Skip to content

Commit

Permalink
Merge pull request #516 from GavinHuttley/develop
Browse files Browse the repository at this point in the history 
STY: black and isort changes
  • Loading branch information
@GavinHuttley
GavinHuttley committed Feb 1, 2020
2 parents 8e533f1 + dee257e commit 5a09fd7
Showing 1 changed file with 47 additions and 30 deletions.
77 changes: 47 additions & 30 deletions tests/test_core/test_alignment.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,15 @@

import numpy

from numpy import arange, array, nan, transpose, log2
from numpy import arange, array, log2, nan, transpose
from numpy.testing import assert_allclose

from cogent3 import load_aligned_seqs, load_unaligned_seqs, make_seq, make_aligned_seqs
from cogent3 import (
load_aligned_seqs,
load_unaligned_seqs,
make_aligned_seqs,
make_seq,
)
from cogent3.core.alignment import (
Aligned,
Alignment,
Expand Down Expand Up @@ -1260,8 +1265,7 @@ def test_to_moltype_info(self):
self.assertEqual(dna.info["key"], "value")

def test_get_lengths(self):
"""returns correct seq lengths"""
"""SequenceCollection.test_get_lengths handles motif length, allow_gaps etc.."""
"""get_lengths handles motif length, allow_gaps etc.."""
data = {"a": "AAAA??????", "b": "CCCGGG--NN"}
coll = self.Class(data=data, moltype=DNA)
got = coll.get_lengths()
Expand Down Expand Up @@ -1534,44 +1538,39 @@ def test_alignment_quality(self):
"""Tests that the alignment_quality generates the right alignment quality
value based on the Hertz-Stormo metric. expected values are hand calculated
using the formula in the paper."""
aln = make_aligned_seqs(["AATTGA",
"AGGTCC",
"AGGATG",
"AGGCGT"], moltype="dna")
aln = make_aligned_seqs(["AATTGA", "AGGTCC", "AGGATG", "AGGCGT"], moltype="dna")
got = aln.alignment_quality(equifreq_mprobs=True)
expect = log2(4) + (3 / 2) * log2(3) + (1 / 2) * log2(2) + (1 / 2) * log2(2)
assert_allclose(got, expect)

aln = make_aligned_seqs(["AAAC",
"ACGC",
"AGCC",
"A-TC"], moltype="dna")
aln = make_aligned_seqs(["AAAC", "ACGC", "AGCC", "A-TC"], moltype="dna")
got = aln.alignment_quality(equifreq_mprobs=False)
expect = 2 * log2(1 / 0.4) + log2(1 / (4 * 0.4)) + (1 / 2) * log2(1 / (8 / 15)) + (
1 / 4) * log2(1 / (4 / 15))
expect = (
2 * log2(1 / 0.4)
+ log2(1 / (4 * 0.4))
+ (1 / 2) * log2(1 / (8 / 15))
+ (1 / 4) * log2(1 / (4 / 15))
)
assert_allclose(got, expect)

#1. Alignment just gaps (Gap chars need to be fixed for unspecified moltype, before uncommenting).
# 1. Alignment just gaps (Gap chars need to be fixed for unspecified moltype, before uncommenting).
# aln = make_aligned_seqs(["----"])
# got = aln.alignment_quality(equifreq_mprobs=True)
# assert_allclose(got, 0)

#2 Just one sequence (I've made an assumption that if there is one sequence,
# 2 Just one sequence (I've made an assumption that if there is one sequence,
# the alignment quality should also return None, correct me if I'm wrong).
aln = make_aligned_seqs(["AAAC"])
got = aln.alignment_quality(equifreq_mprobs=True)
assert got is None

#3.1 Two seqs, one all gaps. (equifreq_mprobs=True)
aln = make_aligned_seqs(["----",
"ACAT"])
# 3.1 Two seqs, one all gaps. (equifreq_mprobs=True)
aln = make_aligned_seqs(["----", "ACAT"])
got = aln.alignment_quality(equifreq_mprobs=True)
assert_allclose(got, 28)


#3.2 Two seqs, one all gaps. (equifreq_mprobs=False)
aln = make_aligned_seqs(["----",
"AAAA"])
# 3.2 Two seqs, one all gaps. (equifreq_mprobs=False)
aln = make_aligned_seqs(["----", "AAAA"])
got = aln.alignment_quality(equifreq_mprobs=False)
assert_allclose(got, -2)

Expand Down Expand Up @@ -2275,22 +2274,28 @@ def test_counts(self):
def test_counts_per_seq(self):
"""SequenceCollection.counts_per_seq handles motif length, allow_gaps etc.."""
data = {"a": "AAAA??????", "b": "CCCGGG--NN", "c": "CCGGTTCCAA"}
coll = self.Class(data=data, moltype=DNA)
coll = self.Class(data=data, moltype="dna")
mtype = coll.moltype
got = coll.counts_per_seq()
self.assertEqual(got["a", "A"], 4)
self.assertEqual(len(got.motifs), 4)
self.assertEqual(len(got.motifs), len(mtype.alphabet))
got = coll.counts_per_seq(include_ambiguity=True, allow_gap=True)
# N, -, ? are the additional states
self.assertEqual(len(got.motifs), 7)
self.assertEqual(
got["b"].to_dict(), {"-": 2, "?": 0, "A": 0, "C": 3, "G": 3, "N": 2, "T": 0}
)
expect = {"-": 2, "?": 0, "A": 0, "C": 3, "G": 3, "N": 2, "T": 0}
b = got["b"].to_dict()
for k in expect:
self.assertEqual(b[k], expect[k])

got = coll.counts_per_seq(motif_length=2)
self.assertEqual(len(got.motifs), 16)
self.assertEqual(len(got.motifs), len(mtype.alphabet) ** 2)
self.assertEqual(got["a", "AA"], 2)
self.assertEqual(got["b", "GG"], 1)
got = coll.counts_per_seq(exclude_unobserved=True)
self.assertEqual(got["c"].to_dict(), {"C": 4, "G": 2, "T": 2, "A": 2})
expect = {"C": 4, "G": 2, "T": 2, "A": 2}
c = got["c"].to_dict()
for k in expect:
self.assertEqual(c[k], expect[k])

def test_counts_per_pos(self):
"""correctly count motifs"""
Expand Down Expand Up @@ -2332,6 +2337,18 @@ def test_counts_per_pos(self):
obs = aln.counts_per_pos(allow_gap=True)
self.assertEqual(obs.array, exp_gap)

def test_counts_per_seq_default_moltype(self):
"""produce correct counts per seq with default moltypes"""
data = {"a": "AAAA??????", "b": "CCCGGG--NN", "c": "CCGGTTCCAA"}
coll = self.Class(data=data)
got = coll.counts_per_seq()
try:
self.assertEqual(got.col_sum()["-"], 0)
except KeyError:
pass # text moltype in Alignment excludes '-'
got = coll.counts_per_seq(include_ambiguity=True, allow_gap=True)
self.assertEqual(got.col_sum()["-"], 2)

def test_get_seq_entropy(self):
"""ArrayAlignment get_seq_entropy should get entropy of each seq"""
seqs = [AB.make_seq(s, preserve_case=True) for s in ["abab", "bbbb", "abbb"]]
Expand Down

0 comments on commit 5a09fd7

Please sign in to comment.