allpy: allpy/base.py annotate

allpy

annotate allpy/base.py @ 313:316122b6b70e

Changed interfaces of allpy.fasta, updated allpy.base accordingly * Renamed allpy.fasta.parse_fasta -> parse_file, save_fasta -> save_file * parse_file returns a list of 3-tuples instead of dict

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Thu, 16 Dec 2010 23:42:14 +0300
parents	5417b9d6b63e
children	3347b5f31477

rev	line source
me@261	1 import sys
me@261	2
me@261	3 import config
me@284	4 import fasta
me@261	5 from graph import Graph
me@260	6 import data.codes
me@260	7
me@306	8 default_gaps = set((".", "-", "~"))
me@306	9 """Set of characters to recoginze as gaps when parsing alignment."""
me@306	10
me@260	11 class MonomerType(object):
me@260	12 """Class of monomer types.
me@260	13
me@260	14 Each MonomerType object represents a known monomer type, e.g. Valine,
me@260	15 and is referenced to by each instance of monomer in a given sequence.
me@260	16
me@260	17 - `name`: full name of monomer type
me@260	18 - `code1`: one-letter code
me@260	19 - `code3`: three-letter code
me@260	20 - `is_modified`: either of True or False
me@260	21
me@260	22 class atributes:
me@260	23
me@260	24 - `by_code1`: a mapping from one-letter code to MonomerType object
me@260	25 - `by_code3`: a mapping from three-letter code to MonomerType object
me@260	26 - `by_name`: a mapping from monomer name to MonomerType object
me@260	27 - `instance_type`: class of Monomer objects to use when creating new
me@260	28 objects; this must be redefined in descendent classes
me@260	29
me@260	30 All of the class attributes MUST be redefined when subclassing.
me@260	31 """
me@260	32
me@260	33 by_code1 = {}
me@260	34 by_code3 = {}
me@260	35 by_name = {}
me@260	36 instance_type = None
me@260	37
me@260	38 def __init__(self, name="", code1="", code3="", is_modified=False):
me@310	39 super(MonomerType, self).__init__()
me@260	40 self.name = name.capitalize()
me@260	41 self.code1 = code1.upper()
me@260	42 self.code3 = code3.upper()
me@260	43 self.is_modified = bool(is_modified)
me@260	44 if not is_modified:
me@260	45 self.by_code1[self.code1] = self
me@260	46 self.by_code3[code3] = self
me@260	47 self.by_name[name] = self
me@260	48 # We duplicate distinguished long names into MonomerType itself,
me@260	49 # so that we can use MonomerType.from_code3 to create the relevant
me@260	50 # type of monomer.
me@260	51 MonomerType.by_code3[code3] = self
me@260	52 MonomerType.by_name[name] = self
me@260	53
me@260	54 @classmethod
me@260	55 def _initialize(cls, type_letter, codes=data.codes.codes):
me@260	56 """Create all relevant instances of MonomerType.
me@260	57
me@260	58 `type_letter` is either of:
me@260	59
me@260	60 - 'p' for protein
me@260	61 - 'd' for DNA
me@260	62 - 'r' for RNA
me@260	63
me@260	64 `codes` is a table of monomer codes
me@260	65 """
me@260	66 for type, code1, is_modified, code3, name in codes:
me@260	67 if type == type_letter:
me@260	68 cls(name, code1, code3, is_modified)
me@260	69
me@260	70 @classmethod
me@260	71 def from_code1(cls, code1):
me@260	72 """Return monomer type by one-letter code."""
me@260	73 return cls.by_code1[code1.upper()]
me@260	74
me@260	75 @classmethod
me@260	76 def from_code3(cls, code3):
me@260	77 """Return monomer type by three-letter code."""
me@260	78 return cls.by_code3[code3.upper()]
me@260	79
me@260	80 @classmethod
me@260	81 def from_name(cls, name):
me@260	82 """Return monomer type by name."""
me@260	83 return cls.by_name[name.capitalize()]
me@260	84
me@260	85 def instance(self):
me@260	86 """Create a new monomer of given type."""
me@260	87 return self.instance_type(self)
me@260	88
me@260	89 def __eq__(self, other):
me@260	90 if hasattr(other, "type"):
me@260	91 return self is other.type
me@260	92 return self is other
me@260	93
me@260	94 class Monomer(object):
me@260	95 """Monomer object.
me@260	96
me@260	97 attributes:
me@260	98
me@260	99 - `type`: type of monomer (a MonomerType object)
me@260	100
me@282	101 class attributes:
me@282	102
me@282	103 - `monomer_type`: either MonomerType or one of it's subclasses, it is used
me@282	104 when creating new monomers. It SHOULD be redefined when subclassing
me@282	105 Monomer.
me@260	106 """
me@260	107 monomer_type = MonomerType
me@260	108
me@260	109 def __init__(self, type):
me@310	110 super(Monomer, self).__init__()
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@313	182 sequence, = fasta.parse_file(file)
me@313	183 name, description, body = sequence
me@313	184 return cls(body, name, description, file.name)
me@284	185
me@295	186 class Alignment(object):
me@295	187 """Alignment. It is a list of Columns."""
bnagaev@249	188
me@287	189 sequence_type = Sequence
me@289	190 """Type of sequences in alignment. SHOULD be redefined when subclassing."""
me@288	191
me@289	192 sequences = None
me@289	193 """Ordered list of sequences in alignment. Read, but DO NOT FIDDLE!"""
bnagaev@249	194
me@287	195 def __init__(self):
me@287	196 """Initialize empty alignment."""
me@287	197 super(Alignment, self).__init__()
me@287	198 self.sequences = []
me@295	199 self.columns = []
me@282	200
me@299	201 # Alignment modification methods
me@299	202 # ==============================
me@299	203
me@294	204 def append_sequence(self, sequence):
me@294	205 """Add sequence to alignment.
me@294	206
me@294	207 If sequence is too short, pad it with gaps on the right.
me@294	208 """
me@294	209 self.sequences.append(sequence)
me@294	210 for i, monomer in enumerate(sequence):
me@302	211 self.column_at(i)[sequence] = monomer
me@294	212
me@306	213 def append_gapped_line(self, line, name='', description='', source='',
me@306	214 gaps=default_gaps):
me@287	215 """Add row from a line of one-letter codes and gaps."""
me@313	216 Sequence = self.sequence_type
me@306	217 not_gap = lambda (i, char): char not in gaps
me@306	218 without_gaps = util.remove_each(line, gaps)
me@306	219 sequence = Sequence(without_gaps, name, description, source)
me@303	220 # The following line has some simple magic:
me@303	221 # 1. attach natural numbers to monomers
me@303	222 # 2. delete gaps
me@303	223 # 3. attach numbers again
me@303	224 # This way we have a pair of numbers attached to monomer:
me@303	225 # - it's position in alignment (the first attached number, j)
me@303	226 # - it's position in sequence (the second attached number, i)
me@287	227 for i, (j, char) in enumerate(filter(not_gap, enumerate(line))):
me@313	228 self.column_at(j)[sequence] = sequence[i]
me@287	229 self.sequences.append(sequence)
me@287	230
me@302	231 def column_at(self, n):
me@302	232 """Return column by index. Create required new columns if required.
me@302	233
me@302	234 Do NOT use this method, unless you are sure it is what you want.
me@302	235 """
me@302	236 for i in range(len(self.columns), n + 1):
me@302	237 self.columns.append(Column())
me@302	238 return self.columns[n]
me@302	239
me@299	240 # Alignment IO methods
me@299	241 # ====================
me@299	242
me@287	243 @classmethod
me@306	244 def from_fasta(cls, file, gaps=default_gaps):
me@287	245 """Create new alignment from FASTA file."""
me@287	246 self = cls()
me@313	247 for (name, description, body) in fasta.parse_file(file):
me@306	248 self.append_gapped_line(body, name, description, gaps)
me@287	249 return self
bnagaev@249	250
me@292	251 def to_fasta(self, file):
me@292	252 """Write alignment in FASTA file as sequences with gaps."""
me@292	253 def char(monomer):
me@292	254 if monomer:
me@292	255 return monomer.code1
me@292	256 return "-"
me@292	257 for row in self.rows_as_lists():
me@292	258 seq = row.sequence
me@292	259 line = "".join(map(char, row))
me@292	260 fasta.save_file(file, line, seq.name, seq.description)
me@292	261
me@299	262 # Data access methods for alignment
me@299	263 # =================================
me@299	264
me@299	265 def rows(self):
me@299	266 """Return list of rows (temporary objects) in alignment.
me@299	267
me@299	268 Each row is a dictionary of { column : monomer }.
me@299	269
me@299	270 For gap positions there is no key for the column in row.
me@299	271
me@299	272 Each row has attribute `sequence` pointing to the sequence the row is
me@299	273 describing.
me@299	274
me@299	275 Modifications of row have no effect on the alignment.
me@299	276 """
me@299	277 # For now, the function returns a list rather than iterator.
me@299	278 # It is yet to see, whether memory performance here becomes critical,
me@299	279 # or is random access useful.
me@299	280 rows = []
me@299	281 for sequence in self.sequences:
me@299	282 row = util.UserDict()
me@299	283 row.sequence = sequence
me@299	284 for column in self.columns:
me@299	285 if sequence in column:
me@299	286 row[column] = column[sequence]
me@299	287 rows.append(row)
me@299	288 return rows
me@299	289
me@299	290 def rows_as_lists(self):
me@299	291 """Return list of rows (temporary objects) in alignment.
me@299	292
me@299	293 Each row here is a list of either monomer or None (for gaps).
me@299	294
me@299	295 Each row has attribute `sequence` pointing to the sequence of row.
me@299	296
me@299	297 Modifications of row have no effect on the alignment.
me@299	298 """
me@299	299 rows = []
me@299	300 for sequence in self.sequences:
me@299	301 row = util.UserList()
me@299	302 row.sequence = sequence
me@299	303 for column in self.columns:
me@299	304 row.append(column.get(sequence))
me@299	305 rows.append(row)
me@299	306 return rows
me@299	307
me@299	308 def columns_as_lists(self):
me@299	309 """Return list of columns (temorary objects) in alignment.
me@299	310
me@299	311 Each column here is a list of either monomer or None (for gaps).
me@299	312
me@299	313 Items of column are sorted in the same way as alignment.sequences.
me@299	314
me@299	315 Modifications of column have no effect on the alignment.
me@299	316 """
me@299	317 columns = []
me@299	318 for column in self.columns:
me@299	319 col = []
me@299	320 for sequence in self.sequences:
me@299	321 col.append(column.get(sequence))
me@299	322 columns.append(col)
me@299	323 return columns
me@299	324
me@300	325 class Column(dict):
me@300	326 """Column of alignment.
me@300	327
me@300	328 Column is a dict of { sequence : monomer }.
me@300	329
me@300	330 For sequences that have gaps in current row, given key is not present in
me@300	331 the column.
me@300	332 """
me@300	333 pass
me@300	334
me@307	335 class Block(object):
me@307	336 """Block of alignment.
me@301	337
me@307	338 Block is intersection of a set of columns & a set of rows. Most of blocks
me@307	339 look like rectangular part of alignment if you shuffle alignment rows the
me@307	340 right way.
me@261	341 """
me@270	342
me@307	343 alignment = None
me@307	344 """Alignment the block belongs to."""
me@270	345
me@307	346 sequences = ()
me@307	347 """List of sequences in block."""
me@307	348
me@307	349 columns = ()
me@307	350 """List of columns in block."""
me@307	351
me@307	352 def __init__(self, alignment, sequences=None, columns=None):
me@307	353 """Build new block from alignment.
me@307	354
me@307	355 If sequences are not given, the block uses all sequences in alignment.
me@307	356
me@307	357 If columns are not given, the block uses all columns in alignment.
me@307	358
me@307	359 In both cases we use exactly the list used in alignment, thus, if new
me@307	360 sequences or columns are added to alignment, the block tracks this too.
me@261	361 """
me@310	362 super(Block, self).__init__()
me@307	363 if sequences is None:
me@307	364 sequences = alignment.sequences
me@307	365 if colums is None:
me@307	366 columns = alignment.columns
me@261	367 self.alignment = alignment
me@261	368 self.sequences = sequences
me@261	369 self.positions = positions
me@270	370
me@312	371 def flush_left(self):
me@312	372 """Move all monomers to the left, gaps to the right within block."""
me@312	373 padding = [None] * len(self.columns)
me@312	374 for row in self.rows_as_lists():
me@312	375 sequence = row.sequence
me@312	376 row = filter(None, row) + padding
me@312	377 for monomer, column in zip(row, self.columns):
me@312	378 if monomer:
me@312	379 column[sequence] = monomer
me@312	380 elif sequence in column:
me@312	381 del column[sequence]
me@312	382
me@312	383
me@260	384 # vim: set ts=4 sts=4 sw=4 et: