.body[sequence]
me@261	466 return (alignment_sequence[i] for i in self.positions)
me@270	467
me@261	468 def ca_atoms(self, sequence, pdb_chain):
me@261	469 """ Iterates Ca-atom of monomers of this sequence from this block """
me@261	470 return (sequence.pdb_residues[pdb_chain][monomer] for monomer in self.monomers())
me@270	471
me@261	472 def sequences_chains(self):
me@261	473 """ Iterates pairs (sequence, chain) """
me@261	474 for sequence in self.alignment.sequences:
me@261	475 if sequence in self.sequences:
me@261	476 for chain in sequence.pdb_chains:
me@261	477 yield (sequence, chain)
me@270	478
me@261	479 def superimpose(self):
me@261	480 """ Superimpose all pdb_chains in this block """
me@261	481 sequences_chains = list(self.sequences_chains())
me@261	482 if len(sequences_chains) >= 1:
me@261	483 sup = Superimposer()
me@261	484 fixed_sequence, fixed_chain = sequences_chains.pop()
me@261	485 fixed_atoms = self.ca_atoms(fixed_sequence, fixed_chain)
me@261	486 for sequence, chain in sequences_chains:
me@261	487 moving_atoms = self.ca_atoms(sequence, chain)
me@261	488 sup.set_atoms(fixed_atoms, moving_atoms)
me@261	489 # Apply rotation/translation to the moving atoms
me@261	490 sup.apply(moving_atoms)
me@270	491
me@261	492 def pdb_save(self, out_file):
me@270	493 """ Save all sequences
me@270	494
me@261	495 Returns {(sequence, chain): CHAIN}
me@261	496 CHAIN is chain letter in new file
me@261	497 """
me@261	498 tmp_file = NamedTemporaryFile(delete=False)
me@261	499 tmp_file.close()
me@270	500
me@261	501 for sequence, chain in self.sequences_chains():
me@261	502 sequence.pdb_save(tmp_file.name, chain)
me@261	503 # TODO: read from tmp_file.name
me@261	504 # change CHAIN
me@261	505 # add to out_file
me@270	506
me@261	507 os.unlink(NamedTemporaryFile)
bnagaev@239	508
me@260	509 # vim: set ts=4 sts=4 sw=4 et: