allpy: allpy/base.py annotate

allpy

annotate allpy/base.py @ 420:438e1951f559

Backed out changeset 3a802644d798 (see #26)

author	boris <bnagaev@gmail.com>
date	Mon, 14 Feb 2011 12:06:30 +0300
parents	3a802644d798
children	42a05616a09b

rev	line source
me@261	1 import sys
bnagaev@357	2 import re
me@261	3
me@315	4 import util
me@284	5 import fasta
me@260	6
dendik@382	7 # import this very module as means of having all related classes in one place
dendik@382	8 import base
dendik@382	9
me@306	10 default_gaps = set((".", "-", "~"))
me@306	11 """Set of characters to recoginze as gaps when parsing alignment."""
me@306	12
me@328	13 class Monomer(object):
me@328	14 """Monomer object."""
me@260	15
me@328	16 type = None
me@328	17 """Either of 'dna', 'rna', 'protein'."""
me@260	18
dendik@382	19 types = base
dendik@382	20 """Mapping of related types. SHOULD be redefined in subclasses."""
dendik@382	21
me@260	22 by_code1 = {}
me@328	23 """A mapping from 1-letter code to Monomer subclass."""
me@328	24
me@260	25 by_code3 = {}
me@328	26 """A mapping from 3-letter code to Monomer subclass."""
me@328	27
me@260	28 by_name = {}
me@328	29 """A mapping from full monomer name to Monomer subclass."""
me@260	30
me@260	31 @classmethod
me@328	32 def _subclass(cls, name='', code1='', code3='', is_modified=False):
me@328	33 """Create new subclass of Monomer for given monomer type."""
me@328	34 class TheMonomer(cls):
me@328	35 pass
me@328	36 name = name.strip().capitalize()
me@328	37 code1 = code1.upper()
me@328	38 code3 = code3.upper()
bnagaev@357	39 TheMonomer.__name__ = re.sub(r"[^\w]", "_", name)
me@328	40 TheMonomer.name = name
me@328	41 TheMonomer.code1 = code1
me@328	42 TheMonomer.code3 = code3
me@328	43 TheMonomer.is_modified = is_modified
me@328	44 if not is_modified:
me@328	45 cls.by_code1[code1] = TheMonomer
me@328	46 cls.by_code3[code3] = TheMonomer
me@328	47 cls.by_name[name] = TheMonomer
me@328	48 # We duplicate distinguished long names into Monomer itself, so that we
me@328	49 # can use Monomer.from_code3 to create the relevant type of monomer.
me@328	50 Monomer.by_code3[code3] = TheMonomer
me@328	51 Monomer.by_name[name] = TheMonomer
me@260	52
me@328	53 @classmethod
me@353	54 def _initialize(cls, codes=None):
me@328	55 """Create all relevant subclasses of Monomer."""
me@328	56 # NB. The table uses letters d, r, p for types,
me@328	57 # while we use full words; hence, we compare by first letter
bnagaev@378	58 for code1, is_modified, code3, name in codes:
bnagaev@378	59 cls._subclass(name, code1, code3, is_modified)
me@260	60
me@260	61 @classmethod
me@260	62 def from_code1(cls, code1):
me@328	63 """Create new monomer from 1-letter code."""
me@328	64 return cls.by_code1[code1.upper()]()
me@260	65
me@260	66 @classmethod
me@260	67 def from_code3(cls, code3):
me@328	68 """Create new monomer from 3-letter code."""
me@328	69 return cls.by_code3[code3.upper()]()
me@260	70
me@260	71 @classmethod
me@260	72 def from_name(cls, name):
me@328	73 """Create new monomer from full name."""
me@328	74 return cls.by_name[name.strip().capitalize()]()
me@260	75
me@329	76 def __repr__(self):
me@329	77 return '<Monomer %s>' % self.code3
me@329	78
me@329	79 def __str__(self):
me@329	80 """Returns one-letter code"""
me@329	81 return self.code1
me@329	82
me@260	83 def __eq__(self, other):
me@328	84 """Monomers within same monomer type are compared by code1."""
me@328	85 assert self.type == other.type
me@328	86 return self.code1 == other.code1
bnagaev@239	87
bnagaev@239	88 class Sequence(list):
me@274	89 """Sequence of Monomers.
bnagaev@243	90
me@274	91 This behaves like list of monomer objects. In addition to standard list
me@274	92 behaviour, Sequence has the following attributes:
me@270	93
me@274	94 * name -- str with the name of the sequence
me@274	95 * description -- str with description of the sequence
me@274	96 * source -- str denoting source of the sequence
me@266	97
me@274	98 Any of them may be empty (i.e. hold empty string)
me@274	99 """
me@270	100
dendik@382	101 types = base
dendik@382	102 """Mapping of related types. SHOULD be redefined in subclasses."""
me@270	103
me@275	104 name = ''
me@275	105 description = ''
me@275	106 source = ''
me@275	107
me@347	108 @classmethod
me@347	109 def from_monomers(cls, monomers=[], name=None, description=None, source=None):
me@347	110 """Create sequence from a list of monomer objecst."""
bnagaev@378	111 result = cls(monomers)
me@275	112 if name:
me@347	113 result.name = name
me@275	114 if description:
me@347	115 result.description = description
me@275	116 if source:
me@347	117 result.source = source
me@347	118 return result
me@347	119
me@347	120 @classmethod
me@347	121 def from_string(cls, string, name='', description='', source=''):
me@347	122 """Create sequences from string of one-letter codes."""
dendik@382	123 monomer = cls.types.Monomer.from_code1
me@347	124 monomers = [monomer(letter) for letter in string]
me@347	125 return cls.from_monomers(monomers, name, description, source)
me@270	126
me@329	127 def __repr__(self):
me@329	128 return '<Sequence %s>' % str(self)
me@329	129
me@262	130 def __str__(self):
me@329	131 """Returns sequence of one-letter codes."""
me@275	132 return ''.join(monomer.code1 for monomer in self)
me@270	133
me@316	134 def __hash__(self):
me@316	135 """Hash sequence by identity."""
me@316	136 return id(self)
me@316	137
me@295	138 class Alignment(object):
me@295	139 """Alignment. It is a list of Columns."""
bnagaev@249	140
dendik@382	141 types = base
dendik@382	142 """Mapping of related types. SHOULD be redefined in subclasses."""
me@288	143
me@289	144 sequences = None
me@289	145 """Ordered list of sequences in alignment. Read, but DO NOT FIDDLE!"""
bnagaev@249	146
me@287	147 def __init__(self):
me@287	148 """Initialize empty alignment."""
me@287	149 self.sequences = []
me@295	150 self.columns = []
me@282	151
me@362	152 # Alignment grow & IO methods
me@299	153 # ==============================
me@299	154
me@294	155 def append_sequence(self, sequence):
me@365	156 """Add sequence to alignment. Return self.
me@294	157
me@294	158 If sequence is too short, pad it with gaps on the right.
me@294	159 """
me@294	160 self.sequences.append(sequence)
dendik@388	161 self._pad_to_width(len(sequence))
dendik@388	162 for column, monomer in zip(self.columns, sequence):
dendik@388	163 column[sequence] = monomer
me@365	164 return self
me@294	165
me@364	166 def append_row_from_string(self, string,
me@364	167 name='', description='', source='', gaps=default_gaps):
me@364	168 """Add row from a string of one-letter codes and gaps. Return self."""
dendik@382	169 Sequence = self.types.Sequence
me@349	170 without_gaps = util.remove_each(string, gaps)
me@321	171 sequence = Sequence.from_string(without_gaps, name, description, source)
dendik@388	172 self._pad_to_width(len(string))
dendik@388	173 non_gap_columns = [column
dendik@390	174 for column, char in zip(self.columns, string)
dendik@388	175 if char not in gaps
dendik@388	176 ]
dendik@388	177 for monomer, column in zip(sequence, non_gap_columns):
dendik@388	178 column[sequence] = monomer
me@287	179 self.sequences.append(sequence)
me@364	180 return self
me@287	181
dendik@388	182 def _pad_to_width(self, n):
dendik@388	183 """Pad alignment with empty columns on the right to width n."""
dendik@388	184 for i in range(len(self.columns), n):
me@302	185 self.columns.append(Column())
me@302	186
me@362	187 def append_file(self, file, format='fasta', gaps=default_gaps):
me@365	188 """Append sequences from file to alignment. Return self.
me@299	189
me@362	190 If sequences in file have gaps (detected as characters belonging to
me@362	191 `gaps` set), treat them accordingly.
me@362	192 """
me@367	193 assert format == 'fasta', "We don't support other formats yet"
me@313	194 for (name, description, body) in fasta.parse_file(file):
bnagaev@378	195 self.append_row_from_string(body, name, description, file.name, gaps)
me@287	196 return self
bnagaev@249	197
me@367	198 def to_file(self, file, format='fasta'):
me@292	199 """Write alignment in FASTA file as sequences with gaps."""
me@367	200 assert format == "fasta", "We don't support other formats yet"
me@292	201 def char(monomer):
me@292	202 if monomer:
me@292	203 return monomer.code1
me@292	204 return "-"
me@292	205 for row in self.rows_as_lists():
me@292	206 seq = row.sequence
me@292	207 line = "".join(map(char, row))
me@292	208 fasta.save_file(file, line, seq.name, seq.description)
me@292	209
me@299	210 # Data access methods for alignment
me@299	211 # =================================
me@299	212
me@299	213 def rows(self):
me@299	214 """Return list of rows (temporary objects) in alignment.
me@299	215
me@299	216 Each row is a dictionary of { column : monomer }.
me@363	217
me@299	218 For gap positions there is no key for the column in row.
me@299	219
me@299	220 Each row has attribute `sequence` pointing to the sequence the row is
me@299	221 describing.
me@299	222
me@299	223 Modifications of row have no effect on the alignment.
me@299	224 """
me@299	225 # For now, the function returns a list rather than iterator.
me@299	226 # It is yet to see, whether memory performance here becomes critical,
me@299	227 # or is random access useful.
me@299	228 rows = []
me@299	229 for sequence in self.sequences:
me@299	230 row = util.UserDict()
me@299	231 row.sequence = sequence
me@299	232 for column in self.columns:
me@299	233 if sequence in column:
me@299	234 row[column] = column[sequence]
me@299	235 rows.append(row)
me@299	236 return rows
me@299	237
me@299	238 def rows_as_lists(self):
me@299	239 """Return list of rows (temporary objects) in alignment.
me@299	240
me@299	241 Each row here is a list of either monomer or None (for gaps).
me@299	242
me@299	243 Each row has attribute `sequence` pointing to the sequence of row.
me@299	244
me@299	245 Modifications of row have no effect on the alignment.
me@299	246 """
me@299	247 rows = []
me@299	248 for sequence in self.sequences:
me@299	249 row = util.UserList()
me@299	250 row.sequence = sequence
me@299	251 for column in self.columns:
me@299	252 row.append(column.get(sequence))
me@299	253 rows.append(row)
me@299	254 return rows
me@299	255
me@299	256 def columns_as_lists(self):
me@299	257 """Return list of columns (temorary objects) in alignment.
me@299	258
me@299	259 Each column here is a list of either monomer or None (for gaps).
me@299	260
me@299	261 Items of column are sorted in the same way as alignment.sequences.
me@299	262
me@299	263 Modifications of column have no effect on the alignment.
me@299	264 """
me@299	265 columns = []
me@299	266 for column in self.columns:
me@299	267 col = []
me@299	268 for sequence in self.sequences:
me@299	269 col.append(column.get(sequence))
me@299	270 columns.append(col)
me@299	271 return columns
me@299	272
me@368	273 # Alignment / Block editing methods
me@368	274 # =================================
me@368	275
me@368	276 def _flush_row(self, row, whence='left'):
me@368	277 """Helper for `flush`: flush to one side all monomers in one row."""
me@368	278 row = filter(None, row)
me@368	279 padding = [None] * len(self.columns)
me@368	280 if whence == 'left':
me@368	281 return row + padding
me@368	282 if whence == 'right':
me@368	283 return padding + row
me@368	284 if whence == 'center':
me@368	285 pad_len = (len(self.columns) - len(row)) // 2
me@368	286 # vvv fix padding for case when length is odd: better have more
me@368	287 pad_len += len(self.columns) - 2 * pad_len
me@368	288 padding = [None] * pad_len
me@368	289 return padding + row + padding
me@368	290 assert True, "whence must be either 'left' or 'right' or 'center'"
me@368	291
me@368	292 def flush(self, whence='left'):
me@368	293 """Remove all gaps from alignment and flush results to one side.
me@368	294
me@368	295 `whence` must be one of 'left', 'right' or 'center'
me@368	296 """
me@368	297 for row in self.rows_as_lists():
me@368	298 sequence = row.sequence
me@368	299 row = self._flush_row(row, whence)
me@368	300 for monomer, column in zip(row, self.columns):
me@368	301 if monomer:
me@368	302 column[sequence] = monomer
me@368	303 elif sequence in column:
me@368	304 del column[sequence]
me@368	305
me@369	306 def remove_gap_columns(self):
me@369	307 """Remove all empty columns."""
me@369	308 for n, column in reversed(enumerate(self.columns)):
me@369	309 if column == {}:
me@369	310 self.columns[n:n+1] = []
me@369	311
me@371	312 def _wipe(self):
me@371	313 """Make all positions gaps (but keep sequences intact)."""
me@371	314 for column in self.columns:
bnagaev@378	315 for sequence in list(column.keys()):
me@371	316 del column[sequence]
me@371	317
me@372	318 def _merge(self, dst, new, merge):
me@373	319 """Replace contents of `dst` with those of `new`.
me@372	320
me@372	321 Replace contents of elements using function `merge(dst_el, new_le)`.
me@372	322 """
bnagaev@384	323 for el, new_el in zip(dst, new):
bnagaev@384	324 merge(el, new_el)
me@372	325 dst[len(dst):] = new[len(dst):]
me@372	326 del dst[len(new):]
me@371	327
me@373	328 def _replace_sequence_contents(self, new, copy_descriptions):
me@373	329 """Replace contents of sequences with those of `new` alignment."""
me@371	330 # XXX: we manually copy sequence contents here
me@372	331 # XXX: we only copy, overlapping parts and link to the rest
me@372	332 def merge_monomers(dst, new):
me@372	333 dst.__class__ = new.__class__
me@372	334 def merge_sequences(dst, new):
me@373	335 if copy_descriptions:
me@373	336 vars(dst).update(vars(new))
me@372	337 self._merge(dst, new, merge_monomers)
me@372	338 self._merge(self.sequences, new.sequences, merge_sequences)
me@371	339
me@371	340 def _replace_column_contents(self, new):
me@373	341 """Replace column contents with those of `new` alignment.
me@371	342
me@373	343 Synonym: copy gap patterns from `new` to `self`.
me@372	344
me@373	345 `self.sequences` and `new.sequences` should have the same contents.
me@371	346 """
me@371	347 self._wipe()
me@371	348 not_gap = lambda (a,b): a != None
me@371	349 for sequence, new_row in zip(self.sequences, new.rows_as_lists()):
me@371	350 assert len(sequence) == len(new_row.sequence)
dendik@388	351 non_gap_columns = [column
dendik@388	352 for column, monomer in zip(self.columns, new_row)
dendik@388	353 if monomer
dendik@388	354 ]
dendik@388	355 for monomer, column in zip(sequence, non_gap_columns):
dendik@388	356 column[sequence] = monomer
me@371	357
me@373	358 def _replace_contents(self, new, copy_descriptions, copy_contents):
me@371	359 """Replace alignment contents with those of other alignment."""
me@373	360 if copy_contents:
me@373	361 self._replace_sequence_contents(new, copy_descriptions)
bnagaev@378	362 self._replace_column_contents(new)
me@371	363
me@373	364 def process(self, function, copy_descriptions=True, copy_contents=True):
me@371	365 """Apply function to the alignment (or block); inject results back.
me@371	366
me@373	367 - `function(block)` must return block with same line order.
me@373	368 - if `copy_descriptions` is False, ignore new sequence names.
me@373	369 - if `copy_contents` is False, don't copy sequence contents too.
dendik@380	370
dendik@380	371 `function` (object) may have attributes `copy_descriptions` and
dendik@380	372 `copy_contents`, which override the same named arguments.
me@371	373 """
me@371	374 new = function(self)
dendik@380	375 if hasattr(function, 'copy_descriptions'):
dendik@380	376 copy_descriptions = function.copy_descriptions
dendik@380	377 if hasattr(function, 'copy_contents'):
dendik@380	378 copy_contents = function.copy_contents
me@373	379 self._replace_contents(new, copy_descriptions, copy_contents)
me@371	380
me@300	381 class Column(dict):
me@300	382 """Column of alignment.
me@300	383
me@300	384 Column is a dict of { sequence : monomer }.
me@300	385
me@300	386 For sequences that have gaps in current row, given key is not present in
me@300	387 the column.
me@300	388 """
me@325	389
dendik@382	390 types = base
dendik@382	391 """Mapping of related types. SHOULD be redefined in subclasses."""
dendik@382	392
me@325	393 def __hash__(self):
me@325	394 """Return hash by identity."""
me@325	395 return id(self)
me@300	396
me@317	397 class Block(Alignment):
me@307	398 """Block of alignment.
me@301	399
me@307	400 Block is intersection of a set of columns & a set of rows. Most of blocks
me@307	401 look like rectangular part of alignment if you shuffle alignment rows the
me@307	402 right way.
me@261	403 """
me@270	404
me@307	405 alignment = None
me@307	406 """Alignment the block belongs to."""
me@270	407
me@307	408 sequences = ()
me@307	409 """List of sequences in block."""
me@307	410
me@307	411 columns = ()
me@307	412 """List of columns in block."""
me@307	413
me@317	414 @classmethod
me@317	415 def from_alignment(cls, alignment, sequences=None, columns=None):
me@307	416 """Build new block from alignment.
me@307	417
me@307	418 If sequences are not given, the block uses all sequences in alignment.
me@307	419
me@307	420 If columns are not given, the block uses all columns in alignment.
me@307	421
me@307	422 In both cases we use exactly the list used in alignment, thus, if new
me@307	423 sequences or columns are added to alignment, the block tracks this too.
me@261	424 """
me@307	425 if sequences is None:
me@307	426 sequences = alignment.sequences
me@318	427 if columns is None:
me@307	428 columns = alignment.columns
me@320	429 block = cls()
me@320	430 block.alignment = alignment
me@320	431 block.sequences = sequences
me@320	432 block.columns = columns
me@320	433 return block
me@270	434
me@260	435 # vim: set ts=4 sts=4 sw=4 et: