Python BinarySearchTree.find_smallest_ge方法代码示例

# 需要导入模块: from bst import BinarySearchTree [as 别名]
# 或者: from bst.BinarySearchTree import find_smallest_ge [as 别名]
class Genotype(object):
    #---------------------------------------------
    # Constructors
    #---------------------------------------------
    def __init__(self, data, snp, sample_id):
        '''
        Construct a genotype set from data arrays:
        - snp: SNP metadata record array (contains chromosome, name, morgans, base-pair location)
        - data: a 3-D genotype data array: (individual x SNP x allele)
        - sample_id: genotyped individuals' ID set
        '''       
        # People's IDs
        self.sample_id = sample_id
        self.data = data
        self._num_snps = self.data.shape[0]
        self._num_samples = self.data.shape[1]
        self._snp_range = None
        
        # SNP metadata: SNP label, chromosome number, Genetic distance in Morgans, and
        # base pair location for each SNP
        self.snp = snp
        # Base-pair-location to snp-index map, lazily-initialized + cached
        base_pair = self.snp['base_pair']
        self._base_pair = base_pair  # np.array([int(base_pair)]) if base_pair.size == 1 else base_pair
        self._bp_to_snp = dict_invert(dict(enumerate(self._base_pair)))
        # Construct a BST for fast bp queries
        self._snp_tree = BinarySearchTree(values=self._base_pair[optimal_insertion_order(self._num_snps)])
        self._snp_index_tree = util.list_index_tree(self._base_pair)
        # A genetic map: lists the two allele letters corresponding to 1 and 2 for each SNP, according
        # their order in the self.snp array.
        self.map = []
        # General metadata, for easy handling of CGI data
        self.metadata = []
                    
        # samples for which the parent-of-origin phase is determined
        self.poo_phase = np.zeros((self._num_samples,), dtype=np.byte)

    @staticmethod
    def empty(snp, sample_id, sz):
        '''Allocate an empty data array of size sz.'''
        return Genotype(snp, sample_id, np.zeros(sz, dtype=np.byte))
    
    def copy(self):
        '''Return a deep copy of this object.'''
        return Genotype(self.data.copy(), self.snp.copy(), self.sample_id.copy())
    
    #---------------------------------------------
    # Operators
    #---------------------------------------------
    def __key(self):
        '''Uniquely-identifying key of this object.'''
        return (self.data.tolist(), self.snp.tolist(),
                self.sample_id.tolist() if self.sample_id is not None else None)

    def __eq__(self, y):
        '''Equality of objects.'''
        return self.__key() == y.__key()

    def __ne__(self, y):
        '''Inequality of objects.'''
        return self.__key() != y.__key()

    def __hash__(self):
        '''Object hash code.'''
        return hash(self.__key())

    def __repr__(self):
        return 'Genotype[snps=%d, samples=%d]' % (self.num_snps, self.num_samples)
     
    #---------------------------------------------
    # Methods
    #---------------------------------------------
    def clear(self, snp, person):
        '''Set the data for the individuals whose index is person at snp indices snp
        to MISSING.'''
        self.data[snp, person, :] = constants.MISSING
        
    def nearest_snp(self, bp):
        '''Nearest SNP neighbor to a base pair location bp.'''
        return util.nearest_neighbor_in_list_tree(bp, self._base_pair, self._snp_index_tree)

    def nearest_snp_multiple(self, bp):
        '''Nearest SNP neighbor to each element of a base pair collection bp.'''
        return util.nearest_neighbor_in_list_tree_multiple(bp, self._base_pair, self._snp_index_tree)

    def segment_intersect(self, segment_in_bp):
        '''Return endpoints of the SNP index range contained in the base-pair segment segment.
        If segment does not intersect our SNP range, return None. The range is [start_index,stop_index)
        where start=inclusive and stop is exclsive.'''
        left = self._snp_tree.find_smallest_ge(segment_in_bp[0])
        if left is None: return None
        right = self._snp_tree.find_largest_le(segment_in_bp[1])
        if right is None: return None
        return (self._bp_to_snp[left], self._bp_to_snp[right] + 1)

    def segments_intersect(self, segments_in_bp):
        '''Find SNP range of each segment in the list segments_in_bp whose unit is base pairs.'''
        segments = []
        for x in segments_in_bp:
            y = self.segment_intersect(x)
#.........这里部分代码省略.........