491 lines
15 KiB
Python
491 lines
15 KiB
Python
from scipy import ndarray,atleast_2d,asarray,intersect1d,zeros
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from scipy import sort as array_sort
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from itertools import izip
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import shelve
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import copy
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import re
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class Dataset:
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"""The Dataset base class.
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A Dataset is an n-way array with defined string identifiers across
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all dimensions.
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example of use:
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---
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dim_name_rows = 'rows'
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names_rows = ('row_a','row_b')
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ids_1 = [dim_name_rows, names_rows]
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dim_name_cols = 'cols'
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names_cols = ('col_a','col_b','col_c','col_d')
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ids_2 = [dim_name_cols, names_cols]
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Array_X = rand(2,4)
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data = Dataset(Array_X,(ids_1,ids_2),name="Testing")
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dim_names = [dim for dim in data]
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column_identifiers = [id for id in data['cols'].keys()]
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column_index = [index for index in data['cols'].values()]
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'cols' in data -> True
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---
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data = Dataset(rand(10,20)) (generates dims and ids (no links))
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"""
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def __init__(self, array, identifiers=None, name='Unnamed dataset'):
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self._dims = [] #existing dimensions in this dataset
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self._map = {} # internal mapping for dataset: identifier <--> index
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self._name = name
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self._identifiers = identifiers
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self._type = 'n'
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if len(array.shape)==1:
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array = atleast_2d(asarray(array))
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# vectors are column vectors
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if array.shape[0]==1:
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array = array.T
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self.shape = array.shape
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if identifiers!=None:
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identifier_shape = [len(i[1]) for i in identifiers]
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if len(identifier_shape)!=len(self.shape):
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raise ValueError, "Identifier list length must equal array dims"
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for ni, na in zip(identifier_shape, self.shape):
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if ni!=na:
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raise ValueError, "identifier-array mismatch in %s: (idents: %s, array: %s)" %(self._name, ni, na)
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self._set_identifiers(identifiers, self._all_dims)
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else:
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self._identifiers = self._create_identifiers(self.shape, self._all_dims)
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self._set_identifiers(self._identifiers, self._all_dims)
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self._array = array
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def __iter__(self):
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"""Returns an iterator over dimensions of dataset."""
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return self._dims.__iter__()
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def __contains__(self,dim):
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"""Returns True if dim is a dimension name in dataset."""
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# return self._dims.__contains__(dim)
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return self._map.__contains__(dim)
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def __len__(self):
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"""Returns the number of dimensions in the dataset"""
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return len(self._map)
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def __getitem__(self,dim):
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"""Return the identifers along the dimension dim."""
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return self._map[dim]
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def _create_identifiers(self,shape,all_dims):
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"""Creates dimension names and identifier names, and returns
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identifiers."""
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dim_names = ['rows','cols']
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ids = []
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for axis,n in enumerate(shape):
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if axis<2:
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dim_suggestion = dim_names[axis]
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else:
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dim_suggestion = 'dim'
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dim_suggestion = self._suggest_dim_name(dim_suggestion,all_dims)
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identifier_creation = [str(axis) + "_" + i for i in map(str,range(n))]
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ids.append((dim_suggestion,identifier_creation))
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all_dims.add(dim_suggestion)
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return ids
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def _set_identifiers(self, identifiers, all_dims):
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"""Creates internal mapping of identifiers structure."""
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for dim, ids in identifiers:
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pos_map = ReverseDict()
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if dim not in self._dims:
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self._dims.append(dim)
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all_dims.add(dim)
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else:
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raise ValueError, "Dimension names must be unique whitin dataset"
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for pos, id in enumerate(ids):
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pos_map[id] = pos
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self._map[dim] = pos_map
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def _suggest_dim_name(self,dim_name,all_dims):
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"""Suggests a unique name for dim and returns it"""
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c = 0
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new_name = dim_name
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while new_name in all_dims:
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new_name = dim_name + "_" + str(c)
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c+=1
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return new_name
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def asarray(self):
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"""Returns the numeric array (data) of dataset"""
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return self._array
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def add_array(self, array):
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"""Adds array as an ArrayType object.
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A one-dim array is transformed to a two-dim array (row-vector)
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"""
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if self.shape!=array.shape:
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raise ValueError, "Input array must be of similar dimensions as dataset"
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self._array = atleast_2d(asarray(array))
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def get_name(self):
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"""Returns dataset name"""
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return self._name
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def get_all_dims(self):
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"""Returns all dimensions in project"""
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return self._all_dims
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def get_dim_name(self, axis=None):
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"""Returns dim name for an axis, if no axis is provided it
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returns a list of dims"""
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if type(axis)==int:
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return self._dims[axis]
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else:
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return [dim for dim in self]
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def get_identifiers(self, dim, indices=None,sorted=False):
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"""Returns identifiers along dim, sorted by position (index)
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is optional.
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You can optionally provide a list/ndarray of indices to get
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only the identifiers of a given position.
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Identifiers are the unique names (strings) for a variable in a
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given dim. Index (Indices) are the Identifiers position in a
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matrix in a given dim.
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"""
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if indices!=None:
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if len(indices)==0:# if empty list or empty array
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return []
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if indices != None:
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# be sure to match intersection
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#indices = intersect1d(self.get_indices(dim),indices)
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ids = [self._map[dim].reverse[i] for i in indices]
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else:
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if sorted==True:
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ids = [self._map[dim].reverse[i] for i in array_sort(self._map[dim].values())]
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else:
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ids = self._map[dim].keys()
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return ids
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def get_indices(self, dim, idents=None):
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"""Returns indices for identifiers along dimension.
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You can optionally provide a list of identifiers to retrieve a
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index subset.
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Identifiers are the unique names (strings) for a variable in a
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given dim. Index (Indices) are the Identifiers position in a
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matrix in a given dim. If none of the input identifiers are
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found an empty index is returned
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"""
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if not isinstance(idents, list) and not isinstance(idents, set):
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raise ValueError("idents needs to be a list/set got: %s" %type(idents))
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if idents==None:
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index = array_sort(self._map[dim].values())
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else:
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index = [self._map[dim][key]
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for key in idents if self._map[dim].has_key(key)]
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return asarray(index)
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def copy(self):
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""" Returns deepcopy of dataset.
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"""
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return copy.deepcopy(self)
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class CategoryDataset(Dataset):
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"""The category dataset class.
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A dataset for representing class information as binary
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matrices (0/1-matrices).
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There is support for using a less memory demanding, and
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fast intersection look-ups by representing the binary matrix as a
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dictionary in each dimension.
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Always has linked dimension in first dim:
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ex matrix:
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. go_term1 go_term2 ...
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gene_1
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gene_2
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gene_3
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.
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.
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.
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"""
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def __init__(self, array, identifiers=None, name='C'):
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Dataset.__init__(self, array, identifiers=identifiers, name=name)
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self.has_dictlists = False
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self._type = 'c'
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def as_dict_lists(self):
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"""Returns data as dict of indices along first dim.
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ex: data['gene_id'] = ['map0030','map0010', ...]
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"""
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data={}
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for name, ind in self._map[self.get_dim_name(0)].items():
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data[name] = self.get_identifiers(self.get_dim_name(1),
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list(self._array[ind,:].nonzero()))
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self._dictlists = data
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self.has_dictlists = True
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return data
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def as_selections(self):
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"""Returns data as a list of Selection objects.
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"""
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ret_list = []
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for cat_name, ind in self._map[self.get_dim_name(1)].items():
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ids = self.get_identifiers(self.get_dim_name(0),
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self._array[:,ind].nonzero()[0])
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selection = Selection(cat_name)
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selection.select(self.get_dim_name(0), ids)
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ret_list.append(selection)
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return ret_list
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class GraphDataset(Dataset):
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"""The graph dataset class.
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A dataset class for representing graphs using an (weighted)
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adjacency matrix
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(restricted to square symmetric matrices)
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If the library NetworkX is installed, there is support for
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representing the graph as a NetworkX.Graph, or NetworkX.XGraph structure.
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"""
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def __init__(self, array=None, identifiers=None, shape=None, all_dims=[],**kwds):
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Dataset.__init__(self, array=array, identifiers=identifiers, name='A')
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self._graph = None
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self._type = 'g'
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def asnetworkx(self, nx_type='graph'):
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dim = self.get_dim_name()[0]
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ids = self.get_identifiers(dim, sorted=True)
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adj_mat = self.asarray()
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G = self._graph_from_adj_matrix(adj_mat, labels=ids)
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self._graph = G
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return G
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def _graph_from_adj_matrix(self, A, labels=None):
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"""Creates a networkx graph class from adjacency
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(possibly weighted) matrix and ordered labels.
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nx_type = ['graph',['xgraph']]
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labels = None, results in string-numbered labels
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"""
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try:
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import networkx as nx
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except:
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print "Failed in import of NetworkX"
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return
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m, n = A.shape# adjacency matrix must be of type that evals to true/false for neigbours
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if m!=n:
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raise IOError, "Adjacency matrix must be square"
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if A[A[:,0].nonzero()[0][0],0]==1: #unweighted graph
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G = nx.Graph()
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else:
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G = nx.XGraph()
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if labels==None: # if labels not provided mark vertices with numbers
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labels = [str(i) for i in range(m)]
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for nbrs, head in izip(A, labels):
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for i, nbr in enumerate(nbrs):
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if nbr:
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tail = labels[i]
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if type(G)==nx.XGraph:
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G.add_edge(head, tail, nbr)
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else:
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G.add_edge(head, tail)
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return G
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Dataset._all_dims = set()
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class ReverseDict(dict):
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"""
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A dictionary which can lookup values by key, and keys by value.
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All values and keys must be hashable, and unique.
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d = ReverseDict((['a',1],['b',2]))
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print d['a'] --> 1
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print d.reverse[1] --> 'a'
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"""
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def __init__(self, *args, **kw):
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dict.__init__(self, *args, **kw)
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self.reverse = dict([[v,k] for k,v in self.items()])
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def __setitem__(self, key, value):
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dict.__setitem__(self, key, value)
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try:
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self.reverse[value] = key
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except:
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self.reverse = {value:key}
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def to_file(filepath,dataset,name=None):
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"""Write dataset to file. A file may contain multiple datasets.
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append to file by using option mode='a'
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"""
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if not name:
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name = dataset._name
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data = shelve.open(filepath, flag='c', protocol=2)
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if data: #we have an append
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names = data.keys()
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if name in names:
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print "Data with name: %s overwritten" %dataset._name
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sub_data = {'array':dataset._array,
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'idents':dataset._identifiers,
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'type':dataset._type}
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data[name] = sub_data
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data.close()
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def from_file(filepath):
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"""Read dataset(s) from file """
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data = shelve.open(filepath, flag='r')
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out_data = []
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for name in data.keys():
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sub_data = data[name]
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if sub_data['type']=='c':
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out_data.append(CategoryDataset(sub_data['array'], identifiers=sub_data['idents'], name=name))
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elif sub_data['type']=='g':
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out_data.append(GraphDataset(sub_data['array'], identifiers=sub_data['idents'], name=name))
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else:
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out_data.append(Dataset(sub_data['array'], identifiers=sub_data['idents'], name=name))
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return out_data
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class Selection(dict):
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"""Handles selected identifiers along each dimension of a dataset"""
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def __init__(self, title='Unnamed Selecton'):
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self.title = title
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def __getitem__(self, key):
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if not self.has_key(key):
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return None
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return dict.__getitem__(self, key)
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def dims(self):
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return self.keys()
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def axis_len(self, axis):
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if self._selection.has_key(axis):
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return len(self._selection[axis])
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return 0
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def select(self, axis, labels):
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self[axis] = labels
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def write_ftsv(fd, ds):
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# Write header information
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if isinstance(ds, CategoryDataset):
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type = 'category'
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elif isinstance(ds, GraphDataset):
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type = 'network'
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elif isinstance(ds, Dataset):
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type = 'dataset'
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else:
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raise Exception("Unknown object")
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print >> fd, "# type: %s" % type
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for dim in ds.get_dim_name():
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print >> fd, "# dimension: %s" % dim,
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for id in ds.get_identifiers(dim, None, True):
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print >> fd, id,
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print >> fd
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print >> fd, "# name: %s" % ds.get_name()
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print >> fd
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# Write data
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m = ds.asarray()
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y, x = m.shape
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for j in range(y):
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for i in range(x):
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print >> fd, "%s\t" % m[j, i],
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print >> fd
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def read_ftsv(fd):
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split_re = re.compile('^#\s*(\w+)\s*:\s*(.+)')
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dimensions = []
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identifiers = {}
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type = 'dataset'
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name = 'Unnamed dataset'
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graphtype = 'graph'
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# Read header lines from file.
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line = fd.readline()
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while line:
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m = split_re.match(line)
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if m:
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key, val = m.groups()
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# The line is on the form;
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# dimension: dimname id1 id2 id3 ...
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if key == 'dimension':
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values = [v.strip() for v in val.split(' ')]
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dimensions.append(values[0])
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identifiers[values[0]] = values[1:]
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# Read type of dataset.
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# Should be dataset, category, or network
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elif key == 'type':
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type = val
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elif key == 'name':
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name = val
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elif key == 'graphtype':
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graphtype = val
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else:
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break
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line = fd.readline()
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# Dimensions in the form [(dim1, [id1, id2, id3 ..) ...]
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dims = [(x, identifiers[x]) for x in dimensions]
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dim_lengths = [len(identifiers[x]) for x in dimensions]
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# Create matrix
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if type == 'category':
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matrix = zeros(dim_lengths, dtype=bool)
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elif type == 'network':
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matrix = zeros(dim_lengths)
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else:
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matrix = zeros(dim_lengths)
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line = fd.readline()
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y = 0
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while line:
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values = line.split()
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for x, v in enumerate(values):
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matrix[y,x] = float(v)
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y += 1
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line = fd.readline()
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# Create dataset of specified type
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if type == 'category':
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ds = CategoryDataset(matrix, dims, name)
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elif type == 'network':
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ds = GraphDataset(matrix, dims, name)
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else:
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ds = Dataset(matrix, dims, name)
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return ds
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