def gappy_pair_data(sequences, maximum_distance, **args) :
"""generate a dataset object that contains all pairs of letters in a sequence that are
within a certain distance of each other.
:Parameters:
- `sequences` - a list of sequences from which to construct the gappy pair
representation or a Fasta file that contains the sequences
- `maximum_distance` - the maximum distance between pairs of length of the
substrings to consider
:Keywords:
- `normalize` - whether to normalize the dataset [default: True]
- `prefix` - a string to be added to the name of each feature
(useful when combining spectrum features from several sources)
- `skip` - a list of characters that should be skipped in computing
the features
"""
prefix = ''
if 'prefix' in args :
prefix = args['prefix']
normalize = True
if 'normalize' in args :
normalize = args['normalize']
skip = []
if 'skip' in args :
skip = args['skip']
if type(sequences) == type('') :
sequences = fasta_read(sequences)
data = SparseDataSet(generate_gappy_pairs(sequences, maximum_distance, prefix, skip))
if normalize :
data.normalize(2)
return data
def gappy_pair_data(sequences, maximum_distance, **args):
"""generate a dataset object that contains all pairs of letters in a sequence that are
within a certain distance of each other.
:Parameters:
- `sequences` - a list of sequences from which to construct the gappy pair
representation or a Fasta file that contains the sequences
- `maximum_distance` - the maximum distance between pairs of length of the
substrings to consider
:Keywords:
- `normalize` - whether to normalize the dataset [default: True]
- `prefix` - a string to be added to the name of each feature
(useful when combining spectrum features from several sources)
- `skip` - a list of characters that should be skipped in computing
the features
"""
prefix = ''
if 'prefix' in args:
prefix = args['prefix']
normalize = True
if 'normalize' in args:
normalize = args['normalize']
skip = []
if 'skip' in args:
skip = args['skip']
if type(sequences) == type(''):
sequences = fasta_read(sequences)
data = SparseDataSet(
generate_gappy_pairs(sequences, maximum_distance, prefix, skip))
if normalize:
data.normalize(2)
return data
def spectrum_data(sequences, k1, k2=None, **args) :
"""generate a dataset object that represents the spectrum of a sequence,
i.e. its kernel function is the spectrum kernel.
Reference:
C. Leslie, E. Eskin, and WS Noble.
The spectrum kernel: A string kernel for SVM protein classification.
:Parameters:
- `sequences` - either a name of a fasta file that contains the sequences or
a list of sequences
- `k1` - the length of the substrings to consider
- `k2` - if k2 is provided then strings whose length is between k1
and k2 are used in constructing the spectrum.
:Keywords:
- `normalize` - whether to normalize the dataset [default: True]
- `prefix` - a string to be added to the name of each feature
(useful when combining spectrum features from several sources)
- `skip` - a list of characters that should be skipped in computing
the spectrum [default: []]. Whenever a character in this list is
encountered, the substring is not included in the spectrum
- `mismatch` - whether to allow a single mismatch [default: False]
"""
prefix = ''
if 'prefix' in args :
prefix = args['prefix']
normalize = True
if 'normalize' in args :
normalize = args['normalize']
if k2 is None :
k2 = k1 + 1
skip = []
if 'skip' in args :
skip = args['skip']
mismatch = False
if 'mismatch' in args :
mismatch = args['mismatch']
if mismatch :
spectrum_generator = generate_single_mismatch_spectrum
else :
spectrum_generator = generate_spectrum
if type(sequences) == type('') :
sequences = fasta_read(sequences)
data = SparseDataSet(spectrum_generator(sequences, k1, prefix, skip))
if normalize :
data.normalize(2)
for k in range(k1+1, k2 + 1) :
data2 = SparseDataSet(spectrum_generator(sequences, k, prefix, skip))
if normalize :
data2.normalize(2)
data.addFeatures(data2)
return data
def spectrum_data(sequences, k1, k2=None, **args):
"""generate a dataset object that represents the spectrum of a sequence,
i.e. its kernel function is the spectrum kernel.
Reference:
C. Leslie, E. Eskin, and WS Noble.
The spectrum kernel: A string kernel for SVM protein classification.
:Parameters:
- `sequences` - either a name of a fasta file that contains the sequences or
a list of sequences
- `k1` - the length of the substrings to consider
- `k2` - if k2 is provided then strings whose length is between k1
and k2 are used in constructing the spectrum.
:Keywords:
- `normalize` - whether to normalize the dataset [default: True]
- `prefix` - a string to be added to the name of each feature
(useful when combining spectrum features from several sources)
- `skip` - a list of characters that should be skipped in computing
the spectrum [default: []]. Whenever a character in this list is
encountered, the substring is not included in the spectrum
- `mismatch` - whether to allow a single mismatch [default: False]
"""
prefix = ''
if 'prefix' in args:
prefix = args['prefix']
normalize = True
if 'normalize' in args:
normalize = args['normalize']
if k2 is None:
k2 = k1 + 1
skip = []
if 'skip' in args:
skip = args['skip']
mismatch = False
if 'mismatch' in args:
mismatch = args['mismatch']
if mismatch:
spectrum_generator = generate_single_mismatch_spectrum
else:
spectrum_generator = generate_spectrum
if type(sequences) == type(''):
sequences = fasta_read(sequences)
data = SparseDataSet(spectrum_generator(sequences, k1, prefix, skip))
if normalize:
data.normalize(2)
for k in range(k1 + 1, k2 + 1):
data2 = SparseDataSet(spectrum_generator(sequences, k, prefix, skip))
if normalize:
data2.normalize(2)
data.addFeatures(data2)
return data
def positional_kmer_data(sequences, k1, k2=None, **args) :
"""generate a dataset object that represents kmers that occur in specific
positions. When using weighting, this is essentially the 'weighted degree'
kernel of Sonenburg et al.
:Parameters:
- `sequences` - the name of a fasta file that contains the sequences or
a list of sequences
- `k1` - the smallest length kmer to consider
- `k2` - if k2 is provided then strings whose length is between k1
and k2 are used in constructing the kernel
:Keywords:
- `normalize` - whether to normalize the dataset [default: True]
- `prefix` - a string to be added to the name of each feature
(useful when combining spectrum features from several sources)
- `skip` - a list of characters that should be skipped in computing
the spectrum [default: []]. Whenever a character in this list is
encountered, the substring is not included in the spectrum
- `weighted` - whether to use the weighting of sonenborg et al
[default: equal weights]
- `shift` - whether to consider a shift [default: False]
- `shift_start` - the position in the seq to start shifting [default: 0]
- `shift_end` - the position in the sequence to stop shifting
[default: end of sequence]
"""
prefix = ''
if 'prefix' in args :
prefix = args['prefix']
normalize = True
if 'normalize' in args :
normalize = args['normalize']
if k2 is None :
k2 = k1 + 1
skip = []
if 'skip' in args :
skip = args['skip']
shift = False
if 'shift' in args :
shift = args['shift']
shift_start = 0
if 'shift_start' in args :
shift_start = args['shift_start']
if type(sequences) == type('') :
sequences = fasta_read(sequences)
if 'shift_end' in args :
shift_end = args['shift_end']
else :
shift_end = len(sequences[0]) - 1
weighted = False
if weighted in args :
weighted = args['weighted']
if weighted :
weights = [1.0 for i in range(k1, k2 + 1)]
else :
weights = [1.0 for i in range(k1, k2 + 1)]
data = SparseDataSet(generate_positional_kmers(
sequences, k1, prefix, skip, weights[0], shift, shift_start, shift_end))
if normalize :
data.normalize(2)
for k in range(k1 + 1, k2 + 1) :
data2 = SparseDataSet(generate_positional_kmers(
sequences, k, prefix, skip, weights[k - k1], shift, shift_start, shift_end))
if normalize :
data2.normalize(2)
data.addFeatures(data2)
return data
def positional_kmer_data(sequences, k1, k2=None, **args):
"""generate a dataset object that represents kmers that occur in specific
positions. When using weighting, this is essentially the 'weighted degree'
kernel of Sonenburg et al.
:Parameters:
- `sequences` - the name of a fasta file that contains the sequences or
a list of sequences
- `k1` - the smallest length kmer to consider
- `k2` - if k2 is provided then strings whose length is between k1
and k2 are used in constructing the kernel
:Keywords:
- `normalize` - whether to normalize the dataset [default: True]
- `prefix` - a string to be added to the name of each feature
(useful when combining spectrum features from several sources)
- `skip` - a list of characters that should be skipped in computing
the spectrum [default: []]. Whenever a character in this list is
encountered, the substring is not included in the spectrum
- `weighted` - whether to use the weighting of sonenborg et al
[default: equal weights]
- `shift` - whether to consider a shift [default: False]
- `shift_start` - the position in the seq to start shifting [default: 0]
- `shift_end` - the position in the sequence to stop shifting
[default: end of sequence]
"""
prefix = ''
if 'prefix' in args:
prefix = args['prefix']
normalize = True
if 'normalize' in args:
normalize = args['normalize']
if k2 is None:
k2 = k1 + 1
skip = []
if 'skip' in args:
skip = args['skip']
shift = False
if 'shift' in args:
shift = args['shift']
shift_start = 0
if 'shift_start' in args:
shift_start = args['shift_start']
if type(sequences) == type(''):
sequences = fasta_read(sequences)
if 'shift_end' in args:
shift_end = args['shift_end']
else:
shift_end = len(sequences[0]) - 1
weighted = False
if weighted in args:
weighted = args['weighted']
if weighted:
weights = [1.0 for i in range(k1, k2 + 1)]
else:
weights = [1.0 for i in range(k1, k2 + 1)]
data = SparseDataSet(
generate_positional_kmers(sequences, k1, prefix, skip, weights[0],
shift, shift_start, shift_end))
if normalize:
data.normalize(2)
for k in range(k1 + 1, k2 + 1):
data2 = SparseDataSet(
generate_positional_kmers(sequences, k, prefix, skip,
weights[k - k1], shift, shift_start,
shift_end))
if normalize:
data2.normalize(2)
data.addFeatures(data2)
return data