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# Copyright 2000-2003 Jeff Chang. 

# Copyright 2001-2008 Brad Chapman. 

# Copyright 2005-2012 by Peter Cock. 

# Copyright 2006-2009 Michiel de Hoon. 

# All rights reserved. 

# This code is part of the Biopython distribution and governed by its 

# 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: 

o SeqFeature 

 

Hold information about a Reference. 

---------------------------------- 

 

This is an attempt to create a General class to hold Reference type 

information. 

 

classes: 

o Reference 

 

Specify locations of a feature on a Sequence. 

--------------------------------------------- 

 

This aims to handle, in Ewan's words, 'the dreaded fuzziness issue' in 

much the same way as Biocorba. This has the advantages of allowing us 

to handle fuzzy stuff in case anyone needs it, and also be compatible 

with Biocorba. 

 

classes: 

o FeatureLocation - Specify the start and end location of a feature. 

o CompoundLocation - Collection of FeatureLocation objects (for joins etc). 

 

o ExactPosition - Specify the position as being exact. 

o WithinPosition - Specify a position occuring within some range. 

o BetweenPosition - Specify a position occuring between a range (OBSOLETE?). 

o BeforePosition - Specify the position as being found before some base. 

o AfterPosition - Specify the position as being found after some base. 

o OneOfPosition - Specify a position where the location can be multiple positions. 

o UnknownPosition - Represents missing information like '?' in UniProt. 

""" 

 

from __future__ import print_function 

 

from Bio.Seq import MutableSeq, reverse_complement 

 

 

class SeqFeature(object): 

    """Represent a Sequence Feature on an object. 

 

    Attributes: 

    o location - the location of the feature on the sequence (FeatureLocation) 

    o type - the specified type of the feature (ie. CDS, exon, repeat...) 

    o 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. 

    o 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. 

    o id - A string identifier for the feature. 

    o 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. 

    o ref_db - A different database for the reference accession number. 

    Note this is a shortcut for the reference property of the location 

    o 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. 

    o sub_features - Obsolete list of additional SeqFeatures which was 

    used for holding compound locations (e.g. joins in GenBank/EMBL). 

    This is now superceded by a CompoundFeatureLocation as the location, 

    and should not be used (DEPRECATED). 

    """ 

    def __init__(self, location = None, type = '', location_operator = '', 

                 strand = None, id = "<unknown id>", 

                 qualifiers = None, sub_features = None, 

                 ref = None, ref_db = None): 

        """Initialize a SeqFeature on a Sequence. 

 

        location can either be a FeatureLocation (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, FeatureLocation 

        >>> f1 = SeqFeature(FeatureLocation(5, 10), type="domain") 

        >>> f1.strand == f1.location.strand == None 

        True 

        >>> f2 = SeqFeature(FeatureLocation(7, 110, strand=1), type="CDS") 

        >>> f2.strand == f2.location.strand == +1 

        True 

        >>> f3 = SeqFeature(FeatureLocation(9, 108, strand=-1), type="CDS") 

        >>> f3.strand == f3.location.strand == -1 

        True 

 

        An invalid strand will trigger an exception: 

 

        >>> f4 = SeqFeature(FeatureLocation(50, 60), strand=2) 

        Traceback (most recent call last): 

           ... 

        ValueError: Strand should be +1, -1, 0 or None, not 2 

 

        Similarly if set via the FeatureLocation directly: 

 

        >>> loc4 = FeatureLocation(50, 60, strand=2) 

        Traceback (most recent call last): 

           ... 

        ValueError: Strand should be +1, -1, 0 or None, not 2 

 

        For exact start/end positions, an integer can be used (as shown above) 

        as shorthand for the ExactPosition object. For non-exact locations, the 

        FeatureLocation must be specified via the appropriate position objects. 

 

        Note that the strand, ref and ref_db arguments to the SeqFeature are 

        now obsolete and will be deprecated in a future release (which will 

        give warning messages) and later 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, FeatureLocation) \ 

        and not isinstance(location, CompoundLocation): 

            raise TypeError("FeatureLocation, CompoundLocation (or None) required for the location") 

        self.location = location 

        self.type = type 

        if location_operator: 

            #TODO - Deprecation warning 

            self.location_operator = location_operator 

        if strand is not None: 

            #TODO - Deprecation warning 

            self.strand = strand 

        self.id = id 

        if qualifiers is None: 

            qualifiers = {} 

        self.qualifiers = qualifiers 

        if sub_features is None: 

            sub_features = [] 

        else: 

            import warnings 

            from Bio import BiopythonDeprecationWarning 

            warnings.warn("Rather than sub_features, use a CompoundFeatureLocation", 

                          BiopythonDeprecationWarning) 

        self._sub_features = sub_features 

        if ref is not None: 

            #TODO - Deprecation warning 

            self.ref = ref 

        if ref_db is not None: 

            #TODO - Deprecation warning 

            self.ref_db = ref_db 

 

    def _get_sub_features(self): 

        if self._sub_features: 

            import warnings 

            from Bio import BiopythonDeprecationWarning 

            warnings.warn("Rather using f.sub_features, f.location should be a CompoundFeatureLocation", 

                          BiopythonDeprecationWarning) 

        return self._sub_features 

    def _set_sub_features(self, value): 

        if value: 

            import warnings 

            from Bio import BiopythonDeprecationWarning 

            warnings.warn("Rather than f.sub_features, use a CompoundFeatureLocation for f.location", 

                          BiopythonDeprecationWarning) 

        self._sub_features = value 

    sub_features = property(fget = _get_sub_features, fset = _set_sub_features, 

                            doc = "Obsolete representation of compound locations (DEPRECATED).") 

 

    def _get_strand(self): 

        return self.location.strand 

 

    def _set_strand(self, value): 

        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.") 

            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): 

        try: 

            return self.location.ref 

        except AttributeError: 

            return None 

    def _set_ref(self, value): 

        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.") 

            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): 

        try: 

            return self.location.ref_db 

        except AttributeError: 

            return None 

    def _set_ref_db(self, value): 

        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): 

        try: 

            return self.location.operator 

        except AttributeError: 

            return None 

    def _set_location_operator(self, value): 

        if value: 

            if isinstance(self.location, CompoundLocation): 

                self.location.operator = value 

            elif self.location is None: 

                raise ValueError("Location is None so can't set its operator (to %r)" % value) 

            else: 

                raise ValueError("Only CompoundLocation gets an operator (%r)" % value) 

    location_operator = property(fget = _get_location_operator, fset = _set_location_operator, 

                                 doc = "Location operator for compound locations (e.g. join).") 

 

    def __repr__(self): 

        """A string representation of the record for debugging.""" 

        answer = "%s(%s" % (self.__class__.__name__, repr(self.location)) 

        if self.type: 

            answer += ", type=%s" % repr(self.type) 

        if self.location_operator: 

            answer += ", location_operator=%s" % repr(self.location_operator) 

        if self.id and self.id != "<unknown id>": 

            answer += ", id=%s" % repr(self.id) 

        if self.ref: 

            answer += ", ref=%s" % repr(self.ref) 

        if self.ref_db: 

            answer += ", ref_db=%s" % repr(self.ref_db) 

        answer += ")" 

        return answer 

 

    def __str__(self): 

        """A readable summary of the feature intended to be printed to screen. 

        """ 

        out = "type: %s\n" % self.type 

        out += "location: %s\n" % self.location 

        if self.id and self.id != "<unknown id>": 

            out += "id: %s\n" % self.id 

        out += "qualifiers: \n" 

        for qual_key in sorted(self.qualifiers): 

            out += "    Key: %s, Value: %s\n" % (qual_key, 

                                               self.qualifiers[qual_key]) 

        #TODO - Remove this from __str__ since deprecated 

        if len(self._sub_features) != 0: 

            out += "Sub-Features\n" 

            for sub_feature in self._sub_features: 

                out +="%s\n" % sub_feature 

        return out 

 

    def _shift(self, offset): 

        """Returns a copy of the feature with its location shifted (PRIVATE). 

 

        The annotation qaulifiers are copied.""" 

        answer = SeqFeature(location = self.location._shift(offset), 

                            type = self.type, 

                            location_operator = self.location_operator, 

                            id = self.id, 

                            qualifiers = dict(self.qualifiers.items())) 

        #This is to avoid the deprecation warning: 

        answer._sub_features = [f._shift(offset) for f in self._sub_features] 

        return answer 

 

    def _flip(self, length): 

        """Returns 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 qaulifiers are copied. 

        """ 

        answer = SeqFeature(location = self.location._flip(length), 

                            type = self.type, 

                            location_operator = self.location_operator, 

                            id = self.id, 

                            qualifiers = dict(self.qualifiers.items())) 

        #This is to avoid the deprecation warning:  

        answer._sub_features = [f._flip(length) for f in self._sub_features[::-1]] 

        return answer 

 

    def extract(self, parent_sequence): 

        """Extract feature sequence from the 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. 

 

        >>> from Bio.Seq import Seq 

        >>> from Bio.Alphabet import generic_protein 

        >>> from Bio.SeqFeature import SeqFeature, FeatureLocation 

        >>> seq = Seq("MKQHKAMIVALIVICITAVVAAL", generic_protein) 

        >>> f = SeqFeature(FeatureLocation(8, 15), type="domain") 

        >>> f.extract(seq) 

        Seq('VALIVIC', ProteinAlphabet()) 

 

        Note - currently only sub-features of type "join" are supported. 

        """ 

        return self.location.extract(parent_sequence) 

 

    #Python 3: 

    def __bool__(self): 

        """Boolean value of an instance of this class (True). 

 

        This behaviour 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 behaviour)! 

        """ 

        return True 

 

    #Python 2: 

    __nonzero__= __bool__ 

 

    def __len__(self): 

        """Returns the length of the region described by a feature. 

 

        >>> from Bio.Seq import Seq 

        >>> from Bio.Alphabet import generic_protein 

        >>> from Bio.SeqFeature import SeqFeature, FeatureLocation 

        >>> seq = Seq("MKQHKAMIVALIVICITAVVAAL", generic_protein) 

        >>> f = SeqFeature(FeatureLocation(8, 15), type="domain") 

        >>> len(f) 

        7 

        >>> f.extract(seq) 

        Seq('VALIVIC', ProteinAlphabet()) 

        >>> 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, FeatureLocation 

        >>> f = SeqFeature(FeatureLocation(5, 10), type="domain", strand=-1) 

        >>> 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, FeatureLocation 

        >>> f = SeqFeature(FeatureLocation(5, 10), type="domain", strand=-1) 

        >>> 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, FeatureLocation 

        >>> from Bio.SeqFeature import BeforePosition 

        >>> f = SeqFeature(FeatureLocation(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(object): 

    """Represent a Generic Reference object. 

 

    Attributes: 

    o 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. 

    o authors - A big old string, or a list split by author, of authors 

    for the reference. 

    o title - The title of the reference. 

    o journal - Journal the reference was published in. 

    o medline_id - A medline reference for the article. 

    o pubmed_id - A pubmed reference for the article. 

    o comment - A place to stick any comments about the reference. 

    """ 

    def __init__(self): 

        self.location = [] 

        self.authors = '' 

        self.consrtm = '' 

        self.title = '' 

        self.journal = '' 

        self.medline_id = '' 

        self.pubmed_id = '' 

        self.comment = '' 

 

    def __str__(self): 

        """Output an informative string for debugging. 

        """ 

        out = "" 

        for single_location in self.location: 

            out += "location: %s\n" % single_location 

        out += "authors: %s\n" % self.authors 

        if self.consrtm: 

            out += "consrtm: %s\n" % self.consrtm 

        out += "title: %s\n" % self.title 

        out += "journal: %s\n" % self.journal 

        out += "medline id: %s\n" % self.medline_id 

        out += "pubmed id: %s\n" % self.pubmed_id 

        out += "comment: %s\n" % self.comment 

        return out 

 

    def __repr__(self): 

        #TODO - Update this is __init__ later accpets values 

        return "%s(title=%s, ...)" % (self.__class__.__name__, 

                                      repr(self.title)) 

 

 

# --- Handling feature locations 

 

class FeatureLocation(object): 

    """Specify the location of a feature along a sequence. 

 

    The FeatureLocation is used for simple continous 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 currently described using a 

    SeqFeature with sub-features. 

 

    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 FeatureLocation 

    >>> f = FeatureLocation(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 FeatureLocation 

    >>> f = FeatureLocation(122, 150, strand=+1) 

    >>> print(f) 

    [122:150](+) 

    >>> print(f.strand) 

    1 

 

    Note that for a parent sequence of length n, the FeatureLocation 

    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 FeatureLocation 

    >>> r = FeatureLocation(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 manor, 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): 

        """Specify the start, end, strand etc of a sequence feature. 

 

        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 AbstractPosition, 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 FeatureLocation 

        >>> loc = FeatureLocation(5, 10, strand=-1) 

        >>> print(loc) 

        [5:10](-) 

 

        Explicit form: 

 

        >>> from Bio.SeqFeature import FeatureLocation, ExactPosition 

        >>> loc = FeatureLocation(ExactPosition(5), ExactPosition(10), strand=-1) 

        >>> print(loc) 

        [5:10](-) 

 

        Other fuzzy positions are used similarly, 

 

        >>> from Bio.SeqFeature import FeatureLocation 

        >>> from Bio.SeqFeature import BeforePosition, AfterPosition 

        >>> loc2 = FeatureLocation(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 = FeatureLocation(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 = FeatureLocation(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, AbstractPosition): 

            self._start = start 

        elif isinstance(start, int) or isinstance(start, long): 

            self._start = ExactPosition(start) 

        else: 

            raise TypeError("start=%r %s" % (start, type(start))) 

        if isinstance(end, AbstractPosition): 

            self._end = end 

        elif isinstance(end, int) or isinstance(end, long): 

            self._end = ExactPosition(end) 

        else: 

            raise TypeError("end=%r %s" % (end, type(end))) 

        self.strand = strand 

        self.ref = ref 

        self.ref_db = ref_db 

 

    def _get_strand(self): 

        return self._strand 

 

    def _set_strand(self, value): 

        if value not in [+1, -1, 0, None]: 

            raise ValueError("Strand should be +1, -1, 0 or None, not %r" 

                             % value) 

        self._strand = value 

 

    strand = property(fget = _get_strand, fset = _set_strand, 

                      doc = "Strand of the location (+1, -1, 0 or None).") 

 

    def __str__(self): 

        """Returns a representation of the location (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 = "[%s:%s]" % (self._start, self._end) 

        if self.ref and self.ref_db: 

            answer = "%s:%s%s" % (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): 

        """A string representation of the location for debugging.""" 

        optional = "" 

        if self.strand is not None: 

            optional += ", strand=%r" % self.strand 

        if self.ref is not None: 

            optional += ", ref=%r" % self.ref 

        if self.ref_db is not None: 

            optional += ", ref_db=%r" % self.ref_db 

        return "%s(%r, %r%s)" \ 

                   % (self.__class__.__name__, self.start, self.end, optional) 

 

    def __add__(self, other): 

        """Combine location with another feature location, or shift it. 

 

        You can add two feature locations to make a join CompoundLocation: 

 

        >>> from Bio.SeqFeature import FeatureLocation 

        >>> f1 = FeatureLocation(5, 10) 

        >>> f2 = FeatureLocation(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 FeatureLocation with a CompoundLocation 

        in this way. 

 

        Separately, adding an integer will give a new FeatureLocation 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, FeatureLocation): 

            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): 

        if isinstance(other, int): 

            return self._shift(other) 

        else: 

            return NotImplemented 

 

    def __nonzero__(self): 

        """Returns True regardless of the length of the feature. 

 

        This behaviour is for backwards compatibility, since until the 

        __len__ method was added, a FeatureLocation 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 FeatureLocation may in future evaluate to False when its 

        length is zero (in order to better match normal python behaviour)! 

        """ 

        return True 

 

    def __len__(self): 

        """Returns the length of the region described by the FeatureLocation. 

 

        Note that extra care may be needed for fuzzy locations, e.g. 

 

        >>> from Bio.SeqFeature import FeatureLocation 

        >>> from Bio.SeqFeature import BeforePosition, AfterPosition 

        >>> loc = FeatureLocation(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 FeatureLocation. 

 

        Note that extra care may be needed for fuzzy locations, e.g. 

 

        >>> from Bio.SeqFeature import FeatureLocation 

        >>> from Bio.SeqFeature import BeforePosition, AfterPosition 

        >>> loc = FeatureLocation(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 FeatureLocation.") 

        if value < self._start or value >= self._end: 

            return False 

        else: 

            return True 

 

    def __iter__(self): 

        """Iterate over the parent positions within the FeatureLocation. 

 

        >>> from Bio.SeqFeature import FeatureLocation 

        >>> from Bio.SeqFeature import BeforePosition, AfterPosition 

        >>> loc = FeatureLocation(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 = FeatureLocation(BeforePosition(5), AfterPosition(10), strand = -1) 

        >>> list(loc) 

        [9, 8, 7, 6, 5] 

        """ 

        if self.strand == -1: 

            for i in range(self._end - 1, self._start - 1, -1): 

                yield i 

        else: 

            for i in range(self._start, self._end): 

                yield i 

 

    def _shift(self, offset): 

        """Returns a copy of the location shifted by the offset (PRIVATE).""" 

        #TODO - What if offset is a fuzzy position? 

        if self.ref or self.ref_db: 

            #TODO - Return self? 

            raise ValueError("Feature references another sequence.") 

        return FeatureLocation(start = self._start._shift(offset), 

                               end = self._end._shift(offset), 

                               strand = self.strand) 

 

    def _flip(self, length): 

        """Returns a copy of the location after the parent is reversed (PRIVATE).""" 

        if self.ref or self.ref_db: 

            #TODO - Return self? 

            raise ValueError("Feature references another sequence.") 

        #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 FeatureLocation(start = self._end._flip(length), 

                               end = self._start._flip(length), 

                               strand = flip_strand) 

 

    @property 

    def parts(self): 

        """Read only list of parts (always one, the Feature Location). 

 

        This is a convience property allowing you to write code handling 

        both simple FeatureLocation objects (with one part) and more complex 

        CompoundLocation objects (with multiple parts) interchangably. 

        """ 

        return [self] 

 

    @property 

    def start(self): 

        """Start location (integer like, possibly a fuzzy position, read only).""" 

        return self._start 

 

    @property 

    def end(self): 

        """End location (integer like, possibly a fuzzy position, read only).""" 

        return self._end 

 

    @property 

    def nofuzzy_start(self): 

        """Start position (integer, approximated if fuzzy, read only) (OBSOLETE). 

 

        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. 

        """ 

        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) (OBSOLETE). 

 

        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. 

        """ 

        try: 

            return int(self._end) 

        except TypeError: 

            if isinstance(self._end, UnknownPosition): 

                return None 

            raise 

 

    def extract(self, parent_sequence): 

        """Extract feature sequence from the supplied parent sequence.""" 

        if self.ref or self.ref_db: 

            #TODO - Take a dictionary as an optional argument? 

            raise ValueError("Feature references another sequence.") 

        if isinstance(parent_sequence, MutableSeq): 

            #This avoids complications with reverse complements 

            #(the MutableSeq reverse complement acts in situ) 

            parent_sequence = parent_sequence.toseq() 

        f_seq = parent_sequence[self.nofuzzy_start:self.nofuzzy_end] 

        if self.strand == -1: 

            try: 

                f_seq = f_seq.reverse_complement() 

            except AttributeError: 

                assert isinstance(f_seq, str) 

                f_seq = reverse_complement(f_seq) 

        return f_seq 

 

 

class CompoundLocation(object): 

    """For handling joins etc where a feature location has several parts.""" 

    def __init__(self, parts, operator="join"): 

        """Create a compound location with several parts. 

 

        >>> from Bio.SeqFeature import FeatureLocation, CompoundLocation 

        >>> f1 = FeatureLocation(10, 40, strand=+1) 

        >>> f2 = FeatureLocation(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([FeatureLocation(3, 6, strand=+1), 

        ...                       FeatureLocation(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 range covered, 0 <= start <= end <= full sequence length. 

 

        >>> f.start == min(f) 

        True 

        >>> f.end == max(f) + 1 

        True 

 

        This is consistent with the behaviour of the simple FeatureLocation 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 = FeatureLocation(3, 6, strand=+1) + FeatureLocation(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, FeatureLocation): 

                raise ValueError("CompoundLocation should be given a list of " 

                                 "FeatureLocation objects, not %s" % loc.__class__) 

        if len(parts) < 2: 

            raise ValueError("CompoundLocation should have at least 2 parts, not %r" % parts) 

 

    def __str__(self): 

        """Returns a representation of the location (with python counting).""" 

        return "%s{%s}" % (self.operator, ", ".join(str(loc) for loc in self.parts)) 

 

    def __repr__(self): 

        """String representation of the location for debugging.""" 

        return "%s(%r, %r)" % (self.__class__.__name__, \ 

                               self.parts, self.operator) 

 

    def _get_strand(self): 

        # 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(set(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): 

        # 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 FeatureLocation, CompoundLocation 

        >>> f1 = FeatureLocation(15, 17, strand=1) 

        >>> f2 = FeatureLocation(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 FeatureLocation, CompoundLocation 

        >>> f1 = FeatureLocation(15, 17) + FeatureLocation(20, 30) 

        >>> print(f1) 

        join{[15:17], [20:30]} 

 

        You can add another FeatureLocation: 

 

        >>> print(f1 + FeatureLocation(40, 50)) 

        join{[15:17], [20:30], [40:50]} 

        >>> print(FeatureLocation(5, 10) + f1) 

        join{[5:10], [15:17], [20:30]} 

 

        You can also add another CompoundLocation: 

 

        >>> f2 = FeatureLocation(40, 50) + FeatureLocation(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 FeatureLocation, adding an integer shifts the 

        location's co-ordinates 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, FeatureLocation): 

            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("Mixed operators %s and %s" \ 

                                 % (self.operator, 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): 

        """Combine locations.""" 

        if isinstance(other, FeatureLocation): 

            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 location.""" 

        for loc in self.parts: 

            if value in loc: 

                return True 

        return False 

 

    def __nonzero__(self): 

        """Returns True regardless of the length of the feature. 

 

        This behaviour is for backwards compatibility, since until the 

        __len__ method was added, a FeatureLocation 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 FeatureLocation may in future evaluate to False when its 

        length is zero (in order to better match normal python behaviour)! 

        """ 

        return True 

 

    def __len__(self): 

        return sum(len(loc) for loc in self.parts) 

 

    def __iter__(self): 

        for loc in self.parts: 

            for pos in loc: 

                yield pos 

 

    def _shift(self, offset): 

        """Returns a copy of the location shifted by the offset (PRIVATE).""" 

        return CompoundLocation([loc._shift(offset) for loc in self.parts], 

                                self.operator) 

 

    def _flip(self, length): 

        """Returns a copy of the location after the parent is reversed (PRIVATE). 

 

        Note that the order of the parts is reversed too. 

        """ 

        return CompoundLocation([loc._flip(length) for loc in self.parts[::-1]], 

                                self.operator) 

 

    @property 

    def start(self): 

        """Start location (integer like, possibly a fuzzy position, read only).""" 

        return min(loc.start for loc in self.parts) 

 

    @property 

    def end(self): 

        """End location (integer like, possibly a fuzzy position, read only).""" 

        return max(loc.end for loc in self.parts) 

 

    @property 

    def nofuzzy_start(self): 

        """Start position (integer, approximated if fuzzy, read only) (OBSOLETE). 

 

        This is an alias for int(feature.start), which should be used in 

        preference -- unless you are trying to support old versions of 

        Biopython. 

        """ 

        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) (OBSOLETE). 

 

        This is an alias for int(feature.end), which should be used in 

        preference -- unless you are trying to support old versions of 

        Biopython. 

        """ 

        try: 

            return int(self.end) 

        except TypeError: 

            if isinstance(self.end, UnknownPosition): 

                return None 

            raise 

 

    @property 

    def ref(self): 

        """CompoundLocation's don't have a ref (dummy method for API compatibility).""" 

        return None 

 

    @property 

    def ref_db(self): 

        """CompoundLocation's don't have a ref_db (dummy method for API compatibility).""" 

        return None 

 

    def extract(self, parent_sequence): 

        """Extract feature sequence from the supplied parent sequence.""" 

        #This copes with mixed strand features & all on reverse: 

        parts = [loc.extract(parent_sequence) for loc in self.parts] 

        #We use addition rather than a join to avoid alphabet issues: 

        f_seq = parts[0] 

        for part in parts[1:]: 

            f_seq += part 

        return f_seq 

 

 

class AbstractPosition(object): 

    """Abstract base class representing a position. 

    """ 

 

    def __repr__(self): 

        """String representation of the location for debugging.""" 

        return "%s(...)" % (self.__class__.__name__) 

 

 

class ExactPosition(int, AbstractPosition): 

    """Specify the specific position of a boundary. 

 

    o position - The position of the boundary. 

    o 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, AbstractPosition) 

    True 

    >>> isinstance(p, int) 

    True 

 

    Integer comparisons and operations should work as expected: 

 

    >>> p == 5 

    True 

    >>> p < 6 

    True 

    >>> p <= 5 

    True 

    >>> p + 10 

    15 

 

    """ 

    def __new__(cls, position, extension = 0): 

        if extension != 0: 

            raise AttributeError("Non-zero extension %s for exact position." 

                                 % extension) 

        return int.__new__(cls, position) 

 

    def __repr__(self): 

        """String representation of the ExactPosition location for debugging.""" 

        return "%s(%i)" % (self.__class__.__name__, int(self)) 

 

    @property 

    def position(self): 

        """Legacy attribute to get position as integer (OBSOLETE).""" 

        return int(self) 

 

    @property 

    def extension(self): 

        """Legacy attribute to get extension (zero) as integer (OBSOLETE).""" 

        return 0 

 

    def _shift(self, offset): 

        #By default preserve any subclass 

        return self.__class__(int(self) + offset) 

 

    def _flip(self, length): 

        #By default perserve 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(AbstractPosition): 

    """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): 

        """String representation of the UnknownPosition location for debugging.""" 

        return "%s()" % self.__class__.__name__ 

 

    def __hash__(self): 

        return hash(None) 

 

    @property 

    def position(self): 

        """Legacy attribute to get position (None) (OBSOLETE).""" 

        return None 

 

    @property 

    def extension(self): 

        """Legacy attribute to get extension (zero) as integer (OBSOLETE).""" 

        return 0 

 

    def _shift(self, offset): 

        return self 

 

    def _flip(self, length): 

        return self 

 

 

class WithinPosition(int, AbstractPosition): 

    """Specify the position of a boundary within some coordinates. 

 

    Arguments: 

    o position - The default integer position 

    o left - The start (left) position of the boundary 

    o right - The end (right) position of the boundary 

 

    This allows dealing with a position like ((1.4)..100). This 

    indicates that the start of the sequence is somewhere between 1 

    and 4. Since this is a start coordinate, it should acts like 

    it is at position 1 (or in Python counting, 0). 

 

    >>> 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 

    20 

 

    >>> isinstance(p, WithinPosition) 

    True 

    >>> isinstance(p, AbstractPosition) 

    True 

    >>> isinstance(p, int) 

    True 

 

    Note this also applies for comparison to other position objects, 

    where again the integer behaviour 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: 

 

    >>> 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 

 

    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: 

 

    >>> p.position == p2.position == 10 

    True 

    >>> p.extension == p2.extension == 3 

    True 

    >>> int(p) == int(p2) 

    False 

    >>> p == 10 

    True 

    >>> p2 == 13 

    True 

 

    """ 

    def __new__(cls, position, left, right): 

        assert position==left or position==right, \ 

            "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 __repr__(self): 

        """String representation of the WithinPosition location for debugging.""" 

        return "%s(%i, left=%i, right=%i)" \ 

               % (self.__class__.__name__, int(self), 

                  self._left, self._right) 

 

    def __str__(self): 

        return "(%s.%s)" % (self._left, self._right) 

 

    @property 

    def position(self): 

        """Legacy attribute to get (left) position as integer (OBSOLETE).""" 

        return self._left 

 

    @property 

    def extension(self): 

        """Legacy attribute to get extension (from left to right) as an integer (OBSOLETE).""" 

        return self._right - self._left 

 

    def _shift(self, offset): 

        return self.__class__(int(self) + offset, 

                              self._left + offset, 

                              self._right + offset) 

 

    def _flip(self, length): 

        return self.__class__(length - int(self), 

                              length - self._right, 

                              length - self._left) 

 

 

class BetweenPosition(int, AbstractPosition): 

    """Specify the position of a boundary between two coordinates (OBSOLETE?). 

 

    Arguments: 

    o position - The default integer position 

    o left - The start (left) position of the boundary 

    o 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) 

    >>> p.position == p2.position == 123 

    True 

    >>> p.extension 

    333 

    >>> p2.extension 

    333 

    >>> p.extension == p2.extension == 333 

    True 

    >>> int(p) == int(p2) 

    False 

    >>> p == 456 

    True 

    >>> p2 == 123 

    True 

 

    Note this potentially surprising behaviour: 

 

    >>> 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): 

        assert position==left or position==right 

        obj = int.__new__(cls, position) 

        obj._left = left 

        obj._right = right 

        return obj 

 

    def __repr__(self): 

        """String representation of the WithinPosition location for debugging.""" 

        return "%s(%i, left=%i, right=%i)" \ 

               % (self.__class__.__name__, int(self), 

                  self._left, self._right) 

 

    def __str__(self): 

        return "(%s^%s)" % (self._left, self._right) 

 

    @property 

    def position(self): 

        """Legacy attribute to get (left) position as integer (OBSOLETE).""" 

        return self._left 

 

    @property 

    def extension(self): 

        """Legacy attribute to get extension (from left to right) as an integer (OBSOLETE).""" 

        return self._right - self._left 

 

    def _shift(self, offset): 

        return self.__class__(int(self) + offset, 

                              self._left + offset, 

                              self._right + offset) 

 

    def _flip(self, length): 

        return self.__class__(length - int(self), 

                              length - self._right, 

                              length - self._left) 

 

 

class BeforePosition(int, AbstractPosition): 

    """Specify a position where the actual location occurs before it. 

 

    Arguments: 

    o position - The upper boundary of where the location can occur. 

    o 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 

    15 

 

    Note this potentially surprising behaviour: 

 

    >>> 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): 

        if extension != 0: 

            raise AttributeError("Non-zero extension %s for exact position." 

                                 % extension) 

        return int.__new__(cls, position) 

 

    @property 

    def position(self): 

        """Legacy attribute to get position as integer (OBSOLETE).""" 

        return int(self) 

 

    @property 

    def extension(self): 

        """Legacy attribute to get extension (zero) as integer (OBSOLETE).""" 

        return 0 

 

    def __repr__(self): 

        """A string representation of the location for debugging.""" 

        return "%s(%i)" % (self.__class__.__name__, int(self)) 

 

    def __str__(self): 

        return "<%s" % self.position 

 

    def _shift(self, offset): 

        return self.__class__(int(self) + offset) 

 

    def _flip(self, length): 

        return AfterPosition(length - int(self)) 

 

 

class AfterPosition(int, AbstractPosition): 

    """Specify a position where the actual location is found after it. 

 

    Arguments: 

    o position - The lower boundary of where the location can occur. 

    o 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 

    17 

 

    >>> isinstance(p, AfterPosition) 

    True 

    >>> isinstance(p, AbstractPosition) 

    True 

    >>> isinstance(p, int) 

    True 

 

    Note this potentially surprising behaviour: 

 

    >>> 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): 

        if extension != 0: 

            raise AttributeError("Non-zero extension %s for exact position." 

                                 % extension) 

        return int.__new__(cls, position) 

 

    @property 

    def position(self): 

        """Legacy attribute to get position as integer (OBSOLETE).""" 

        return int(self) 

 

    @property 

    def extension(self): 

        """Legacy attribute to get extension (zero) as integer (OBSOLETE).""" 

        return 0 

 

    def __repr__(self): 

        """A string representation of the location for debugging.""" 

        return "%s(%i)" % (self.__class__.__name__, int(self)) 

 

    def __str__(self): 

        return ">%s" % self.position 

 

    def _shift(self, offset): 

        return self.__class__(int(self) + offset) 

 

    def _flip(self, length): 

        return BeforePosition(length - int(self)) 

 

 

class OneOfPosition(int, AbstractPosition): 

    """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 

 

    Interget comparisons and operators act like using int(p), 

 

    >>> p == 1888 

    True 

    >>> p <= 1888 

    True 

    >>> p > 1888 

    False 

    >>> p + 100 

    1988 

 

    >>> isinstance(p, OneOfPosition) 

    True 

    >>> isinstance(p, AbstractPosition) 

    True 

    >>> isinstance(p, int) 

    True 

 

    The old legacy properties of position and extension give the 

    starting/lowest/left-most position as an integer, and the 

    distance to the ending/highest/right-most position as an integer. 

    Note that the position object will act like one of the list of 

    possible locations depending on how it was created: 

 

    >>> p2 = OneOfPosition(1901, [ExactPosition(1888), ExactPosition(1901)]) 

    >>> p.position == p2.position == 1888 

    True 

    >>> p.extension == p2.extension == 13 

    True 

    >>> int(p) == int(p2) 

    False 

    >>> p == 1888 

    True 

    >>> p2 == 1901 

    True 

 

    """ 

    def __new__(cls, position, choices): 

        """Initialize with a set of posssible positions. 

 

        position_list is a list of AbstractPosition derived objects, 

        specifying possible locations. 

 

        position is an integer specifying the default behaviour. 

        """ 

        assert position in choices, \ 

            "OneOfPosition: %r should match one of %r" % (position, choices) 

        obj = int.__new__(cls, position) 

        obj.position_choices = choices 

        return obj 

 

    @property 

    def position(self): 

        """Legacy attribute to get (left) position as integer (OBSOLETE).""" 

        return min(int(pos) for pos in self.position_choices) 

 

    @property 

    def extension(self): 

        """Legacy attribute to get extension as integer (OBSOLETE).""" 

        positions = [int(pos) for pos in self.position_choices] 

        return max(positions) - min(positions) 

 

    def __repr__(self): 

        """String representation of the OneOfPosition location for debugging.""" 

        return "%s(%i, choices=%r)" % (self.__class__.__name__, 

                                       int(self), self.position_choices) 

 

    def __str__(self): 

        out = "one-of(" 

        for position in self.position_choices: 

            out += "%s," % position 

        # replace the last comma with the closing parenthesis 

        out = out[:-1] + ")" 

        return out 

 

    def _shift(self, offset): 

        return self.__class__(int(self) + offset, 

                              [p._shift(offset) for p in self.position_choices]) 

 

    def _flip(self, length): 

        return self.__class__(length - int(self), 

                              [p._flip(length) for p in self.position_choices[::-1]]) 

 

 

class PositionGap(object): 

    """Simple class to hold information about a gap between positions. 

    """ 

    def __init__(self, gap_size): 

        """Intialize with a position object containing the gap information. 

        """ 

        self.gap_size = gap_size 

 

    def __repr__(self): 

        """A string representation of the position gap for debugging.""" 

        return "%s(%s)" % (self.__class__.__name__, repr(self.gap_size)) 

 

    def __str__(self): 

        out = "gap(%s)" % self.gap_size 

        return out 

 

 

if __name__ == "__main__": 

    from Bio._utils import run_doctest 

    run_doctest()