allpy: allpy/base.py annotate

allpy

annotate allpy/base.py @ 353:24a058450d72

Fixed references to monomer code tables. (closes #17)

author	Daniil Alexeyevsky <me.dendik@gmail.com>
date	Fri, 21 Jan 2011 15:28:26 +0300
parents	424f815b7515
children	0bdf8e55dd86

rev	line source
me@261	1 import sys
me@261	2
me@315	3 import util
me@284	4 import fasta
me@260	5
me@306	6 default_gaps = set((".", "-", "~"))
me@306	7 """Set of characters to recoginze as gaps when parsing alignment."""
me@306	8
me@328	9 class Monomer(object):
me@328	10 """Monomer object."""
me@260	11
me@328	12 type = None
me@328	13 """Either of 'dna', 'rna', 'protein'."""
me@260	14
me@260	15 by_code1 = {}
me@328	16 """A mapping from 1-letter code to Monomer subclass."""
me@328	17
me@260	18 by_code3 = {}
me@328	19 """A mapping from 3-letter code to Monomer subclass."""
me@328	20
me@260	21 by_name = {}
me@328	22 """A mapping from full monomer name to Monomer subclass."""
me@260	23
me@260	24 @classmethod
me@328	25 def _subclass(cls, name='', code1='', code3='', is_modified=False):
me@328	26 """Create new subclass of Monomer for given monomer type."""
me@328	27 class TheMonomer(cls):
me@328	28 pass
me@328	29 name = name.strip().capitalize()
me@328	30 code1 = code1.upper()
me@328	31 code3 = code3.upper()
me@328	32 TheMonomer.__name__ = "Monomer"
me@328	33 TheMonomer.name = name
me@328	34 TheMonomer.code1 = code1
me@328	35 TheMonomer.code3 = code3
me@328	36 TheMonomer.is_modified = is_modified
me@328	37 if not is_modified:
me@328	38 cls.by_code1[code1] = TheMonomer
me@328	39 cls.by_code3[code3] = TheMonomer
me@328	40 cls.by_name[name] = TheMonomer
me@328	41 # We duplicate distinguished long names into Monomer itself, so that we
me@328	42 # can use Monomer.from_code3 to create the relevant type of monomer.
me@328	43 Monomer.by_code3[code3] = TheMonomer
me@328	44 Monomer.by_name[name] = TheMonomer
me@260	45
me@328	46 @classmethod
me@353	47 def _initialize(cls, codes=None):
me@328	48 """Create all relevant subclasses of Monomer."""
me@328	49 # NB. The table uses letters d, r, p for types,
me@328	50 # while we use full words; hence, we compare by first letter
me@260	51 for type, code1, is_modified, code3, name in codes:
me@328	52 if type[0] == cls.type[0]:
me@328	53 cls._subclass(name, code1, code3, is_modified)
me@260	54
me@260	55 @classmethod
me@260	56 def from_code1(cls, code1):
me@328	57 """Create new monomer from 1-letter code."""
me@328	58 return cls.by_code1[code1.upper()]()
me@260	59
me@260	60 @classmethod
me@260	61 def from_code3(cls, code3):
me@328	62 """Create new monomer from 3-letter code."""
me@328	63 return cls.by_code3[code3.upper()]()
me@260	64
me@260	65 @classmethod
me@260	66 def from_name(cls, name):
me@328	67 """Create new monomer from full name."""
me@328	68 return cls.by_name[name.strip().capitalize()]()
me@260	69
me@329	70 def __repr__(self):
me@329	71 return '<Monomer %s>' % self.code3
me@329	72
me@329	73 def __str__(self):
me@329	74 """Returns one-letter code"""
me@329	75 return self.code1
me@329	76
me@260	77 def __eq__(self, other):
me@328	78 """Monomers within same monomer type are compared by code1."""
me@328	79 assert self.type == other.type
me@328	80 return self.code1 == other.code1
bnagaev@239	81
bnagaev@239	82 class Sequence(list):
me@274	83 """Sequence of Monomers.
bnagaev@243	84
me@274	85 This behaves like list of monomer objects. In addition to standard list
me@274	86 behaviour, Sequence has the following attributes:
me@270	87
me@274	88 * name -- str with the name of the sequence
me@274	89 * description -- str with description of the sequence
me@274	90 * source -- str denoting source of the sequence
me@266	91
me@274	92 Any of them may be empty (i.e. hold empty string)
me@275	93
me@275	94 Class attributes:
me@282	95
me@275	96 * monomer_type -- type of monomers in sequence, must be redefined when
me@275	97 subclassing
me@274	98 """
me@270	99
me@275	100 monomer_type = Monomer
me@270	101
me@275	102 name = ''
me@275	103 description = ''
me@275	104 source = ''
me@275	105
me@347	106 @classmethod
me@347	107 def from_monomers(cls, monomers=[], name=None, description=None, source=None):
me@347	108 """Create sequence from a list of monomer objecst."""
me@347	109 result = cls()
me@275	110 if name:
me@347	111 result.name = name
me@275	112 if description:
me@347	113 result.description = description
me@275	114 if source:
me@347	115 result.source = source
me@347	116 return result
me@347	117
me@347	118 @classmethod
me@347	119 def from_string(cls, string, name='', description='', source=''):
me@347	120 """Create sequences from string of one-letter codes."""
me@347	121 monomer = cls.monomer_type.from_code1
me@347	122 monomers = [monomer(letter) for letter in string]
me@347	123 return cls.from_monomers(monomers, name, description, source)
me@270	124
me@329	125 def __repr__(self):
me@329	126 return '<Sequence %s>' % str(self)
me@329	127
me@262	128 def __str__(self):
me@329	129 """Returns sequence of one-letter codes."""
me@275	130 return ''.join(monomer.code1 for monomer in self)
me@270	131
me@316	132 def __hash__(self):
me@316	133 """Hash sequence by identity."""
me@316	134 return id(self)
me@316	135
me@295	136 class Alignment(object):
me@295	137 """Alignment. It is a list of Columns."""
bnagaev@249	138
me@287	139 sequence_type = Sequence
me@289	140 """Type of sequences in alignment. SHOULD be redefined when subclassing."""
me@288	141
me@289	142 sequences = None
me@289	143 """Ordered list of sequences in alignment. Read, but DO NOT FIDDLE!"""
bnagaev@249	144
me@287	145 def __init__(self):
me@287	146 """Initialize empty alignment."""
me@287	147 self.sequences = []
me@295	148 self.columns = []
me@282	149
me@299	150 # Alignment modification methods
me@299	151 # ==============================
me@299	152
me@294	153 def append_sequence(self, sequence):
me@294	154 """Add sequence to alignment.
me@294	155
me@294	156 If sequence is too short, pad it with gaps on the right.
me@294	157 """
me@294	158 self.sequences.append(sequence)
me@294	159 for i, monomer in enumerate(sequence):
me@302	160 self.column_at(i)[sequence] = monomer
me@294	161
me@349	162 def append_row(self, string, name='', description='', source='',
me@306	163 gaps=default_gaps):
me@349	164 """Add row from a string of one-letter codes and gaps."""
me@313	165 Sequence = self.sequence_type
me@306	166 not_gap = lambda (i, char): char not in gaps
me@349	167 without_gaps = util.remove_each(string, gaps)
me@321	168 sequence = Sequence.from_string(without_gaps, name, description, source)
me@303	169 # The following line has some simple magic:
me@303	170 # 1. attach natural numbers to monomers
me@303	171 # 2. delete gaps
me@303	172 # 3. attach numbers again
me@303	173 # This way we have a pair of numbers attached to monomer:
me@303	174 # - it's position in alignment (the first attached number, j)
me@303	175 # - it's position in sequence (the second attached number, i)
me@349	176 for i, (j, char) in enumerate(filter(not_gap, enumerate(string))):
me@313	177 self.column_at(j)[sequence] = sequence[i]
me@287	178 self.sequences.append(sequence)
me@287	179
me@302	180 def column_at(self, n):
me@302	181 """Return column by index. Create required new columns if required.
me@302	182
me@302	183 Do NOT use this method, unless you are sure it is what you want.
me@302	184 """
me@302	185 for i in range(len(self.columns), n + 1):
me@302	186 self.columns.append(Column())
me@302	187 return self.columns[n]
me@302	188
me@299	189 # Alignment IO methods
me@299	190 # ====================
me@299	191
me@287	192 @classmethod
me@349	193 def from_file(cls, file, format='fasta', gaps=default_gaps):
me@349	194 """Create new alignment from file."""
me@287	195 self = cls()
me@349	196 assert format == 'fasta'
me@313	197 for (name, description, body) in fasta.parse_file(file):
me@349	198 self.append_row(body, name, description, file.name, gaps)
me@287	199 return self
bnagaev@249	200
me@292	201 def to_fasta(self, file):
me@292	202 """Write alignment in FASTA file as sequences with gaps."""
me@292	203 def char(monomer):
me@292	204 if monomer:
me@292	205 return monomer.code1
me@292	206 return "-"
me@292	207 for row in self.rows_as_lists():
me@292	208 seq = row.sequence
me@292	209 line = "".join(map(char, row))
me@292	210 fasta.save_file(file, line, seq.name, seq.description)
me@292	211
me@299	212 # Data access methods for alignment
me@299	213 # =================================
me@299	214
me@299	215 def rows(self):
me@299	216 """Return list of rows (temporary objects) in alignment.
me@299	217
me@299	218 Each row is a dictionary of { column : monomer }.
me@299	219
me@299	220 For gap positions there is no key for the column in row.
me@299	221
me@299	222 Each row has attribute `sequence` pointing to the sequence the row is
me@299	223 describing.
me@299	224
me@299	225 Modifications of row have no effect on the alignment.
me@299	226 """
me@299	227 # For now, the function returns a list rather than iterator.
me@299	228 # It is yet to see, whether memory performance here becomes critical,
me@299	229 # or is random access useful.
me@299	230 rows = []
me@299	231 for sequence in self.sequences:
me@299	232 row = util.UserDict()
me@299	233 row.sequence = sequence
me@299	234 for column in self.columns:
me@299	235 if sequence in column:
me@299	236 row[column] = column[sequence]
me@299	237 rows.append(row)
me@299	238 return rows
me@299	239
me@299	240 def rows_as_lists(self):
me@299	241 """Return list of rows (temporary objects) in alignment.
me@299	242
me@299	243 Each row here is a list of either monomer or None (for gaps).
me@299	244
me@299	245 Each row has attribute `sequence` pointing to the sequence of row.
me@299	246
me@299	247 Modifications of row have no effect on the alignment.
me@299	248 """
me@299	249 rows = []
me@299	250 for sequence in self.sequences:
me@299	251 row = util.UserList()
me@299	252 row.sequence = sequence
me@299	253 for column in self.columns:
me@299	254 row.append(column.get(sequence))
me@299	255 rows.append(row)
me@299	256 return rows
me@299	257
me@299	258 def columns_as_lists(self):
me@299	259 """Return list of columns (temorary objects) in alignment.
me@299	260
me@299	261 Each column here is a list of either monomer or None (for gaps).
me@299	262
me@299	263 Items of column are sorted in the same way as alignment.sequences.
me@299	264
me@299	265 Modifications of column have no effect on the alignment.
me@299	266 """
me@299	267 columns = []
me@299	268 for column in self.columns:
me@299	269 col = []
me@299	270 for sequence in self.sequences:
me@299	271 col.append(column.get(sequence))
me@299	272 columns.append(col)
me@299	273 return columns
me@299	274
me@300	275 class Column(dict):
me@300	276 """Column of alignment.
me@300	277
me@300	278 Column is a dict of { sequence : monomer }.
me@300	279
me@300	280 For sequences that have gaps in current row, given key is not present in
me@300	281 the column.
me@300	282 """
me@325	283
me@325	284 def __hash__(self):
me@325	285 """Return hash by identity."""
me@325	286 return id(self)
me@300	287
me@317	288 class Block(Alignment):
me@307	289 """Block of alignment.
me@301	290
me@307	291 Block is intersection of a set of columns & a set of rows. Most of blocks
me@307	292 look like rectangular part of alignment if you shuffle alignment rows the
me@307	293 right way.
me@261	294 """
me@270	295
me@307	296 alignment = None
me@307	297 """Alignment the block belongs to."""
me@270	298
me@307	299 sequences = ()
me@307	300 """List of sequences in block."""
me@307	301
me@307	302 columns = ()
me@307	303 """List of columns in block."""
me@307	304
me@317	305 @classmethod
me@317	306 def from_alignment(cls, alignment, sequences=None, columns=None):
me@307	307 """Build new block from alignment.
me@307	308
me@307	309 If sequences are not given, the block uses all sequences in alignment.
me@307	310
me@307	311 If columns are not given, the block uses all columns in alignment.
me@307	312
me@307	313 In both cases we use exactly the list used in alignment, thus, if new
me@307	314 sequences or columns are added to alignment, the block tracks this too.
me@261	315 """
me@307	316 if sequences is None:
me@307	317 sequences = alignment.sequences
me@318	318 if columns is None:
me@307	319 columns = alignment.columns
me@320	320 block = cls()
me@320	321 block.alignment = alignment
me@320	322 block.sequences = sequences
me@320	323 block.columns = columns
me@320	324 return block
me@270	325
me@312	326 def flush_left(self):
me@312	327 """Move all monomers to the left, gaps to the right within block."""
me@312	328 padding = [None] * len(self.columns)
me@312	329 for row in self.rows_as_lists():
me@312	330 sequence = row.sequence
me@312	331 row = filter(None, row) + padding
me@312	332 for monomer, column in zip(row, self.columns):
me@312	333 if monomer:
me@312	334 column[sequence] = monomer
me@312	335 elif sequence in column:
me@312	336 del column[sequence]
me@312	337
me@312	338
me@260	339 # vim: set ts=4 sts=4 sw=4 et: