if not was_high:
start = max(i_lo, i - window)
if d_segments and start-d_segments[-1][1] < min_gap_length:
(start, jumped_end) = d_segments.pop()
was_high = True
else:
if was_high:
d_segments.append((start, i))
was_high = False
if was_high:
d_segments.append((start, i_hi))
return d_segments
try:
_compare = importVersionedModule('_compare', globals(),
(1, 3), "slow Python dotplot")
segments_from_diagonal = _compare.segments_from_diagonal
except ExpectedImportError:
segments_from_diagonal = py_segments_from_diagonal
@UI.display_wrap
def dotplot(seq1, seq2, window, threshold, min_gap_length=0, band=None, ui=None):
"""A list of line segments covering the window-mers with identical matches > threshold
Gaps of size less than min_gap will be hidden, which saves on line segments.
if 'band' is not None then it limits the searched area
"""
def one_diagonal(dia):
segs = segments_from_diagonal(seq1, seq2, window, threshold,
min_gap_length, dia)
return [((start, start+dia), (end, end+dia)) for (start, end) in segs]
def _importedPyrexAligningModule(name):
try:
return importVersionedModule(name, globals(), (3, 1),
"slow Python alignment implementation")
except ExpectedImportError:
return None
start = max(i_lo, i - window)
if d_segments and start - d_segments[-1][1] < min_gap_length:
(start, jumped_end) = d_segments.pop()
was_high = True
else:
if was_high:
d_segments.append((start, i))
was_high = False
if was_high:
d_segments.append((start, i_hi))
return d_segments
try:
_compare = importVersionedModule('_compare', globals(), (1, 3),
"slow Python dotplot")
segments_from_diagonal = _compare.segments_from_diagonal
except ExpectedImportError:
segments_from_diagonal = py_segments_from_diagonal
@UI.display_wrap
def dotplot(seq1,
seq2,
window,
threshold,
min_gap_length=0,
band=None,
ui=None):
"""A list of line segments covering the window-mers with identical matches > threshold
numpy.seterr(all='ignore')
numerictypes = numpy.core.numerictypes.sctype2char
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2011, The Cogent Project"
__credits__ = ["Peter Maxwell", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.6.0dev"
__maintainer__ = "Peter Maxwell"
__email__ = "*****@*****.**"
__status__ = "Production"
try:
pyrex = importVersionedModule('_likelihood_tree', globals(),
(2, 1), "pure Python/NumPy likelihoodihood tree")
except ExpectedImportError:
pyrex = None
class _LikelihoodTreeEdge(object):
def __init__(self, children, edge_name, alignment=None):
self.edge_name = edge_name
self.alphabet = children[0].alphabet
self.comm = None # for MPI
M = children[0].shape[-1]
for child in children:
assert child.shape[-1] == M
# Unique positions are unique combos of input positions
if alignment is None:
def _importedPyrexAligningModule(name):
try:
return importVersionedModule(name, globals(), (3, 1),
"slow Python alignment implementation")
except ExpectedImportError:
return None
numpy.seterr(all='ignore')
numerictypes = numpy.core.numerictypes.sctype2char
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Peter Maxwell", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3-dev"
__maintainer__ = "Peter Maxwell"
__email__ = "*****@*****.**"
__status__ = "Production"
try:
pyrex = importVersionedModule('_likelihood_tree', globals(),
(2, 1), "pure Python/NumPy likelihoodihood tree")
except ExpectedImportError:
pyrex = None
class _LikelihoodTreeEdge(object):
def __init__(self, children, edge_name, alignment=None):
self.edge_name = edge_name
self.alphabet = children[0].alphabet
self.comm = None # for MPI
M = children[0].shape[-1]
for child in children:
assert child.shape[-1] == M
# Unique positions are unique combos of input positions
if alignment is None:
# in case it needs to be put back in a more runtime way.
#numpy.seterr(all='ignore')
import warnings
from cogent.align.traceback import alignment_traceback
from cogent.evolve.likelihood_tree import LikelihoodTreeEdge
from indel_positions import leaf2pog
from cogent import LoadSeqs
from cogent.core.alignment import Aligned
from cogent.align.traceback import map_traceback
from cogent.util import parallel
from cogent.util.modules import importVersionedModule, ExpectedImportError
try:
pyrex_align_module = importVersionedModule('_pairwise_pogs', globals(),
(3, 1), "slow Python alignment implementation")
except ExpectedImportError:
pyrex_align_module = None
try:
pyrex_seq_align_module = importVersionedModule('_pairwise_seqs', globals(),
(3, 1), "slow Python alignment implementation")
except ExpectedImportError:
pyrex_seq_align_module = None
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2011, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.6.0dev"
__maintainer__ = "Peter Maxwell"
__email__ = "*****@*****.**"
"""P matrices for some DNA models can be calculated without going via the
intermediate rate matrix Q. A Cython implementation of this calculation can
be used when Q is not required, for example during likelihood tree optimisation.
Equivalent pure python code is NOT provided because it is typically slower
than the rate-matrix based alternative and provides no extra functionality.
"""
from cogent.evolve.substitution_model import Nucleotide, CalcDefn
from cogent.evolve.predicate import MotifChange
from cogent.maths.matrix_exponentiation import FastExponentiator
import numpy
from cogent.util.modules import importVersionedModule, ExpectedImportError
try:
_solved_models = importVersionedModule('_solved_models', globals(),
(1, 0), "only matrix exponentiating DNA models")
except ExpectedImportError:
_solved_models = None
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Peter Maxwell"]
__license__ = "GPL"
__version__ = "1.9"
class PredefinedNucleotide(Nucleotide):
_default_expm_setting = None
# Instead of providing calcExchangeabilityMatrix this subclass overrrides
# makeContinuousPsubDefn to bypass the Q / Qd step.
# in case it needs to be put back in a more runtime way.
#numpy.seterr(all='ignore')
import warnings
from cogent.align.traceback import alignment_traceback
from cogent.evolve.likelihood_tree import LikelihoodTreeEdge
from indel_positions import leaf2pog
from cogent import LoadSeqs
from cogent.core.alignment import Aligned
from cogent.align.traceback import map_traceback
from cogent.util import parallel
from cogent.util.modules import importVersionedModule, ExpectedImportError
try:
pyrex_align_module = importVersionedModule('_pairwise_pogs', globals(),
(3, 1), "slow Python alignment implementation")
except ExpectedImportError:
pyrex_align_module = None
try:
pyrex_seq_align_module = importVersionedModule('_pairwise_seqs', globals(),
(3, 1), "slow Python alignment implementation")
except ExpectedImportError:
pyrex_seq_align_module = None
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Peter Maxwell"
__email__ = "*****@*****.**"
