allpy
view allpy/base.py @ 748:15633bca9c90
extract_pfam: Added sequence case markup. (closes #76)
| author | Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
|---|---|
| date | Mon, 11 Jul 2011 14:36:57 +0400 |
| parents | 0a7917b4ca71 |
| children | fbf79117dd18 |
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."""
75 @classmethod
77 """Create new monomer from 3-letter code."""
80 @classmethod
82 """Create new monomer from full name."""
89 """Returns one-letter code"""
93 """Monomers within same monomer type are compared by code1."""
103 """Sequence of Monomers.
105 This behaves like list of monomer objects. In addition to standard list
106 behaviour, Sequence has the following attributes:
108 * name -- str with the name of the sequence
109 * description -- str with description of the sequence
110 * source -- str denoting source of the sequence
112 Any of them may be empty (i.e. hold empty string)
113 """
116 """Mapping of related types. SHOULD be redefined in subclasses."""
126 @classmethod
128 """Create sequence from a list of monomer objecst."""
138 @classmethod
140 """Create sequences from string of one-letter codes."""
153 """Returns sequence of one-letter codes."""
157 """Hash sequence by identity."""
162 """Alignment. It is a list of Columns."""
165 """Mapping of related types. SHOULD be redefined in subclasses."""
168 """Ordered list of sequences in alignment. Read, but DO NOT FIDDLE!"""
171 """Initialize empty alignment."""
176 # Alignment grow & IO methods
177 # ==============================
180 """Add sequence to alignment. Return self.
182 If sequence is too short, pad it with gaps on the right.
183 """
192 """Add row from a string of one-letter codes and gaps. Return self."""
200 ]
207 """Add row from row_as_list representation and sequence. Return self."""
216 """Pad alignment with empty columns on the right to width n."""
221 """Append sequences from file to alignment. Return self.
223 If sequences in file have gaps (detected as characters belonging to
224 `gaps` set), treat them accordingly.
225 """
230 """Write alignment in FASTA file as sequences with gaps."""
234 # Data access methods for alignment
235 # =================================
238 """Return list of rows (temporary objects) in alignment.
240 Each row is a dictionary of { column : monomer }.
242 For gap positions there is no key for the column in row.
244 Each row has attribute `sequence` pointing to the sequence the row is
245 describing.
247 Modifications of row have no effect on the alignment.
248 """
249 # For now, the function returns a list rather than iterator.
250 # It is yet to see, whether memory performance here becomes critical,
251 # or is random access useful.
263 """Return list of rows (temporary objects) in alignment.
265 Each row here is a list of either monomer or None (for gaps).
267 Each row has attribute `sequence` pointing to the sequence of row.
269 Modifications of row have no effect on the alignment.
270 """
281 """Return list of string representation of rows in alignment.
283 Each row has attribute `sequence` pointing to the sequence of row.
285 `gap` is the symbol to use for gap.
286 """
301 """Return representaion of row as list with `Monomers` and `None`s."""
305 """Return string representaion of row in alignment.
307 String will have gaps represented by `gap` symbol (defaults to '-').
308 """
317 """Return list of columns (temorary objects) in alignment.
319 Each column here is a list of either monomer or None (for gaps).
321 Items of column are sorted in the same way as alignment.sequences.
323 Modifications of column have no effect on the alignment.
324 """
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."""
452 """Return hash by identity."""
457 """Block of alignment.
459 Block is an intersection of several rows & columns. (The collections of
460 rows and columns are represented as ordered lists, to retain display order
461 of Alignment or add ability to tweak it). Most of blocks look like
462 rectangular part of alignment if you shuffle alignment rows the right way.
463 """
466 """Alignment the block belongs to."""
469 """List of sequences in block."""
472 """List of columns in block."""
474 @classmethod
476 """Build new block from alignment.
478 If sequences are not given, the block uses all sequences in alignment.
480 If columns are not given, the block uses all columns in alignment.
482 In both cases we use exactly the list used in alignment, thus, if new
483 sequences or columns are added to alignment, the block tracks this too.
484 """
496 """Base class for sequence and alignment markups.
498 We shall call either sequence or alignment a container. And we shall call
499 either monomers or columns elements respectively.
501 Markup behaves like a dictionary of [element] -> value.
503 Every container has a dictionary of [name] -> markup. It is Markup's
504 responsibility to add itself to this dictionary and to avoid collisions
505 while doing it.
506 """
509 """Name of markup elements"""
512 """Register self within container.
514 Assure the name is not taken before. If name is not given, look in the
515 class. Make sure we have some name at all.
516 """
524 """Recalculate markup values (if they are generated automatically)."""
525 pass
527 @classmethod
529 """Restore markup from `record`. (Used for loading from file).
531 `record` is a dict of all metadata and data related to one markup. All
532 keys and values in `record` are strings, markup must parse them itself.
534 Markup values should be stored in `record['markup']`, which is a list
535 of items separated with either `record['separator']` or a comma.
536 """
540 """Save markup to `record`, for saving to file.
542 For description of `record` see docstring for `from_record` method.
543 """
547 """Return list of elements in the container in proper order."""
551 """Return list of markup values in container."""
555 """Markup for sequence.
557 Behaves like a dictionary of [monomer] -> value. Value may be anything
558 or something specific, depending on subclass.
560 Actual values are stored in monomers themselves as attributes.
561 """
569 """Return list of monomers."""
573 """Return list of markup values, if every monomer is marked up."""
577 """Part of Mapping collection interface."""
583 """Part of Mapping collection interface."""
587 """Part of Mapping collection interface."""
591 """Part of Mapping collection interface."""
595 """Markupf for alignment.
597 Is a dictionary of [column] -> value. Value may be anything or something
598 specific, depending on subclass.
599 """
607 """Return a list of columns."""
611 """Return a list of makrup values, if every column is marked up."""
614 # vim: set ts=4 sts=4 sw=4 et: