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#!/usr/bin/env python
import numpy
Float = numpy.core.numerictypes.sctype2char(float)
import logging
LOG = logging.getLogger('cogent.align')
from cogent.align import pairwise, indel_model
from cogent.evolve.likelihood_tree import makeLikelihoodTreeLeaf
try:
from _compare import dotplot
except ImportError:
from pycompare import dotplot
LOG.warning('Using slow Python dotplot implementation')
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2009, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley"]
__license__ = "GPL"
__version__ = "1.4.1"
__maintainer__ = "Peter Maxwell"
__email__ = "pm67nz@gmail.com"
__status__ = "Production"
def make_dna_scoring_dict(match, transition, transversion):
DNA = {}
for a in 'ATCG':
ar = a in 'AG'
for b in 'ATCG':
br = b in 'AG'
if a == b:
score = match
elif ar == br:
score = transition
else:
score = transversion
DNA[a,b] = score
return DNA
def _align_pairwise(s1, s2, mprobs, psub, TM, local, **kw):
"""Generic alignment with any substitution model and indel model"""
[p1, p2] = [makeLikelihoodTreeLeaf(seq) for seq in [s1, s2]]
[p1, p2] = [pairwise.AlignableSeq(leaf) for leaf in [p1, p2]]
pair = pairwise.Pair(p1, p2)
EP = pair.makeSimpleEmissionProbs(mprobs, [psub])
hmm = EP.makePairHMM(TM)
if local:
(score, alignment) = hmm.getLocalViterbiScoreAndAlignment(**kw)
else:
(score, alignment) = hmm.getViterbiScoreAndAlignment(**kw)
return alignment
def classic_align_pairwise(s1, s2, Sd, d, e, local, **kw):
"""Alignment specified by gap costs and a score matrix"""
TM = indel_model.ClassicGapScores(d, e)
a1 = s1.MolType.Alphabet
a2 = s2.MolType.Alphabet
S = numpy.zeros([len(a1), len(a2)], Float)
for (i,m1) in enumerate(a1):
for (j,m2) in enumerate(a2):
S[i, j] = Sd[m1, m2]
psub = numpy.exp(S)
mprobs = numpy.ones(len(psub), Float) / len(psub)
return _align_pairwise(s1, s2, mprobs, psub, TM, local, **kw)
# these can't do codon sequences
# they could be replaced with something more sophisticated, like the HMM
# may not give same answer's as algorithm
def local_pairwise(s1, s2, S, d, e):
return classic_align_pairwise(s1, s2, S, d, e, True)
def global_pairwise(s1, s2, S, d, e):
return classic_align_pairwise(s1, s2, S, d, e, False)
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