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ignores missing entries in .Rtab files #158

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ignores missing entries in .Rtab files #158

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cfed703
ignores missing entries in .Rtab files
julibeg Jun 6, 2021
1359b61
added unit test for missing values in .Rtab file
julibeg Jul 7, 2021
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2 changes: 1 addition & 1 deletion pyseer/input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -421,7 +421,7 @@ def read_variant(infile, p, var_type, burden, burden_regions,
if present == '1':
d[sample] = 1
elif present == ".":
d[sample] = np.nan
continue

# Use common dictionary to format design matrix etc
kstrains = sorted(set(d.keys()).intersection(all_strains)) # This will include missing
Expand Down
28 changes: 28 additions & 0 deletions tests/input_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,6 +35,7 @@
KMER = os.path.join(DATA_DIR, 'kmers.gz')
PRES = os.path.join(DATA_DIR, 'presence_absence_smaller.Rtab')
PRESSPACE = os.path.join(DATA_DIR, 'presence_absence_smaller_space.Rtab')
PRESMISSING = os.path.join(DATA_DIR, 'presence_absence_missing.Rtab')
VCF = os.path.join(DATA_DIR, 'variants_smaller.vcf.gz')
VCFNOGT = os.path.join(DATA_DIR, 'variants_no_gt.vcf.gz')
VCFMISSING = os.path.join(DATA_DIR, 'variants_missing.vcf.gz')
Expand Down Expand Up @@ -424,6 +425,33 @@ def test_read_variant_rtab(self):
self.assertEqual(af, 1.0)
self.assertEqual(missing, 0.0)

def test_read_variant_rtab_missing(self):
infile = open(PRESMISSING)
p = pd.read_csv(P, index_col=0, sep='\t')['binary']
header = infile.readline().rstrip()
sample_order = header.split()[1:]
# check header
self.assertEqual(sample_order, list(p.index))
# check first gene
t = read_variant(infile, p, 'Rtab', False, [], False,
p.index, sample_order)
self.assertEqual(
list(t[1]),
[0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0,
1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0,
0, 1, 0, 0, 0, 0, 1, 0])
# read whole file
vars = []
while not t[0]:
vars.append(t)
t = read_variant(infile, p, 'Rtab', False, [], False,
p.index, sample_order)
_, _, var_names, _, _, afs, _ = zip(*vars)
# test allele frequencies
self.assertEqual(
list(afs),
[0.32, 0.52, 0.44, 0.5, 0.46, 0.48, 0.38, 0.46, 0.4, 0.44])

def test_read_variant_vcf(self):
p = pd.read_csv(P,
index_col=0,
Expand Down
11 changes: 11 additions & 0 deletions tests/presence_absence_missing.Rtab
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Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
Gene sample_1 sample_2 sample_3 sample_4 sample_5 sample_6 sample_7 sample_8 sample_9 sample_10 sample_11 sample_12 sample_13 sample_14 sample_15 sample_16 sample_17 sample_18 sample_19 sample_20 sample_21 sample_22 sample_23 sample_24 sample_25 sample_26 sample_27 sample_28 sample_29 sample_30 sample_31 sample_32 sample_33 sample_34 sample_35 sample_36 sample_37 sample_38 sample_39 sample_40 sample_41 sample_42 sample_43 sample_44 sample_45 sample_46 sample_47 sample_48 sample_49 sample_50
gene_1 0 0 1 0 0 . 1 1 0 0 0 1 0 0 1 0 0 0 0 0 0 1 0 0 0 1 0 0 1 0 1 1 0 0 1 0 1 1 0 0 1 0 . 1 0 0 . . 1 0
gene_2 0 0 1 0 . 0 1 0 1 1 1 0 . 1 1 1 0 0 1 0 0 0 0 0 1 1 0 1 0 1 0 0 1 1 1 1 0 0 0 0 1 1 1 1 1 0 1 1 1 1
gene_3 0 . 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 0 1 1 0 0 0 0 1 1 1 1 0 0 1 0 0 1 1 1 0 . . 1 1 0 1 1 1 . 1 . 0 1
gene_4 0 1 1 1 1 0 0 0 1 1 1 0 0 1 0 0 1 0 0 1 1 1 0 0 . 1 . 0 . . 1 1 1 0 0 1 1 0 1 1 1 0 0 1 0 1 1 0 1 0
gene_5 1 1 0 . 0 0 0 0 1 1 0 1 0 1 1 1 0 . 0 . 1 1 0 1 0 0 0 0 1 1 0 0 1 0 1 1 1 1 1 0 . 1 1 1 1 0 0 0 0 0
gene_6 1 1 1 1 1 1 1 0 0 1 0 0 0 . 1 0 1 0 1 0 0 . 0 1 . 1 0 . 1 0 1 0 0 1 1 1 . 0 0 0 0 1 1 1 1 0 1 0 1 0
gene_7 1 1 0 0 1 0 1 1 . 0 1 0 1 0 . 0 0 1 0 1 . 1 0 0 0 0 1 1 1 0 1 0 . 1 0 . 1 0 1 0 0 0 0 0 1 1 0 0 0 0
gene_8 0 0 0 . 0 0 1 1 0 0 1 1 0 . 1 0 1 0 1 1 1 0 0 . 0 1 1 0 0 0 1 0 1 0 1 0 1 0 1 0 1 1 1 0 1 1 1 1 0 0
gene_9 0 1 1 . 1 0 1 1 0 0 . 1 0 0 0 1 0 1 0 0 0 1 1 0 0 0 1 . 1 . 0 1 1 1 0 . 0 . 1 0 1 1 . 0 0 1 0 0 1 0
gene_10 1 0 1 1 1 1 . 1 0 1 0 0 0 0 0 1 1 0 1 0 0 0 1 0 0 1 0 0 1 1 0 1 1 1 0 . 1 1 0 0 1 . . 1 0 0 0 0 1 0