# Copyright 2000-2003 Jeff Chang. # Copyright 2001-2008 Brad Chapman. # Copyright 2005-2016 by Peter Cock. # Copyright 2006-2009 Michiel de Hoon. # All rights reserved. # # This file is part of the Biopython distribution and governed by your # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". # Please see the LICENSE file that should have been included as part of this # package. """Represent a Sequence Feature holding info about a part of a sequence. This is heavily modeled after the Biocorba SeqFeature objects, and may be pretty biased towards GenBank stuff since I'm writing it for the GenBank parser output... What's here: Base class to hold a Feature ---------------------------- Classes: - SeqFeature Hold information about a Reference ---------------------------------- This is an attempt to create a General class to hold Reference type information. Classes: - Reference Specify locations of a feature on a Sequence -------------------------------------------- This aims to handle, in Ewan Birney's words, 'the dreaded fuzziness issue'. This has the advantages of allowing us to handle fuzzy stuff in case anyone needs it, and also be compatible with BioPerl etc and BioSQL. Classes: - Location - abstract base class of SimpleLocation and CompoundLocation. - SimpleLocation - Specify the start and end location of a feature. - CompoundLocation - Collection of SimpleLocation objects (for joins etc). - Position - abstract base class of ExactPosition, WithinPosition, BetweenPosition, AfterPosition, OneOfPosition, UncertainPosition, and UnknownPosition. - ExactPosition - Specify the position as being exact. - WithinPosition - Specify a position occurring within some range. - BetweenPosition - Specify a position occurring between a range (OBSOLETE?). - BeforePosition - Specify the position as being found before some base. - AfterPosition - Specify the position as being found after some base. - OneOfPosition - Specify a position consisting of multiple alternative positions. - UncertainPosition - Specify a specific position which is uncertain. - UnknownPosition - Represents missing information like '?' in UniProt. Exceptions: - LocationParserError - Exception indicating a failure to parse a location string. """ import functools import re import warnings from abc import ABC, abstractmethod from Bio import BiopythonParserWarning from Bio import BiopythonDeprecationWarning from Bio.Seq import MutableSeq from Bio.Seq import reverse_complement from Bio.Seq import Seq # Regular expressions for location parsing _reference = r"(?:[a-zA-Z][a-zA-Z0-9_\.\|]*[a-zA-Z0-9]?\:)" _oneof_position = r"one\-of\(\d+[,\d+]+\)" _oneof_location = rf"[<>]?(?:\d+|{_oneof_position})\.\.[<>]?(?:\d+|{_oneof_position})" _any_location = rf"({_reference}?{_oneof_location}|complement\({_oneof_location}\)|[^,]+|complement\([^,]+\))" _split = re.compile(_any_location).split assert _split("123..145")[1::2] == ["123..145"] assert _split("123..145,200..209")[1::2] == ["123..145", "200..209"] assert _split("one-of(200,203)..300")[1::2] == ["one-of(200,203)..300"] assert _split("complement(123..145),200..209")[1::2] == [ "complement(123..145)", "200..209", ] assert _split("123..145,one-of(200,203)..209")[1::2] == [ "123..145", "one-of(200,203)..209", ] assert _split("123..145,one-of(200,203)..one-of(209,211),300")[1::2] == [ "123..145", "one-of(200,203)..one-of(209,211)", "300", ] assert _split("123..145,complement(one-of(200,203)..one-of(209,211)),300")[1::2] == [ "123..145", "complement(one-of(200,203)..one-of(209,211))", "300", ] assert _split("123..145,200..one-of(209,211),300")[1::2] == [ "123..145", "200..one-of(209,211)", "300", ] assert _split("123..145,200..one-of(209,211)")[1::2] == [ "123..145", "200..one-of(209,211)", ] assert _split( "complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905" )[1::2] == [ "complement(149815..150200)", "complement(293787..295573)", "NC_016402.1:6618..6676", "181647..181905", ] _pair_location = r"[<>]?-?\d+\.\.[<>]?-?\d+" _between_location = r"\d+\^\d+" _within_position = r"\(\d+\.\d+\)" _within_location = r"([<>]?\d+|%s)\.\.([<>]?\d+|%s)" % ( _within_position, _within_position, ) _within_position = r"\((\d+)\.(\d+)\)" _re_within_position = re.compile(_within_position) assert _re_within_position.match("(3.9)") _oneof_location = r"([<>]?\d+|%s)\.\.([<>]?\d+|%s)" % (_oneof_position, _oneof_position) _oneof_position = r"one\-of\((\d+[,\d+]+)\)" _re_oneof_position = re.compile(_oneof_position) assert _re_oneof_position.match("one-of(6,9)") assert not _re_oneof_position.match("one-of(3)") assert _re_oneof_position.match("one-of(3,6)") assert _re_oneof_position.match("one-of(3,6,9)") _solo_location = r"[<>]?\d+" _solo_bond = r"bond\(%s\)" % _solo_location _re_location_category = re.compile( r"^(?P%s)|(?P%s)|(?P%s)|(?P%s)|(?P%s)|(?P%s)$" % ( _pair_location, _between_location, _within_location, _oneof_location, _solo_bond, _solo_location, ) ) class LocationParserError(ValueError): """Could not parse a feature location string.""" pass class SeqFeature: """Represent a Sequence Feature on an object. Attributes: - location - the location of the feature on the sequence (SimpleLocation) - type - the specified type of the feature (ie. CDS, exon, repeat...) - location_operator - a string specifying how this SeqFeature may be related to others. For example, in the example GenBank feature shown below, the location_operator would be "join". This is a proxy for feature.location.operator and only applies to compound locations. - strand - A value specifying on which strand (of a DNA sequence, for instance) the feature deals with. 1 indicates the plus strand, -1 indicates the minus strand, 0 indicates stranded but unknown (? in GFF3), while the default of None indicates that strand doesn't apply (dot in GFF3, e.g. features on proteins). Note this is a shortcut for accessing the strand property of the feature's location. - id - A string identifier for the feature. - ref - A reference to another sequence. This could be an accession number for some different sequence. Note this is a shortcut for the reference property of the feature's location. - ref_db - A different database for the reference accession number. Note this is a shortcut for the reference property of the location - qualifiers - A dictionary of qualifiers on the feature. These are analogous to the qualifiers from a GenBank feature table. The keys of the dictionary are qualifier names, the values are the qualifier values. """ def __init__( self, location=None, type="", location_operator="", strand=None, id="", qualifiers=None, sub_features=None, ref=None, ref_db=None, ): """Initialize a SeqFeature on a sequence. location can either be a SimpleLocation (with strand argument also given if required), or None. e.g. With no strand, on the forward strand, and on the reverse strand: >>> from Bio.SeqFeature import SeqFeature, SimpleLocation >>> f1 = SeqFeature(SimpleLocation(5, 10), type="domain") >>> f1.strand == f1.location.strand == None True >>> f2 = SeqFeature(SimpleLocation(7, 110, strand=1), type="CDS") >>> f2.strand == f2.location.strand == +1 True >>> f3 = SeqFeature(SimpleLocation(9, 108, strand=-1), type="CDS") >>> f3.strand == f3.location.strand == -1 True For exact start/end positions, an integer can be used (as shown above) as shorthand for the ExactPosition object. For non-exact locations, the SimpleLocation must be specified via the appropriate position objects. Note that the strand, ref and ref_db arguments to the SeqFeature are now deprecated and will later be removed. Set them via the location object instead. Note that location_operator and sub_features arguments can no longer be used, instead do this via the CompoundLocation object. """ if ( location is not None and not isinstance(location, SimpleLocation) and not isinstance(location, CompoundLocation) ): raise TypeError( "SimpleLocation, CompoundLocation (or None) required for the location" ) self.location = location self.type = type if location_operator: warnings.warn( "Using the location_operator argument is deprecated, and will be removed in a future release. " "Please do this via the CompoundLocation object instead.", BiopythonDeprecationWarning, ) self.location_operator = location_operator if strand is not None: warnings.warn( "Using the strand argument is deprecated, and will be removed in a future release. " "Please set it via the location object instead.", BiopythonDeprecationWarning, ) self.strand = strand self.id = id self.qualifiers = {} if qualifiers is not None: self.qualifiers.update(qualifiers) if sub_features is not None: raise TypeError("Rather than sub_features, use a CompoundLocation") if ref is not None: warnings.warn( "Using the ref argument is deprecated, and will be removed in a future release. " "Please set it via the location object instead.", BiopythonDeprecationWarning, ) self.ref = ref if ref_db is not None: warnings.warn( "Using the ref_db argument is deprecated, and will be removed in a future release. " "Please set it via the location object instead.", BiopythonDeprecationWarning, ) self.ref_db = ref_db def _get_strand(self): """Get function for the strand property (PRIVATE).""" return self.location.strand def _set_strand(self, value): """Set function for the strand property (PRIVATE).""" try: self.location.strand = value except AttributeError: if self.location is None: if value is not None: raise ValueError("Can't set strand without a location.") from None else: raise strand = property( fget=_get_strand, fset=_set_strand, doc="""Feature's strand This is a shortcut for feature.location.strand """, ) def _get_ref(self): """Get function for the reference property (PRIVATE).""" try: return self.location.ref except AttributeError: return None def _set_ref(self, value): """Set function for the reference property (PRIVATE).""" try: self.location.ref = value except AttributeError: if self.location is None: if value is not None: raise ValueError("Can't set ref without a location.") from None else: raise ref = property( fget=_get_ref, fset=_set_ref, doc="""Feature location reference (e.g. accession). This is a shortcut for feature.location.ref """, ) def _get_ref_db(self): """Get function for the database reference property (PRIVATE).""" try: return self.location.ref_db except AttributeError: return None def _set_ref_db(self, value): """Set function for the database reference property (PRIVATE).""" self.location.ref_db = value ref_db = property( fget=_get_ref_db, fset=_set_ref_db, doc="""Feature location reference's database. This is a shortcut for feature.location.ref_db """, ) def _get_location_operator(self): """Get function for the location operator property (PRIVATE).""" try: return self.location.operator except AttributeError: return None def _set_location_operator(self, value): """Set function for the location operator property (PRIVATE).""" if value: if isinstance(self.location, CompoundLocation): self.location.operator = value elif self.location is None: raise ValueError( f"Location is None so can't set its operator (to {value!r})" ) else: raise ValueError(f"Only CompoundLocation gets an operator ({value!r})") location_operator = property( fget=_get_location_operator, fset=_set_location_operator, doc="Location operator for compound locations (e.g. join).", ) def __eq__(self, other): """Check if two SeqFeature objects should be considered equal.""" return ( isinstance(other, SeqFeature) and self.id == other.id and self.type == other.type and self.location == other.location and self.qualifiers == other.qualifiers ) def __repr__(self): """Represent the feature as a string for debugging.""" answer = f"{self.__class__.__name__}({self.location!r}" if self.type: answer += f", type={self.type!r}" if self.location_operator: answer += f", location_operator={self.location_operator!r}" if self.id and self.id != "": answer += f", id={self.id!r}" if self.qualifiers: answer += ", qualifiers=..." if self.ref: answer += f", ref={self.ref!r}" if self.ref_db: answer += f", ref_db={self.ref_db!r}" answer += ")" return answer def __str__(self): """Return the full feature as a python string.""" out = f"type: {self.type}\n" out += f"location: {self.location}\n" if self.id and self.id != "": out += f"id: {self.id}\n" out += "qualifiers:\n" for qual_key in sorted(self.qualifiers): out += f" Key: {qual_key}, Value: {self.qualifiers[qual_key]}\n" return out def _shift(self, offset): """Return a copy of the feature with its location shifted (PRIVATE). The annotation qualifiers are copied. """ return SeqFeature( location=self.location._shift(offset), type=self.type, id=self.id, qualifiers=self.qualifiers.copy(), ) def _flip(self, length): """Return a copy of the feature with its location flipped (PRIVATE). The argument length gives the length of the parent sequence. For example a location 0..20 (+1 strand) with parent length 30 becomes after flipping 10..30 (-1 strand). Strandless (None) or unknown strand (0) remain like that - just their end points are changed. The annotation qualifiers are copied. """ return SeqFeature( location=self.location._flip(length), type=self.type, id=self.id, qualifiers=self.qualifiers.copy(), ) def extract(self, parent_sequence, references=None): """Extract the feature's sequence from supplied parent sequence. The parent_sequence can be a Seq like object or a string, and will generally return an object of the same type. The exception to this is a MutableSeq as the parent sequence will return a Seq object. This should cope with complex locations including complements, joins and fuzzy positions. Even mixed strand features should work! This also covers features on protein sequences (e.g. domains), although here reverse strand features are not permitted. If the location refers to other records, they must be supplied in the optional dictionary references. >>> from Bio.Seq import Seq >>> from Bio.SeqFeature import SeqFeature, SimpleLocation >>> seq = Seq("MKQHKAMIVALIVICITAVVAAL") >>> f = SeqFeature(SimpleLocation(8, 15), type="domain") >>> f.extract(seq) Seq('VALIVIC') If the SimpleLocation is None, e.g. when parsing invalid locus locations in the GenBank parser, extract() will raise a ValueError. >>> from Bio.Seq import Seq >>> from Bio.SeqFeature import SeqFeature >>> seq = Seq("MKQHKAMIVALIVICITAVVAAL") >>> f = SeqFeature(None, type="domain") >>> f.extract(seq) Traceback (most recent call last): ... ValueError: The feature's .location is None. Check the sequence file for a valid location. Note - currently only compound features of type "join" are supported. """ if self.location is None: raise ValueError( "The feature's .location is None. Check the " "sequence file for a valid location." ) return self.location.extract(parent_sequence, references=references) def translate( self, parent_sequence, table="Standard", start_offset=None, stop_symbol="*", to_stop=False, cds=None, gap=None, ): """Get a translation of the feature's sequence. This method is intended for CDS or other features that code proteins and is a shortcut that will both extract the feature and translate it, taking into account the codon_start and transl_table qualifiers, if they are present. If they are not present the value of the arguments "table" and "start_offset" are used. The "cds" parameter is set to "True" if the feature is of type "CDS" but can be overridden by giving an explicit argument. The arguments stop_symbol, to_stop and gap have the same meaning as Seq.translate, refer to that documentation for further information. Arguments: - parent_sequence - A DNA or RNA sequence. - table - Which codon table to use if there is no transl_table qualifier for this feature. This can be either a name (string), an NCBI identifier (integer), or a CodonTable object (useful for non-standard genetic codes). This defaults to the "Standard" table. - start_offset - offset at which the first complete codon of a coding feature can be found, relative to the first base of that feature. Has a valid value of 0, 1 or 2. NOTE: this uses python's 0-based numbering whereas the codon_start qualifier in files from NCBI use 1-based numbering. Will override a codon_start qualifier >>> from Bio.Seq import Seq >>> from Bio.SeqFeature import SeqFeature, SimpleLocation >>> seq = Seq("GGTTACACTTACCGATAATGTCTCTGATGA") >>> f = SeqFeature(SimpleLocation(0, 30), type="CDS") >>> f.qualifiers['transl_table'] = [11] Note that features of type CDS are subject to the usual checks at translation. But you can override this behavior by giving explicit arguments: >>> f.translate(seq, cds=False) Seq('GYTYR*CL**') Now use the start_offset argument to change the frame. Note this uses python 0-based numbering. >>> f.translate(seq, start_offset=1, cds=False) Seq('VTLTDNVSD') Alternatively use the codon_start qualifier to do the same thing. Note: this uses 1-based numbering, which is found in files from NCBI. >>> f.qualifiers['codon_start'] = [2] >>> f.translate(seq, cds=False) Seq('VTLTDNVSD') """ # see if this feature should be translated in a different # frame using the "codon_start" qualifier if start_offset is None: try: start_offset = int(self.qualifiers["codon_start"][0]) - 1 except KeyError: start_offset = 0 if start_offset not in [0, 1, 2]: raise ValueError( "The start_offset must be 0, 1, or 2. " f"The supplied value is {start_offset}. " "Check the value of either the codon_start qualifier " "or the start_offset argument" ) feat_seq = self.extract(parent_sequence)[start_offset:] codon_table = self.qualifiers.get("transl_table", [table])[0] if cds is None: cds = self.type == "CDS" return feat_seq.translate( table=codon_table, stop_symbol=stop_symbol, to_stop=to_stop, cds=cds, gap=gap, ) def __bool__(self): """Boolean value of an instance of this class (True). This behavior is for backwards compatibility, since until the __len__ method was added, a SeqFeature always evaluated as True. Note that in comparison, Seq objects, strings, lists, etc, will all evaluate to False if they have length zero. WARNING: The SeqFeature may in future evaluate to False when its length is zero (in order to better match normal python behavior)! """ return True def __len__(self): """Return the length of the region where the feature is located. >>> from Bio.Seq import Seq >>> from Bio.SeqFeature import SeqFeature, SimpleLocation >>> seq = Seq("MKQHKAMIVALIVICITAVVAAL") >>> f = SeqFeature(SimpleLocation(8, 15), type="domain") >>> len(f) 7 >>> f.extract(seq) Seq('VALIVIC') >>> len(f.extract(seq)) 7 This is a proxy for taking the length of the feature's location: >>> len(f.location) 7 For simple features this is the same as the region spanned (end position minus start position using Pythonic counting). However, for a compound location (e.g. a CDS as the join of several exons) the gaps are not counted (e.g. introns). This ensures that len(f) matches len(f.extract(parent_seq)), and also makes sure things work properly with features wrapping the origin etc. """ return len(self.location) def __iter__(self): """Iterate over the parent positions within the feature. The iteration order is strand aware, and can be thought of as moving along the feature using the parent sequence coordinates: >>> from Bio.SeqFeature import SeqFeature, SimpleLocation >>> f = SeqFeature(SimpleLocation(5, 10, strand=-1), type="domain") >>> len(f) 5 >>> for i in f: print(i) 9 8 7 6 5 >>> list(f) [9, 8, 7, 6, 5] This is a proxy for iterating over the location, >>> list(f.location) [9, 8, 7, 6, 5] """ return iter(self.location) def __contains__(self, value): """Check if an integer position is within the feature. >>> from Bio.SeqFeature import SeqFeature, SimpleLocation >>> f = SeqFeature(SimpleLocation(5, 10, strand=-1), type="domain") >>> len(f) 5 >>> [i for i in range(15) if i in f] [5, 6, 7, 8, 9] For example, to see which features include a SNP position, you could use this: >>> from Bio import SeqIO >>> record = SeqIO.read("GenBank/NC_000932.gb", "gb") >>> for f in record.features: ... if 1750 in f: ... print("%s %s" % (f.type, f.location)) source [0:154478](+) gene [1716:4347](-) tRNA join{[4310:4347](-), [1716:1751](-)} Note that for a feature defined as a join of several subfeatures (e.g. the union of several exons) the gaps are not checked (e.g. introns). In this example, the tRNA location is defined in the GenBank file as complement(join(1717..1751,4311..4347)), so that position 1760 falls in the gap: >>> for f in record.features: ... if 1760 in f: ... print("%s %s" % (f.type, f.location)) source [0:154478](+) gene [1716:4347](-) Note that additional care may be required with fuzzy locations, for example just before a BeforePosition: >>> from Bio.SeqFeature import SeqFeature, SimpleLocation >>> from Bio.SeqFeature import BeforePosition >>> f = SeqFeature(SimpleLocation(BeforePosition(3), 8), type="domain") >>> len(f) 5 >>> [i for i in range(10) if i in f] [3, 4, 5, 6, 7] Note that is is a proxy for testing membership on the location. >>> [i for i in range(10) if i in f.location] [3, 4, 5, 6, 7] """ return value in self.location # --- References # TODO -- Will this hold PubMed and Medline information decently? class Reference: """Represent a Generic Reference object. Attributes: - location - A list of Location objects specifying regions of the sequence that the references correspond to. If no locations are specified, the entire sequence is assumed. - authors - A big old string, or a list split by author, of authors for the reference. - title - The title of the reference. - journal - Journal the reference was published in. - medline_id - A medline reference for the article. - pubmed_id - A pubmed reference for the article. - comment - A place to stick any comments about the reference. """ def __init__(self): """Initialize the class.""" self.location = [] self.authors = "" self.consrtm = "" self.title = "" self.journal = "" self.medline_id = "" self.pubmed_id = "" self.comment = "" def __str__(self): """Return the full Reference object as a python string.""" out = "" for single_location in self.location: out += f"location: {single_location}\n" out += f"authors: {self.authors}\n" if self.consrtm: out += f"consrtm: {self.consrtm}\n" out += f"title: {self.title}\n" out += f"journal: {self.journal}\n" out += f"medline id: {self.medline_id}\n" out += f"pubmed id: {self.pubmed_id}\n" out += f"comment: {self.comment}\n" return out def __repr__(self): """Represent the Reference object as a string for debugging.""" # TODO - Update this is __init__ later accepts values return f"{self.__class__.__name__}(title={self.title!r}, ...)" def __eq__(self, other): """Check if two Reference objects should be considered equal. Note prior to Biopython 1.70 the location was not compared, as until then __eq__ for the SimpleLocation class was not defined. """ return ( self.authors == other.authors and self.consrtm == other.consrtm and self.title == other.title and self.journal == other.journal and self.medline_id == other.medline_id and self.pubmed_id == other.pubmed_id and self.comment == other.comment and self.location == other.location ) # --- Handling feature locations class Location(ABC): """Abstract base class representing a location.""" @abstractmethod def __repr__(self): """Represent the Location object as a string for debugging.""" return f"{self.__class__.__name__}(...)" def fromstring(text, length=None, circular=False, stranded=True): """Create a Location object from a string. This should accept any valid location string in the INSDC Feature Table format (https://www.insdc.org/submitting-standards/feature-table/) as used in GenBank, DDBJ and EMBL files. Simple examples: >>> Location.fromstring("123..456", 1000) SimpleLocation(ExactPosition(122), ExactPosition(456), strand=1) >>> Location.fromstring("complement(<123..>456)", 1000) SimpleLocation(BeforePosition(122), AfterPosition(456), strand=-1) A more complex location using within positions, >>> Location.fromstring("(9.10)..(20.25)", 1000) SimpleLocation(WithinPosition(8, left=8, right=9), WithinPosition(25, left=20, right=25), strand=1) Notice how that will act as though it has overall start 8 and end 25. Zero length between feature, >>> Location.fromstring("123^124", 1000) SimpleLocation(ExactPosition(123), ExactPosition(123), strand=1) The expected sequence length is needed for a special case, a between position at the start/end of a circular genome: >>> Location.fromstring("1000^1", 1000) SimpleLocation(ExactPosition(1000), ExactPosition(1000), strand=1) Apart from this special case, between positions P^Q must have P+1==Q, >>> Location.fromstring("123^456", 1000) Traceback (most recent call last): ... Bio.SeqFeature.LocationParserError: invalid feature location '123^456' You can optionally provide a reference name: >>> Location.fromstring("AL391218.9:105173..108462", 2000000) SimpleLocation(ExactPosition(105172), ExactPosition(108462), strand=1, ref='AL391218.9') >>> Location.fromstring("<2644..159", 2868, "circular") CompoundLocation([SimpleLocation(BeforePosition(2643), ExactPosition(2868), strand=1), SimpleLocation(ExactPosition(0), ExactPosition(159), strand=1)], 'join') """ if text.startswith("complement("): if text[-1] != ")": raise ValueError(f"closing bracket missing in '{text}'") text = text[11:-1] strand = -1 elif stranded: strand = 1 else: strand = None # Determine if we have a simple location or a compound location if text.startswith("join("): operator = "join" parts = _split(text[5:-1])[1::2] # assert parts[0] == "" and parts[-1] == "" elif text.startswith("order("): operator = "order" parts = _split(text[6:-1])[1::2] # assert parts[0] == "" and parts[-1] == "" elif text.startswith("bond("): operator = "bond" parts = _split(text[5:-1])[1::2] # assert parts[0] == "" and parts[-1] == "" else: loc = SimpleLocation.fromstring(text, length, circular) loc.strand = strand if strand == -1: loc.parts.reverse() return loc locs = [] for part in parts: loc = SimpleLocation.fromstring(part, length, circular) if loc is None: break if loc.strand == -1: if strand == -1: raise LocationParserError("double complement in '{text}'?") else: loc.strand = strand locs.extend(loc.parts) else: if len(locs) == 1: return loc # Historically a join on the reverse strand has been represented # in Biopython with both the parent SeqFeature and its children # (the exons for a CDS) all given a strand of -1. Likewise, for # a join feature on the forward strand they all have strand +1. # However, we must also consider evil mixed strand examples like # this, join(complement(69611..69724),139856..140087,140625..140650) if strand == -1: # Whole thing was wrapped in complement(...) for loc in locs: assert loc.strand == -1 # Reverse the backwards order used in GenBank files # with complement(join(...)) locs = locs[::-1] return CompoundLocation(locs, operator=operator) # Not recognized if "order" in text and "join" in text: # See Bug 3197 raise LocationParserError( f"failed to parse feature location '{text}' containing a combination of 'join' and 'order' (nested operators) are illegal" ) # See issue #937. Note that NCBI has already fixed this record. if ",)" in text: warnings.warn( "Dropping trailing comma in malformed feature location", BiopythonParserWarning, ) text = text.replace(",)", ")") return Location.fromstring(text) raise LocationParserError(f"failed to parse feature location '{text}'") class SimpleLocation(Location): """Specify the location of a feature along a sequence. The SimpleLocation is used for simple continuous features, which can be described as running from a start position to and end position (optionally with a strand and reference information). More complex locations made up from several non-continuous parts (e.g. a coding sequence made up of several exons) are described using a SeqFeature with a CompoundLocation. Note that the start and end location numbering follow Python's scheme, thus a GenBank entry of 123..150 (one based counting) becomes a location of [122:150] (zero based counting). >>> from Bio.SeqFeature import SimpleLocation >>> f = SimpleLocation(122, 150) >>> print(f) [122:150] >>> print(f.start) 122 >>> print(f.end) 150 >>> print(f.strand) None Note the strand defaults to None. If you are working with nucleotide sequences you'd want to be explicit if it is the forward strand: >>> from Bio.SeqFeature import SimpleLocation >>> f = SimpleLocation(122, 150, strand=+1) >>> print(f) [122:150](+) >>> print(f.strand) 1 Note that for a parent sequence of length n, the SimpleLocation start and end must satisfy the inequality 0 <= start <= end <= n. This means even for features on the reverse strand of a nucleotide sequence, we expect the 'start' coordinate to be less than the 'end'. >>> from Bio.SeqFeature import SimpleLocation >>> r = SimpleLocation(122, 150, strand=-1) >>> print(r) [122:150](-) >>> print(r.start) 122 >>> print(r.end) 150 >>> print(r.strand) -1 i.e. Rather than thinking of the 'start' and 'end' biologically in a strand aware manner, think of them as the 'left most' or 'minimum' boundary, and the 'right most' or 'maximum' boundary of the region being described. This is particularly important with compound locations describing non-continuous regions. In the example above we have used standard exact positions, but there are also specialised position objects used to represent fuzzy positions as well, for example a GenBank location like complement(<123..150) would use a BeforePosition object for the start. """ def __init__(self, start, end, strand=None, ref=None, ref_db=None): """Initialize the class. start and end arguments specify the values where the feature begins and ends. These can either by any of the ``*Position`` objects that inherit from Position, or can just be integers specifying the position. In the case of integers, the values are assumed to be exact and are converted in ExactPosition arguments. This is meant to make it easy to deal with non-fuzzy ends. i.e. Short form: >>> from Bio.SeqFeature import SimpleLocation >>> loc = SimpleLocation(5, 10, strand=-1) >>> print(loc) [5:10](-) Explicit form: >>> from Bio.SeqFeature import SimpleLocation, ExactPosition >>> loc = SimpleLocation(ExactPosition(5), ExactPosition(10), strand=-1) >>> print(loc) [5:10](-) Other fuzzy positions are used similarly, >>> from Bio.SeqFeature import SimpleLocation >>> from Bio.SeqFeature import BeforePosition, AfterPosition >>> loc2 = SimpleLocation(BeforePosition(5), AfterPosition(10), strand=-1) >>> print(loc2) [<5:>10](-) For nucleotide features you will also want to specify the strand, use 1 for the forward (plus) strand, -1 for the reverse (negative) strand, 0 for stranded but strand unknown (? in GFF3), or None for when the strand does not apply (dot in GFF3), e.g. features on proteins. >>> loc = SimpleLocation(5, 10, strand=+1) >>> print(loc) [5:10](+) >>> print(loc.strand) 1 Normally feature locations are given relative to the parent sequence you are working with, but an explicit accession can be given with the optional ref and db_ref strings: >>> loc = SimpleLocation(105172, 108462, ref="AL391218.9", strand=1) >>> print(loc) AL391218.9[105172:108462](+) >>> print(loc.ref) AL391218.9 """ # TODO - Check 0 <= start <= end (<= length of reference) if isinstance(start, Position): self._start = start elif isinstance(start, int): self._start = ExactPosition(start) else: raise TypeError(f"start={start!r} {type(start)}") if isinstance(end, Position): self._end = end elif isinstance(end, int): self._end = ExactPosition(end) else: raise TypeError(f"end={end!r} {type(end)}") if ( isinstance(self.start, int) and isinstance(self.end, int) and self.start > self.end ): raise ValueError( f"End location ({self.end}) must be greater than " f"or equal to start location ({self.start})" ) self.strand = strand self.ref = ref self.ref_db = ref_db @staticmethod def fromstring(text, length=None, circular=False): """Create a SimpleLocation object from a string.""" if text.startswith("complement("): text = text[11:-1] strand = -1 else: strand = None # Try simple cases first for speed try: s, e = text.split("..") s = int(s) - 1 e = int(e) except ValueError: pass else: if 0 <= s <= e: return SimpleLocation(s, e, strand) # Try general case try: ref, text = text.split(":") except ValueError: ref = None m = _re_location_category.match(text) if m is None: return None for key, value in m.groupdict().items(): if value is not None: break assert value == text if key == "bond": # e.g. bond(196) warnings.warn( "Dropping bond qualifier in feature location", BiopythonParserWarning, ) text = text[5:-1] s_pos = Position.fromstring(text, -1) e_pos = Position.fromstring(text) elif key == "solo": # e.g. "123" s_pos = Position.fromstring(text, -1) e_pos = Position.fromstring(text) elif key in ("pair", "within", "oneof"): s, e = text.split("..") # Attempt to fix features that span the origin s_pos = Position.fromstring(s, -1) e_pos = Position.fromstring(e) if s_pos > e_pos: # There is likely a problem with origin wrapping. # Create a CompoundLocation of the wrapped feature, # consisting of two SimpleLocation objects to extend to # the list of feature locations. if not circular: raise LocationParserError( f"it appears that '{text}' is a feature that spans the origin, but the sequence topology is undefined" ) warnings.warn( "Attempting to fix invalid location %r as " "it looks like incorrect origin wrapping. " "Please fix input file, this could have " "unintended behavior." % text, BiopythonParserWarning, ) f1 = SimpleLocation(s_pos, length, strand) f2 = SimpleLocation(0, e_pos, strand) if strand == -1: # For complementary features spanning the origin return f2 + f1 else: return f1 + f2 elif key == "between": # A between location like "67^68" (one based counting) is a # special case (note it has zero length). In python slice # notation this is 67:67, a zero length slice. See Bug 2622 # Further more, on a circular genome of length N you can have # a location N^1 meaning the junction at the origin. See Bug 3098. # NOTE - We can imagine between locations like "2^4", but this # is just "3". Similarly, "2^5" is just "3..4" s, e = text.split("^") s = int(s) e = int(e) if s + 1 == e or (s == length and e == 1): s_pos = ExactPosition(s) e_pos = s_pos else: raise LocationParserError(f"invalid feature location '{text}'") if s_pos < 0: raise LocationParserError( f"negative starting position in feature location '{text}'" ) return SimpleLocation(s_pos, e_pos, strand, ref=ref) def _get_strand(self): """Get function for the strand property (PRIVATE).""" return self._strand def _set_strand(self, value): """Set function for the strand property (PRIVATE).""" if value not in [+1, -1, 0, None]: raise ValueError(f"Strand should be +1, -1, 0 or None, not {value!r}") self._strand = value strand = property( fget=_get_strand, fset=_set_strand, doc="Strand of the location (+1, -1, 0 or None).", ) def __str__(self): """Return a representation of the SimpleLocation object (with python counting). For the simple case this uses the python splicing syntax, [122:150] (zero based counting) which GenBank would call 123..150 (one based counting). """ answer = f"[{self._start}:{self._end}]" if self.ref and self.ref_db: answer = f"{self.ref_db}:{self.ref}{answer}" elif self.ref: answer = self.ref + answer # Is ref_db without ref meaningful? if self.strand is None: return answer elif self.strand == +1: return answer + "(+)" elif self.strand == -1: return answer + "(-)" else: # strand = 0, stranded but strand unknown, ? in GFF3 return answer + "(?)" def __repr__(self): """Represent the SimpleLocation object as a string for debugging.""" optional = "" if self.strand is not None: optional += f", strand={self.strand!r}" if self.ref is not None: optional += f", ref={self.ref!r}" if self.ref_db is not None: optional += f", ref_db={self.ref_db!r}" return f"{self.__class__.__name__}({self.start!r}, {self.end!r}{optional})" def __add__(self, other): """Combine location with another SimpleLocation object, or shift it. You can add two feature locations to make a join CompoundLocation: >>> from Bio.SeqFeature import SimpleLocation >>> f1 = SimpleLocation(5, 10) >>> f2 = SimpleLocation(20, 30) >>> combined = f1 + f2 >>> print(combined) join{[5:10], [20:30]} This is thus equivalent to: >>> from Bio.SeqFeature import CompoundLocation >>> join = CompoundLocation([f1, f2]) >>> print(join) join{[5:10], [20:30]} You can also use sum(...) in this way: >>> join = sum([f1, f2]) >>> print(join) join{[5:10], [20:30]} Furthermore, you can combine a SimpleLocation with a CompoundLocation in this way. Separately, adding an integer will give a new SimpleLocation with its start and end offset by that amount. For example: >>> print(f1) [5:10] >>> print(f1 + 100) [105:110] >>> print(200 + f1) [205:210] This can be useful when editing annotation. """ if isinstance(other, SimpleLocation): return CompoundLocation([self, other]) elif isinstance(other, int): return self._shift(other) else: # This will allow CompoundLocation's __radd__ to be called: return NotImplemented def __radd__(self, other): """Return a SimpleLocation object by shifting the location by an integer amount.""" if isinstance(other, int): return self._shift(other) else: return NotImplemented def __sub__(self, other): """Subtracting an integer will shift the start and end by that amount. >>> from Bio.SeqFeature import SimpleLocation >>> f1 = SimpleLocation(105, 150) >>> print(f1) [105:150] >>> print(f1 - 100) [5:50] This can be useful when editing annotation. You can also add an integer to a feature location (which shifts in the opposite direction). """ if isinstance(other, int): return self._shift(-other) else: return NotImplemented def __nonzero__(self): """Return True regardless of the length of the feature. This behavior is for backwards compatibility, since until the __len__ method was added, a SimpleLocation always evaluated as True. Note that in comparison, Seq objects, strings, lists, etc, will all evaluate to False if they have length zero. WARNING: The SimpleLocation may in future evaluate to False when its length is zero (in order to better match normal python behavior)! """ return True def __len__(self): """Return the length of the region described by the SimpleLocation object. Note that extra care may be needed for fuzzy locations, e.g. >>> from Bio.SeqFeature import SimpleLocation >>> from Bio.SeqFeature import BeforePosition, AfterPosition >>> loc = SimpleLocation(BeforePosition(5), AfterPosition(10)) >>> len(loc) 5 """ return int(self._end) - int(self._start) def __contains__(self, value): """Check if an integer position is within the SimpleLocation object. Note that extra care may be needed for fuzzy locations, e.g. >>> from Bio.SeqFeature import SimpleLocation >>> from Bio.SeqFeature import BeforePosition, AfterPosition >>> loc = SimpleLocation(BeforePosition(5), AfterPosition(10)) >>> len(loc) 5 >>> [i for i in range(15) if i in loc] [5, 6, 7, 8, 9] """ if not isinstance(value, int): raise ValueError( "Currently we only support checking for integer " "positions being within a SimpleLocation." ) if value < self._start or value >= self._end: return False else: return True def __iter__(self): """Iterate over the parent positions within the SimpleLocation object. >>> from Bio.SeqFeature import SimpleLocation >>> from Bio.SeqFeature import BeforePosition, AfterPosition >>> loc = SimpleLocation(BeforePosition(5), AfterPosition(10)) >>> len(loc) 5 >>> for i in loc: print(i) 5 6 7 8 9 >>> list(loc) [5, 6, 7, 8, 9] >>> [i for i in range(15) if i in loc] [5, 6, 7, 8, 9] Note this is strand aware: >>> loc = SimpleLocation(BeforePosition(5), AfterPosition(10), strand = -1) >>> list(loc) [9, 8, 7, 6, 5] """ if self.strand == -1: yield from range(self._end - 1, self._start - 1, -1) else: yield from range(self._start, self._end) def __eq__(self, other): """Implement equality by comparing all the location attributes.""" if not isinstance(other, SimpleLocation): return False return ( self._start == other.start and self._end == other.end and self._strand == other.strand and self.ref == other.ref and self.ref_db == other.ref_db ) def _shift(self, offset): """Return a copy of the SimpleLocation shifted by an offset (PRIVATE). Returns self when location is relative to an external reference. """ # TODO - What if offset is a fuzzy position? if self.ref or self.ref_db: return self return SimpleLocation( start=self._start + offset, end=self._end + offset, strand=self.strand, ) def _flip(self, length): """Return a copy of the location after the parent is reversed (PRIVATE). Returns self when location is relative to an external reference. """ if self.ref or self.ref_db: return self # Note this will flip the start and end too! if self.strand == +1: flip_strand = -1 elif self.strand == -1: flip_strand = +1 else: # 0 or None flip_strand = self.strand return SimpleLocation( start=self._end._flip(length), end=self._start._flip(length), strand=flip_strand, ) @property def parts(self): """Read only list of sections (always one, the SimpleLocation object). This is a convenience property allowing you to write code handling both SimpleLocation objects (with one part) and more complex CompoundLocation objects (with multiple parts) interchangeably. """ return [self] @property def start(self): """Start location - left most (minimum) value, regardless of strand. Read only, returns an integer like position object, possibly a fuzzy position. """ return self._start @property def end(self): """End location - right most (maximum) value, regardless of strand. Read only, returns an integer like position object, possibly a fuzzy position. """ return self._end @property def nofuzzy_start(self): """Start position (integer, approximated if fuzzy, read only) (DEPRECATED). This is now an alias for int(feature.start), which should be used in preference -- unless you are trying to support old versions of Biopython. """ warnings.warn( "Use int(feature.start) rather than feature.nofuzzy_start", BiopythonDeprecationWarning, ) try: return int(self._start) except TypeError: if isinstance(self._start, UnknownPosition): return None raise @property def nofuzzy_end(self): """End position (integer, approximated if fuzzy, read only) (DEPRECATED). This is now an alias for int(feature.end), which should be used in preference -- unless you are trying to support old versions of Biopython. """ warnings.warn( "Use int(feature.end) rather than feature.nofuzzy_end", BiopythonDeprecationWarning, ) try: return int(self._end) except TypeError: if isinstance(self._end, UnknownPosition): return None raise def extract(self, parent_sequence, references=None): """Extract the sequence from supplied parent sequence using the SimpleLocation object. The parent_sequence can be a Seq like object or a string, and will generally return an object of the same type. The exception to this is a MutableSeq as the parent sequence will return a Seq object. If the location refers to other records, they must be supplied in the optional dictionary references. >>> from Bio.Seq import Seq >>> from Bio.SeqFeature import SimpleLocation >>> seq = Seq("MKQHKAMIVALIVICITAVVAAL") >>> feature_loc = SimpleLocation(8, 15) >>> feature_loc.extract(seq) Seq('VALIVIC') """ if self.ref or self.ref_db: if not references: raise ValueError( f"Feature references another sequence ({self.ref})," " references mandatory" ) elif self.ref not in references: # KeyError? raise ValueError( f"Feature references another sequence ({self.ref})," " not found in references" ) parent_sequence = references[self.ref] f_seq = parent_sequence[int(self.start) : int(self.end)] if isinstance(f_seq, MutableSeq): f_seq = Seq(f_seq) if self.strand == -1: f_seq = reverse_complement( f_seq, inplace=False ) # TODO: remove inplace=False return f_seq FeatureLocation = SimpleLocation # OBSOLETE; for backward compatability only. class CompoundLocation(Location): """For handling joins etc where a feature location has several parts.""" def __init__(self, parts, operator="join"): """Initialize the class. >>> from Bio.SeqFeature import SimpleLocation, CompoundLocation >>> f1 = SimpleLocation(10, 40, strand=+1) >>> f2 = SimpleLocation(50, 59, strand=+1) >>> f = CompoundLocation([f1, f2]) >>> len(f) == len(f1) + len(f2) == 39 == len(list(f)) True >>> print(f.operator) join >>> 5 in f False >>> 15 in f True >>> f.strand 1 Notice that the strand of the compound location is computed automatically - in the case of mixed strands on the sub-locations the overall strand is set to None. >>> f = CompoundLocation([SimpleLocation(3, 6, strand=+1), ... SimpleLocation(10, 13, strand=-1)]) >>> print(f.strand) None >>> len(f) 6 >>> list(f) [3, 4, 5, 12, 11, 10] The example above doing list(f) iterates over the coordinates within the feature. This allows you to use max and min on the location, to find the range covered: >>> min(f) 3 >>> max(f) 12 More generally, you can use the compound location's start and end which give the full span covered, 0 <= start <= end <= full sequence length. >>> f.start == min(f) True >>> f.end == max(f) + 1 True This is consistent with the behavior of the SimpleLocation for a single region, where again the 'start' and 'end' do not necessarily give the biological start and end, but rather the 'minimal' and 'maximal' coordinate boundaries. Note that adding locations provides a more intuitive method of construction: >>> f = SimpleLocation(3, 6, strand=+1) + SimpleLocation(10, 13, strand=-1) >>> len(f) 6 >>> list(f) [3, 4, 5, 12, 11, 10] """ self.operator = operator self.parts = list(parts) for loc in self.parts: if not isinstance(loc, SimpleLocation): raise ValueError( "CompoundLocation should be given a list of " "SimpleLocation objects, not %s" % loc.__class__ ) if len(parts) < 2: raise ValueError( f"CompoundLocation should have at least 2 parts, not {parts!r}" ) def __str__(self): """Return a representation of the CompoundLocation object (with python counting).""" return "%s{%s}" % (self.operator, ", ".join(str(loc) for loc in self.parts)) def __repr__(self): """Represent the CompoundLocation object as string for debugging.""" return f"{self.__class__.__name__}({self.parts!r}, {self.operator!r})" def _get_strand(self): """Get function for the strand property (PRIVATE).""" # Historically a join on the reverse strand has been represented # in Biopython with both the parent SeqFeature and its children # (the exons for a CDS) all given a strand of -1. Likewise, for # a join feature on the forward strand they all have strand +1. # However, we must also consider evil mixed strand examples like # this, join(complement(69611..69724),139856..140087,140625..140650) if len({loc.strand for loc in self.parts}) == 1: return self.parts[0].strand else: return None # i.e. mixed strands def _set_strand(self, value): """Set function for the strand property (PRIVATE).""" # Should this be allowed/encouraged? for loc in self.parts: loc.strand = value strand = property( fget=_get_strand, fset=_set_strand, doc="""Overall strand of the compound location. If all the parts have the same strand, that is returned. Otherwise for mixed strands, this returns None. >>> from Bio.SeqFeature import SimpleLocation, CompoundLocation >>> f1 = SimpleLocation(15, 17, strand=1) >>> f2 = SimpleLocation(20, 30, strand=-1) >>> f = f1 + f2 >>> f1.strand 1 >>> f2.strand -1 >>> f.strand >>> f.strand is None True If you set the strand of a CompoundLocation, this is applied to all the parts - use with caution: >>> f.strand = 1 >>> f1.strand 1 >>> f2.strand 1 >>> f.strand 1 """, ) def __add__(self, other): """Combine locations, or shift the location by an integer offset. >>> from Bio.SeqFeature import SimpleLocation >>> f1 = SimpleLocation(15, 17) + SimpleLocation(20, 30) >>> print(f1) join{[15:17], [20:30]} You can add another SimpleLocation: >>> print(f1 + SimpleLocation(40, 50)) join{[15:17], [20:30], [40:50]} >>> print(SimpleLocation(5, 10) + f1) join{[5:10], [15:17], [20:30]} You can also add another CompoundLocation: >>> f2 = SimpleLocation(40, 50) + SimpleLocation(60, 70) >>> print(f2) join{[40:50], [60:70]} >>> print(f1 + f2) join{[15:17], [20:30], [40:50], [60:70]} Also, as with the SimpleLocation, adding an integer shifts the location's coordinates by that offset: >>> print(f1 + 100) join{[115:117], [120:130]} >>> print(200 + f1) join{[215:217], [220:230]} >>> print(f1 + (-5)) join{[10:12], [15:25]} """ if isinstance(other, SimpleLocation): return CompoundLocation(self.parts + [other], self.operator) elif isinstance(other, CompoundLocation): if self.operator != other.operator: # Handle join+order -> order as a special case? raise ValueError( f"Mixed operators {self.operator} and {other.operator}" ) return CompoundLocation(self.parts + other.parts, self.operator) elif isinstance(other, int): return self._shift(other) else: raise NotImplementedError def __radd__(self, other): """Add a feature to the left.""" if isinstance(other, SimpleLocation): return CompoundLocation([other] + self.parts, self.operator) elif isinstance(other, int): return self._shift(other) else: raise NotImplementedError def __contains__(self, value): """Check if an integer position is within the CompoundLocation object.""" for loc in self.parts: if value in loc: return True return False def __nonzero__(self): """Return True regardless of the length of the feature. This behavior is for backwards compatibility, since until the __len__ method was added, a SimpleLocation always evaluated as True. Note that in comparison, Seq objects, strings, lists, etc, will all evaluate to False if they have length zero. WARNING: The SimpleLocation may in future evaluate to False when its length is zero (in order to better match normal python behavior)! """ return True def __len__(self): """Return the length of the CompoundLocation object.""" return sum(len(loc) for loc in self.parts) def __iter__(self): """Iterate over the parent positions within the CompoundLocation object.""" for loc in self.parts: yield from loc def __eq__(self, other): """Check if all parts of CompoundLocation are equal to all parts of other CompoundLocation.""" if not isinstance(other, CompoundLocation): return False if len(self.parts) != len(other.parts): return False if self.operator != other.operator: return False for self_part, other_part in zip(self.parts, other.parts): if self_part != other_part: return False return True def _shift(self, offset): """Return a copy of the CompoundLocation shifted by an offset (PRIVATE).""" return CompoundLocation( [loc._shift(offset) for loc in self.parts], self.operator ) def _flip(self, length): """Return a copy of the locations after the parent is reversed (PRIVATE). Note that the order of the parts is NOT reversed too. Consider a CDS on the forward strand with exons small, medium and large (in length). Once we change the frame of reference to the reverse complement strand, the start codon is still part of the small exon, and the stop codon still part of the large exon - so the part order remains the same! Here is an artificial example, were the features map to the two upper case regions and the lower case runs of n are not used: >>> from Bio.Seq import Seq >>> from Bio.SeqFeature import SimpleLocation >>> dna = Seq("nnnnnAGCATCCTGCTGTACnnnnnnnnGAGAMTGCCATGCCCCTGGAGTGAnnnnn") >>> small = SimpleLocation(5, 20, strand=1) >>> large = SimpleLocation(28, 52, strand=1) >>> location = small + large >>> print(small) [5:20](+) >>> print(large) [28:52](+) >>> print(location) join{[5:20](+), [28:52](+)} >>> for part in location.parts: ... print(len(part)) ... 15 24 As you can see, this is a silly example where each "exon" is a word: >>> print(small.extract(dna).translate()) SILLY >>> print(large.extract(dna).translate()) EXAMPLE* >>> print(location.extract(dna).translate()) SILLYEXAMPLE* >>> for part in location.parts: ... print(part.extract(dna).translate()) ... SILLY EXAMPLE* Now, let's look at this from the reverse strand frame of reference: >>> flipped_dna = dna.reverse_complement() >>> flipped_location = location._flip(len(dna)) >>> print(flipped_location.extract(flipped_dna).translate()) SILLYEXAMPLE* >>> for part in flipped_location.parts: ... print(part.extract(flipped_dna).translate()) ... SILLY EXAMPLE* The key point here is the first part of the CompoundFeature is still the small exon, while the second part is still the large exon: >>> for part in flipped_location.parts: ... print(len(part)) ... 15 24 >>> print(flipped_location) join{[37:52](-), [5:29](-)} Notice the parts are not reversed. However, there was a bug here in older versions of Biopython which would have given join{[5:29](-), [37:52](-)} and the translation would have wrongly been "EXAMPLE*SILLY" instead. """ return CompoundLocation( [loc._flip(length) for loc in self.parts], self.operator ) @property def start(self): """Start location - left most (minimum) value, regardless of strand. Read only, returns an integer like position object, possibly a fuzzy position. For the special case of a CompoundLocation wrapping the origin of a circular genome, this will return zero. """ return min(loc.start for loc in self.parts) @property def end(self): """End location - right most (maximum) value, regardless of strand. Read only, returns an integer like position object, possibly a fuzzy position. For the special case of a CompoundLocation wrapping the origin of a circular genome this will match the genome length (minus one given how Python counts from zero). """ return max(loc.end for loc in self.parts) @property def nofuzzy_start(self): """Start position (integer, approximated if fuzzy, read only) (DEPRECATED). This is an alias for int(feature.start), which should be used in preference -- unless you are trying to support old versions of Biopython. """ warnings.warn( "Use int(feature.start) rather than feature.nofuzzy_start", BiopythonDeprecationWarning, ) try: return int(self.start) except TypeError: if isinstance(self.start, UnknownPosition): return None raise @property def nofuzzy_end(self): """End position (integer, approximated if fuzzy, read only) (DEPRECATED). This is an alias for int(feature.end), which should be used in preference -- unless you are trying to support old versions of Biopython. """ warnings.warn( "Use int(feature.end) rather than feature.nofuzzy_end", BiopythonDeprecationWarning, ) try: return int(self.end) except TypeError: if isinstance(self.end, UnknownPosition): return None raise @property def ref(self): """Not present in CompoundLocation, dummy method for API compatibility.""" return None @property def ref_db(self): """Not present in CompoundLocation, dummy method for API compatibility.""" return None def extract(self, parent_sequence, references=None): """Extract the sequence from supplied parent sequence using the CompoundLocation object. The parent_sequence can be a Seq like object or a string, and will generally return an object of the same type. The exception to this is a MutableSeq as the parent sequence will return a Seq object. If the location refers to other records, they must be supplied in the optional dictionary references. >>> from Bio.Seq import Seq >>> from Bio.SeqFeature import SimpleLocation, CompoundLocation >>> seq = Seq("MKQHKAMIVALIVICITAVVAAL") >>> fl1 = SimpleLocation(2, 8) >>> fl2 = SimpleLocation(10, 15) >>> fl3 = CompoundLocation([fl1,fl2]) >>> fl3.extract(seq) Seq('QHKAMILIVIC') """ # This copes with mixed strand features & all on reverse: parts = [ loc.extract(parent_sequence, references=references) for loc in self.parts ] f_seq = functools.reduce(lambda x, y: x + y, parts) return f_seq class Position(ABC): """Abstract base class representing a position.""" @abstractmethod def __repr__(self): """Represent the Position object as a string for debugging.""" return f"{self.__class__.__name__}(...)" @property def position(self): """Legacy attribute to get (left-most) position as an integer (DEPRECATED).""" warnings.warn( "Alias location.position is deprecated and will be removed in a future " "release. Use location directly, or int(location). However, that will " "fail for UnknownPosition, and for OneOfPosition and WithinPosition " "will give the default rather than left-most value.", BiopythonDeprecationWarning, ) return int(self) @property def extension(self): """Legacy attribute to get the position's 'width' as an integer, typically zero (DEPRECATED).""" warnings.warn( "Alias location.extension is deprecated and will be removed in a " "future release. It was undefined or zero except for OneOfPosition, " "WithinPosition and WithinPosition which must now be handled " "explicitly instead.", BiopythonDeprecationWarning, ) return 0 @staticmethod def fromstring(text, offset=0): """Build a Position object from the text string. For an end position, leave offset as zero (default): >>> Position.fromstring("5") ExactPosition(5) For a start position, set offset to minus one (for Python counting): >>> Position.fromstring("5", -1) ExactPosition(4) This also covers fuzzy positions: >>> p = Position.fromstring("<5") >>> p BeforePosition(5) >>> print(p) <5 >>> int(p) 5 >>> Position.fromstring(">5") AfterPosition(5) By default assumes an end position, so note the integer behavior: >>> p = Position.fromstring("one-of(5,8,11)") >>> p OneOfPosition(11, choices=[ExactPosition(5), ExactPosition(8), ExactPosition(11)]) >>> print(p) one-of(5,8,11) >>> int(p) 11 >>> Position.fromstring("(8.10)") WithinPosition(10, left=8, right=10) Fuzzy start positions: >>> p = Position.fromstring("<5", -1) >>> p BeforePosition(4) >>> print(p) <4 >>> int(p) 4 Notice how the integer behavior changes too! >>> p = Position.fromstring("one-of(5,8,11)", -1) >>> p OneOfPosition(4, choices=[ExactPosition(4), ExactPosition(7), ExactPosition(10)]) >>> print(p) one-of(4,7,10) >>> int(p) 4 """ if offset != 0 and offset != -1: raise ValueError( "To convert one-based indices to zero-based indices, offset must be either 0 (for end positions) or -1 (for start positions)." ) if text == "?": return UnknownPosition() if text.startswith("?"): return UncertainPosition(int(text[1:]) + offset) if text.startswith("<"): return BeforePosition(int(text[1:]) + offset) if text.startswith(">"): return AfterPosition(int(text[1:]) + offset) m = _re_within_position.match(text) if m is not None: s, e = m.groups() s = int(s) + offset e = int(e) + offset if offset == -1: default = s else: default = e return WithinPosition(default, left=s, right=e) m = _re_oneof_position.match(text) if m is not None: positions = m.groups()[0] parts = [ExactPosition(int(pos) + offset) for pos in positions.split(",")] if offset == -1: default = min(int(pos) for pos in parts) else: default = max(int(pos) for pos in parts) return OneOfPosition(default, choices=parts) return ExactPosition(int(text) + offset) class ExactPosition(int, Position): """Specify the specific position of a boundary. Arguments: - position - The position of the boundary. - extension - An optional argument which must be zero since we don't have an extension. The argument is provided so that the same number of arguments can be passed to all position types. In this case, there is no fuzziness associated with the position. >>> p = ExactPosition(5) >>> p ExactPosition(5) >>> print(p) 5 >>> isinstance(p, Position) True >>> isinstance(p, int) True Integer comparisons and operations should work as expected: >>> p == 5 True >>> p < 6 True >>> p <= 5 True >>> p + 10 ExactPosition(15) """ def __new__(cls, position, extension=0): """Create an ExactPosition object.""" if extension != 0: raise AttributeError(f"Non-zero extension {extension} for exact position.") return int.__new__(cls, position) # Must define this on Python 3.8 onwards because we redefine __repr__ def __str__(self): """Return a representation of the ExactPosition object (with python counting).""" return str(int(self)) def __repr__(self): """Represent the ExactPosition object as a string for debugging.""" return "%s(%i)" % (self.__class__.__name__, int(self)) def __add__(self, offset): """Return a copy of the position object with its location shifted (PRIVATE).""" # By default preserve any subclass return self.__class__(int(self) + offset) def _flip(self, length): """Return a copy of the location after the parent is reversed (PRIVATE).""" # By default preserve any subclass return self.__class__(length - int(self)) class UncertainPosition(ExactPosition): """Specify a specific position which is uncertain. This is used in UniProt, e.g. ?222 for uncertain position 222, or in the XML format explicitly marked as uncertain. Does not apply to GenBank/EMBL. """ pass class UnknownPosition(Position): """Specify a specific position which is unknown (has no position). This is used in UniProt, e.g. ? or in the XML as unknown. """ def __repr__(self): """Represent the UnknownPosition object as a string for debugging.""" return f"{self.__class__.__name__}()" def __hash__(self): """Return the hash value of the UnknownPosition object.""" return hash(None) @property def position(self): """Legacy attribute to get location (None) (DEPRECATED). In general you can use the location directly as with the exception of UnknownPosition it subclasses int, or use int(location), rather than this location.position legacy attribute. However, the UnknownPosition cannot be cast to an integer, and thus does not subclass int, and int(...) will fail. The legacy attribute would return None instead. Note that while None == None, UnknownPosition() != UnknownPosition() which is like the behavour for NaN. """ warnings.warn( "Alias location.position is deprecated and will be removed in a future release. " "In general use position directly, but not note for UnknownPosition " "int(location) will fail. Use try/except or isinstance(location, UnknownPosition).", BiopythonDeprecationWarning, ) return None def __add__(self, offset): """Return a copy of the position object with its location shifted (PRIVATE).""" return self def _flip(self, length): """Return a copy of the location after the parent is reversed (PRIVATE).""" return self class WithinPosition(int, Position): """Specify the position of a boundary within some coordinates. Arguments: - position - The default integer position - left - The start (left) position of the boundary - right - The end (right) position of the boundary This allows dealing with a location like ((11.14)..100). This indicates that the start of the sequence is somewhere between 11 and 14. Since this is a start coordinate, it should act like it is at position 11 (or in Python counting, 10). >>> p = WithinPosition(10, 10, 13) >>> p WithinPosition(10, left=10, right=13) >>> print(p) (10.13) >>> int(p) 10 Basic integer comparisons and operations should work as though this were a plain integer: >>> p == 10 True >>> p in [9, 10, 11] True >>> p < 11 True >>> p + 10 WithinPosition(20, left=20, right=23) >>> isinstance(p, WithinPosition) True >>> isinstance(p, Position) True >>> isinstance(p, int) True Note this also applies for comparison to other position objects, where again the integer behavior is used: >>> p == 10 True >>> p == ExactPosition(10) True >>> p == BeforePosition(10) True >>> p == AfterPosition(10) True If this were an end point, you would want the position to be 13 (the right/larger value, not the left/smaller value as above): >>> p2 = WithinPosition(13, 10, 13) >>> p2 WithinPosition(13, left=10, right=13) >>> print(p2) (10.13) >>> int(p2) 13 >>> p2 == 13 True >>> p2 == ExactPosition(13) True """ def __new__(cls, position, left, right): """Create a WithinPosition object.""" if not (position == left or position == right): raise RuntimeError( "WithinPosition: %r should match left %r or " "right %r" % (position, left, right) ) obj = int.__new__(cls, position) obj._left = left obj._right = right return obj def __getnewargs__(self): """Return the arguments accepted by __new__. Necessary to allow pickling and unpickling of class instances. """ return (int(self), self._left, self._right) def __repr__(self): """Represent the WithinPosition object as a string for debugging.""" return "%s(%i, left=%i, right=%i)" % ( self.__class__.__name__, int(self), self._left, self._right, ) def __str__(self): """Return a representation of the WithinPosition object (with python counting).""" return f"({self._left}.{self._right})" @property def position(self): """Legacy attribute to get (left) position as integer (DEPRECATED).""" warnings.warn( "Alias location.position is deprecated and will be removed in a future release. " "Use location directly, or int(location) which will return the preferred location " "defined for WithinPosition (which may not be the left-most position).", BiopythonDeprecationWarning, ) return self._left @property def extension(self): """Legacy attribute to get the within-position's 'width' as an integer (DEPRECATED).""" warnings.warn( "Alias location.extension is deprecated and will be removed in a future release. " "This is usually zero, but there is no neat replacement for the WithinPosition object.", BiopythonDeprecationWarning, ) return self._right - self._left def __add__(self, offset): """Return a copy of the position object with its location shifted.""" return self.__class__( int(self) + offset, self._left + offset, self._right + offset ) def _flip(self, length): """Return a copy of the location after the parent is reversed (PRIVATE).""" return self.__class__( length - int(self), length - self._right, length - self._left ) class BetweenPosition(int, Position): """Specify the position of a boundary between two coordinates (OBSOLETE?). Arguments: - position - The default integer position - left - The start (left) position of the boundary - right - The end (right) position of the boundary This allows dealing with a position like 123^456. This indicates that the start of the sequence is somewhere between 123 and 456. It is up to the parser to set the position argument to either boundary point (depending on if this is being used as a start or end of the feature). For example as a feature end: >>> p = BetweenPosition(456, 123, 456) >>> p BetweenPosition(456, left=123, right=456) >>> print(p) (123^456) >>> int(p) 456 Integer equality and comparison use the given position, >>> p == 456 True >>> p in [455, 456, 457] True >>> p > 300 True The old legacy properties of position and extension give the starting/lower/left position as an integer, and the distance to the ending/higher/right position as an integer. Note that the position object will act like either the left or the right end-point depending on how it was created: >>> p2 = BetweenPosition(123, left=123, right=456) >>> int(p) == int(p2) False >>> p == 456 True >>> p2 == 123 True Note this potentially surprising behavior: >>> BetweenPosition(123, left=123, right=456) == ExactPosition(123) True >>> BetweenPosition(123, left=123, right=456) == BeforePosition(123) True >>> BetweenPosition(123, left=123, right=456) == AfterPosition(123) True i.e. For equality (and sorting) the position objects behave like integers. """ def __new__(cls, position, left, right): """Create a new instance in BetweenPosition object.""" assert position == left or position == right # TODO - public API for getting left/right, especially the unknown one obj = int.__new__(cls, position) obj._left = left obj._right = right return obj def __getnewargs__(self): """Return the arguments accepted by __new__. Necessary to allow pickling and unpickling of class instances. """ return (int(self), self._left, self._right) def __repr__(self): """Represent the BetweenPosition object as a string for debugging.""" return "%s(%i, left=%i, right=%i)" % ( self.__class__.__name__, int(self), self._left, self._right, ) def __str__(self): """Return a representation of the BetweenPosition object (with python counting).""" return f"({self._left}^{self._right})" @property def position(self): """Legacy attribute to get (left) position as integer (DEPRECATED).""" warnings.warn( "Alias location.position is deprecated and will be removed in a future release. " "Use location directly, or int(location) which will return the preferred location " "defined for a BetweenPosition (which may not be the left-most position).", BiopythonDeprecationWarning, ) return self._left @property def extension(self): """Legacy attribute to get the between-position's 'width' as an integer (DEPRECATED).""" warnings.warn( "Alias location.extension is deprecated and will be removed in a future release. " "This is usually zero, but there is no neat replacement for the BetweenPosition object.", BiopythonDeprecationWarning, ) return self._right - self._left def __add__(self, offset): """Return a copy of the position object with its location shifted (PRIVATE).""" return self.__class__( int(self) + offset, self._left + offset, self._right + offset ) def _flip(self, length): """Return a copy of the location after the parent is reversed (PRIVATE).""" return self.__class__( length - int(self), length - self._right, length - self._left ) class BeforePosition(int, Position): """Specify a position where the actual location occurs before it. Arguments: - position - The upper boundary of where the location can occur. - extension - An optional argument which must be zero since we don't have an extension. The argument is provided so that the same number of arguments can be passed to all position types. This is used to specify positions like (<10..100) where the location occurs somewhere before position 10. >>> p = BeforePosition(5) >>> p BeforePosition(5) >>> print(p) <5 >>> int(p) 5 >>> p + 10 BeforePosition(15) Note this potentially surprising behavior: >>> p == ExactPosition(5) True >>> p == AfterPosition(5) True Just remember that for equality and sorting the position objects act like integers. """ # Subclasses int so can't use __init__ def __new__(cls, position, extension=0): """Create a new instance in BeforePosition object.""" if extension != 0: raise AttributeError(f"Non-zero extension {extension} for exact position.") return int.__new__(cls, position) def __repr__(self): """Represent the location as a string for debugging.""" return "%s(%i)" % (self.__class__.__name__, int(self)) def __str__(self): """Return a representation of the BeforePosition object (with python counting).""" return f"<{int(self)}" def __add__(self, offset): """Return a copy of the position object with its location shifted (PRIVATE).""" return self.__class__(int(self) + offset) def _flip(self, length): """Return a copy of the location after the parent is reversed (PRIVATE).""" return AfterPosition(length - int(self)) class AfterPosition(int, Position): """Specify a position where the actual location is found after it. Arguments: - position - The lower boundary of where the location can occur. - extension - An optional argument which must be zero since we don't have an extension. The argument is provided so that the same number of arguments can be passed to all position types. This is used to specify positions like (>10..100) where the location occurs somewhere after position 10. >>> p = AfterPosition(7) >>> p AfterPosition(7) >>> print(p) >7 >>> int(p) 7 >>> p + 10 AfterPosition(17) >>> isinstance(p, AfterPosition) True >>> isinstance(p, Position) True >>> isinstance(p, int) True Note this potentially surprising behavior: >>> p == ExactPosition(7) True >>> p == BeforePosition(7) True Just remember that for equality and sorting the position objects act like integers. """ # Subclasses int so can't use __init__ def __new__(cls, position, extension=0): """Create a new instance of the AfterPosition object.""" if extension != 0: raise AttributeError(f"Non-zero extension {extension} for exact position.") return int.__new__(cls, position) def __repr__(self): """Represent the location as a string for debugging.""" return "%s(%i)" % (self.__class__.__name__, int(self)) def __str__(self): """Return a representation of the AfterPosition object (with python counting).""" return f">{int(self)}" def __add__(self, offset): """Return a copy of the position object with its location shifted (PRIVATE).""" return self.__class__(int(self) + offset) def _flip(self, length): """Return a copy of the location after the parent is reversed (PRIVATE).""" return BeforePosition(length - int(self)) class OneOfPosition(int, Position): """Specify a position where the location can be multiple positions. This models the GenBank 'one-of(1888,1901)' function, and tries to make this fit within the Biopython Position models. If this was a start position it should act like 1888, but as an end position 1901. >>> p = OneOfPosition(1888, [ExactPosition(1888), ExactPosition(1901)]) >>> p OneOfPosition(1888, choices=[ExactPosition(1888), ExactPosition(1901)]) >>> int(p) 1888 Integer comparisons and operators act like using int(p), >>> p == 1888 True >>> p <= 1888 True >>> p > 1888 False >>> p + 100 OneOfPosition(1988, choices=[ExactPosition(1988), ExactPosition(2001)]) >>> isinstance(p, OneOfPosition) True >>> isinstance(p, Position) True >>> isinstance(p, int) True """ def __new__(cls, position, choices): """Initialize with a set of possible positions. choices is a list of Position derived objects, specifying possible locations. position is an integer specifying the default behavior. """ if position not in choices: raise ValueError( f"OneOfPosition: {position!r} should match one of {choices!r}" ) obj = int.__new__(cls, position) obj.position_choices = choices return obj def __getnewargs__(self): """Return the arguments accepted by __new__. Necessary to allow pickling and unpickling of class instances. """ return (int(self), self.position_choices) @property def position(self): """Legacy attribute to get (left) position as integer (DEPRECATED).""" warnings.warn( "Alias location.position is deprecated and will be removed in a future release. " "Use location directly, or int(location) which will return the preferred location " "defined for a OneOfPosition (which may not be the left-most position), or " "min(location.position_choices) instead.", BiopythonDeprecationWarning, ) return min(int(pos) for pos in self.position_choices) @property def extension(self): """Legacy attribute to get the one-of-position's 'width' as an integer (DEPRECATED).""" warnings.warn( "Alias location.extension is deprecated and will be removed in a future release. " "This is usually zero, but for a OneOfPosition you can use " "max(position.position_choices) - min(position.position_choices)", BiopythonDeprecationWarning, ) positions = [int(pos) for pos in self.position_choices] return max(positions) - min(positions) def __repr__(self): """Represent the OneOfPosition object as a string for debugging.""" return "%s(%i, choices=%r)" % ( self.__class__.__name__, int(self), self.position_choices, ) def __str__(self): """Return a representation of the OneOfPosition object (with python counting).""" out = "one-of(" for position in self.position_choices: out += f"{position}," # replace the last comma with the closing parenthesis return out[:-1] + ")" def __add__(self, offset): """Return a copy of the position object with its location shifted (PRIVATE).""" return self.__class__( int(self) + offset, [p + offset for p in self.position_choices] ) def _flip(self, length): """Return a copy of the location after the parent is reversed (PRIVATE).""" return self.__class__( length - int(self), [p._flip(length) for p in self.position_choices[::-1]] ) class PositionGap: """Simple class to hold information about a gap between positions (DEPRECATED).""" def __init__(self, gap_size): """Initialize with a position object containing the gap information.""" self.gap_size = gap_size warnings.warn( "The PositionGap class is deprecated and will be removed in a future release. " "It has not been used in Biopython for over ten years.", BiopythonDeprecationWarning, ) def __repr__(self): """Represent the position gap as a string for debugging.""" return f"{self.__class__.__name__}({self.gap_size!r})" def __str__(self): """Return a representation of the PositionGap object (with python counting).""" return f"gap({self.gap_size})" if __name__ == "__main__": from Bio._utils import run_doctest run_doctest()