allpy
view allpy/base.py @ 669:2f016bfda114
Massive changes to my program
| author | Boris Burkov <BurkovBA@gmail.com> |
|---|---|
| date | Fri, 01 Jul 2011 09:52:49 +0400 |
| parents | c32e728b98d7 |
| children | 1a4a04829ba6 |
line source
8 # import this very module as means of having all related classes in one place
12 """Set of characters to recoginze as gaps when parsing alignment."""
15 """Monomer object."""
18 """Either of 'dna', 'rna', 'protein'."""
21 """Mapping of related types. SHOULD be redefined in subclasses."""
24 """A mapping from 1-letter code to Monomer subclass."""
27 """A mapping from 3-letter code to Monomer subclass."""
30 """A mapping from full monomer name to Monomer subclass."""
32 @classmethod
34 """Create new subclass of Monomer for given monomer type."""
36 pass
47 # Save the class in data.monomers so that it can be pickled
48 # Some names are not unique, we append underscores to them
49 # in order to fix it.
57 # We duplicate distinguished long names into Monomer itself, so that we
58 # can use Monomer.from_code3 to create the relevant type of monomer.
62 @classmethod
64 """Create all relevant subclasses of Monomer."""
68 @classmethod
70 """Create new monomer from 1-letter code."""
73 @classmethod
75 """Create new monomer from 3-letter code."""
78 @classmethod
80 """Create new monomer from full name."""
87 """Returns one-letter code"""
91 """Monomers within same monomer type are compared by code1."""
92 #import traceback
93 #for entry in traceback.extract_stack():
94 # if "remove_contained_preblocks" in entry[2]:
95 # print traceback.extract_stack()
105 """Sequence of Monomers.
107 This behaves like list of monomer objects. In addition to standard list
108 behaviour, Sequence has the following attributes:
110 * name -- str with the name of the sequence
111 * description -- str with description of the sequence
112 * source -- str denoting source of the sequence
114 Any of them may be empty (i.e. hold empty string)
115 """
118 """Mapping of related types. SHOULD be redefined in subclasses."""
124 @classmethod
126 """Create sequence from a list of monomer objecst."""
136 @classmethod
138 """Create sequences from string of one-letter codes."""
151 """Returns sequence of one-letter codes."""
155 """Hash sequence by identity."""
160 """Alignment. It is a list of Columns."""
163 """Mapping of related types. SHOULD be redefined in subclasses."""
166 """Ordered list of sequences in alignment. Read, but DO NOT FIDDLE!"""
169 """Initialize empty alignment."""
173 # Alignment grow & IO methods
174 # ==============================
177 """Add sequence to alignment. Return self.
179 If sequence is too short, pad it with gaps on the right.
180 """
189 """Add row from a string of one-letter codes and gaps. Return self."""
197 ]
204 """Add row from row_as_list representation and sequence. Return self."""
213 """Pad alignment with empty columns on the right to width n."""
218 """Append sequences from file to alignment. Return self.
220 If sequences in file have gaps (detected as characters belonging to
221 `gaps` set), treat them accordingly.
222 """
230 """Write alignment in FASTA file as sequences with gaps."""
235 # Data access methods for alignment
236 # =================================
239 """Return list of rows (temporary objects) in alignment.
241 Each row is a dictionary of { column : monomer }.
243 For gap positions there is no key for the column in row.
245 Each row has attribute `sequence` pointing to the sequence the row is
246 describing.
248 Modifications of row have no effect on the alignment.
249 """
250 # For now, the function returns a list rather than iterator.
251 # It is yet to see, whether memory performance here becomes critical,
252 # or is random access useful.
264 """Return list of rows (temporary objects) in alignment.
266 Each row here is a list of either monomer or None (for gaps).
268 Each row has attribute `sequence` pointing to the sequence of row.
270 Modifications of row have no effect on the alignment.
271 """
282 """Return list of string representation of rows in alignment.
284 Each row has attribute `sequence` pointing to the sequence of row.
286 `gap` is the symbol to use for gap.
287 """
302 """Return representaion of row as list with `Monomers` and `None`s."""
306 """Return string representaion of row in alignment.
308 String will have gaps represented by `gap` symbol (defaults to '-').
309 """
318 """Return list of columns (temorary objects) in alignment.
320 Each column here is a list of either monomer or None (for gaps).
322 Items of column are sorted in the same way as alignment.sequences.
324 Modifications of column have no effect on the alignment.
325 """
334 # Alignment / Block editing methods
335 # =================================
338 """Remove all gaps from alignment and flush results to one side.
340 `whence` must be one of 'left', 'right' or 'center'
341 """
353 """Remove all empty columns."""
359 """Turn all row positions into gaps (but keep sequences intact)."""
365 """Replace contents of `dst` with those of `new`.
367 Replace contents of elements using function `merge(dst_el, new_le)`.
368 """
375 """Replace contents of sequences with those of `new` alignment."""
376 # XXX: we manually copy sequence contents here
377 # XXX: we only copy, overlapping parts and link to the rest
387 """Replace column contents with those of `new` alignment.
389 In other words: copy gap patterns from `new` to `self`.
391 `self.sequences` and `new.sequences` should have the same contents.
392 """
401 ]
406 """Replace alignment contents with those of other alignment."""
412 """Apply function to the alignment (or block); inject results back.
414 - `function(block)` must return block with same line order.
415 - if `copy_descriptions` is False, ignore new sequence names.
416 - if `copy_contents` is False, don't copy sequence contents too.
418 `function` (object) may have attributes `copy_descriptions` and
419 `copy_contents`, which override the same named arguments.
420 """
429 """Realign self.
431 I.e.: apply function to self to produce a new alignment, then update
432 self to have the same gap patterns as the new alignment.
434 This is the same as process(function, False, False)
435 """
440 """Column of alignment.
442 Column is a dict of { sequence : monomer }.
444 For sequences that have gaps in current row, given key is not present in
445 the column.
446 """
449 """Mapping of related types. SHOULD be redefined in subclasses."""
456 """Return hash by identity."""
465 #!!!!!!!!! READ HOW index OF LIST COMPARES OBJECTS AND BASIC TYPES
472 """Block of alignment.
474 Block is an intersection of several rows & columns. (The collections of
475 rows and columns are represented as ordered lists, to retain display order
476 of Alignment or add ability to tweak it). Most of blocks look like
477 rectangular part of alignment if you shuffle alignment rows the right way.
478 """
481 """Alignment the block belongs to."""
484 """List of sequences in block."""
487 """List of columns in block."""
489 @classmethod
491 """Build new block from alignment.
493 If sequences are not given, the block uses all sequences in alignment.
495 If columns are not given, the block uses all columns in alignment.
497 In both cases we use exactly the list used in alignment, thus, if new
498 sequences or columns are added to alignment, the block tracks this too.
499 """
510 # vim: set ts=4 sts=4 sw=4 et: