from pyfaidx import Fasta import six import simplejson as json from gffutils import constants from gffutils import helpers from gffutils import parser from gffutils import bins from gffutils.attributes import dict_class _position_lookup = dict(enumerate(['seqid', 'source', 'featuretype', 'start', 'end', 'score', 'strand', 'frame', 'attributes'])) class Feature(object): def __init__(self, seqid=".", source=".", featuretype=".", start=".", end=".", score=".", strand=".", frame=".", attributes=None, extra=None, bin=None, id=None, dialect=None, file_order=None, keep_order=False, sort_attribute_values=False): """ Represents a feature from the database. Usually you won't want to use this directly, since it has various implementation details needed for operating in the context of FeatureDB objects. Instead, try the :func:`gffutils.feature.feature_from_line` function. When printed, reproduces the original line from the file as faithfully as possible using `dialect`. Parameters ---------- seqid : string Name of the sequence (often chromosome) source : string Source of the feature; typically the originating database or program that predicted the feature featuretype : string Type of feature. For example "gene", "exon", "TSS", etc start, end : int or "." 1-based coordinates; start must be <= end. If "." (the default placeholder for GFF files), then the corresponding attribute will be None. score : string Stored as a string. strand : "+" | "-" | "." Strand of the feature; "." when strand is not relevant. frame : "0" | "1" | "2" Coding frame. 0 means in-frame; 1 means there is one extra base at the beginning, so the first codon starts at the second base; 2 means two extra bases at the beginning. Interpretation is strand specific; "beginning" for a minus-strand feature is at the end coordinate. attributes : string or dict If a string, first assume it is serialized JSON; if this fails then assume it's the original key/vals string. If it's a dictionary already, then use as-is. The end result is that this instance's `attributes` attribute will always be a dictionary. Upon printing, the attributes will be reconstructed based on this dictionary and the dialect -- except if the original attributes string was provided, in which case that will be used directly. Notes on encoding/decoding: the only time unquoting (e.g., "%2C" becomes ",") happens is if `attributes` is a string and if `settings.ignore_url_escape_characters = False`. If dict or JSON, the contents are used as-is. Similarly, the only time characters are quoted ("," becomes "%2C") is when the feature is printed (`__str__` method). extra : string or list Additional fields after the canonical 9 fields for GFF/GTF. If a string, then first assume it's serialized JSON; if this fails then assume it's a tab-delimited string of additional fields. If it's a list already, then use as-is. bin : int UCSC genomic bin. If None, will be created based on provided start/end; if start or end is "." then bin will be None. id : None or string Database-specific primary key for this feature. The only time this should not be None is if this feature is coming from a database, in which case it will be filled in automatically. dialect : dict or None The dialect to use when reconstructing attribute strings; defaults to the GFF3 spec. :class:`FeatureDB` objects will automatically attach the dialect from the original file. file_order : int This is the `rowid` special field used in a sqlite3 database; this is provided by FeatureDB. keep_order : bool If True, then the attributes in the printed string will be in the order specified in the dialect. Disabled by default, since this sorting step is time-consuming over many features. sort_attribute_values : bool If True, then the values of each attribute will be sorted when the feature is printed. Mostly useful for testing, where the order is important for checking against expected values. Disabled by default, since it can be time-consuming over many features. """ # start/end can be provided as int-like, ".", or None, but will be # converted to int or None if start == "." or start == "": start = None elif start is not None: start = int(start) if end == "." or end == "": end = None elif end is not None: end = int(end) # Flexible handling of attributes: # If dict, then use that; otherwise assume JSON and convert to a dict; # otherwise assume original string and convert to a dict. # # dict_class is set at the module level above...this is so you can swap # in and out different dict implementations (ordered, defaultdict, etc) # for testing. attributes = attributes or dict_class() if isinstance(attributes, six.string_types): try: attributes = helpers._unjsonify(attributes, isattributes=True) # it's a string but not JSON: assume original attributes string. except json.JSONDecodeError: # But Feature.attributes is still a dict attributes, _dialect = parser._split_keyvals(attributes) # Use this dialect if none provided. dialect = dialect or _dialect # If string, then try un-JSONifying it into a list; if that doesn't # work then assume it's tab-delimited and convert to a list. extra = extra or [] if isinstance(extra, six.string_types): try: extra = helpers._unjsonify(extra) except json.JSONDecodeError: extra = extra.split('\t') self.seqid = seqid self.source = source self.featuretype = featuretype self.start = start self.end = end self.score = score self.strand = strand self.frame = frame self.attributes = attributes self.extra = extra self.bin = self.calc_bin(bin) self.id = id self.dialect = dialect or constants.dialect self.file_order = file_order self.keep_order = keep_order self.sort_attribute_values = sort_attribute_values def calc_bin(self, _bin=None): """ Calculate the smallest UCSC genomic bin that will contain this feature. """ if _bin is None: try: _bin = bins.bins(self.start, self.end, one=True) except TypeError: _bin = None return _bin def __repr__(self): memory_loc = hex(id(self)) # Reconstruct start/end as "." if self.start is None: start = '.' else: start = self.start if self.end is None: end = '.' else: end = self.end return ( "".format(x=self, start=start, end=end, loc=memory_loc)) def __getitem__(self, key): if isinstance(key, int): # TODO: allow access to "extra" fields attr = _position_lookup[key] return getattr(self, attr) else: return self.attributes[key] def __setitem__(self, key, value): if isinstance(key, int): # TODO: allow setting of "extra" fields attr = _position_lookup[key] setattr(self, attr, value) else: self.attributes[key] = value def __str__(self): if six.PY3: return self.__unicode__() else: return unicode(self).encode('utf-8') def __unicode__(self): # All fields but attributes (and extra). items = [getattr(self, k) for k in constants._gffkeys[:-1]] # Handle start/stop, which are either None or int if items[3] is None: items[3] = "." else: items[3] = str(items[3]) if items[4] is None: items[4] = "." else: items[4] = str(items[4]) # Reconstruct from dict and dialect reconstructed_attributes = parser._reconstruct( self.attributes, self.dialect, keep_order=self.keep_order, sort_attribute_values=self.sort_attribute_values) # Final line includes reconstructed as well as any previously-added # "extra" fields items.append(reconstructed_attributes) if self.extra: items.append('\t'.join(self.extra)) return '\t'.join(items) def __hash__(self): return hash(str(self)) def __eq__(self, other): return str(self) == str(other) def __ne__(self, other): return str(self) != str(other) def __len__(self): return self.stop - self.start + 1 # aliases for official GFF field names; this way x.chrom == x.seqid; and # x.stop == x.end. @property def chrom(self): return self.seqid @chrom.setter def chrom(self, value): self.seqid = value @property def stop(self): return self.end @stop.setter def stop(self, value): self.end = value def astuple(self, encoding=None): """ Return a tuple suitable for import into a database. Attributes field and extra field jsonified into strings. The order of fields is such that they can be supplied as arguments for the query defined in :attr:`gffutils.constants._INSERT`. If `encoding` is not None, then convert string fields to unicode using the provided encoding. Returns ------- Tuple """ if not encoding: return ( self.id, self.seqid, self.source, self.featuretype, self.start, self.end, self.score, self.strand, self.frame, helpers._jsonify(self.attributes), helpers._jsonify(self.extra), self.calc_bin() ) return ( self.id.decode(encoding), self.seqid.decode(encoding), self.source.decode(encoding), self.featuretype.decode(encoding), self.start, self.end, self.score.decode(encoding), self.strand.decode(encoding), self.frame.decode(encoding), helpers._jsonify(self.attributes).decode(encoding), helpers._jsonify(self.extra).decode(encoding), self.calc_bin() ) def sequence(self, fasta, use_strand=True): """ Retrieves the sequence of this feature as a string. Uses the pyfaidx package. Parameters ---------- fasta : str If str, then it's a FASTA-format filename; otherwise assume it's a pyfaidx.Fasta object. use_strand : bool If True (default), the sequence returned will be reverse-complemented for minus-strand features. Returns ------- string """ if isinstance(fasta, six.string_types): fasta = Fasta(fasta, as_raw=False) # recall GTF/GFF is 1-based closed; pyfaidx uses Python slice notation # and is therefore 0-based half-open. seq = fasta[self.chrom][self.start-1:self.stop] if use_strand and self.strand == '-': seq = seq.reverse.complement return seq.seq def feature_from_line(line, dialect=None, strict=True, keep_order=False): """ Given a line from a GFF file, return a Feature object Parameters ---------- line : string strict : bool If True (default), assume `line` is a single, tab-delimited string that has at least 9 fields. If False, then the input can have a more flexible format, useful for creating single ad hoc features or for writing tests. In this case, `line` can be a multi-line string (as long as it has a single non-empty line), and, as long as there are only 9 fields (standard GFF/GTF), then it's OK to use spaces instead of tabs to separate fields in `line`. But if >9 fields are to be used, then tabs must be used. keep_order, dialect Passed directly to :class:`Feature`; see docstring for that class for description Returns ------- A new :class:`Feature` object. """ if not strict: lines = line.splitlines(False) _lines = [] for i in lines: i = i.strip() if len(i) > 0: _lines.append(i) assert len(_lines) == 1, _lines line = _lines[0] if '\t' in line: fields = line.rstrip('\n\r').split('\t') else: fields = line.rstrip('\n\r').split(None, 8) else: fields = line.rstrip('\n\r').split('\t') try: attr_string = fields[8] except IndexError: attr_string = "" attrs, _dialect = parser._split_keyvals(attr_string, dialect=dialect) d = dict(list(zip(constants._gffkeys, fields))) d['attributes'] = attrs d['extra'] = fields[9:] d['keep_order'] = keep_order if dialect is None: dialect = _dialect return Feature(dialect=dialect, **d)