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Fix warnings regarding the .ix depreciation #231

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merged 4 commits into from Dec 18, 2018
Merged

Fix warnings regarding the .ix depreciation #231

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d1ad3c5
Replaced .ix with .loc in main concoct
alneberg Dec 14, 2018
55baefb
Merge remote-tracking branch 'upstream/develop' into fix_warnings
alneberg Dec 14, 2018
f19d414
Replaced .ix to .loc in test unittest
alneberg Dec 14, 2018
f6e15fd
Replaced .ix with .loc in test gen input table
alneberg Dec 14, 2018
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2 changes: 1 addition & 1 deletion bin/concoct
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Expand Up @@ -25,7 +25,7 @@ def main(args):
sys.exit(-1)

if cov is not None:
joined = composition.join(cov.ix[:,cov_range[0]:cov_range[1]],how="inner")
joined = composition.join(cov.loc[:,cov_range[0]:cov_range[1]],how="inner")
else:
joined = composition

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16 changes: 8 additions & 8 deletions concoct/input.py
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Expand Up @@ -87,32 +87,32 @@ def load_coverage(cov_file, contig_lengths, no_cov_normalization, add_total_cove
cov_range = (cov.columns[0],cov.columns[-1])

# Adding pseudo count
cov.ix[:,cov_range[0]:cov_range[1]] = cov.ix[:,cov_range[0]:cov_range[1]].add(
cov.loc[:,cov_range[0]:cov_range[1]] = cov.loc[:,cov_range[0]:cov_range[1]].add(
(read_length/contig_lengths),
axis='index')

if not no_cov_normalization:
#Normalize per sample first
cov.ix[:,cov_range[0]:cov_range[1]] = \
_normalize_per_sample(cov.ix[:,cov_range[0]:cov_range[1]])
cov.loc[:,cov_range[0]:cov_range[1]] = \
_normalize_per_sample(cov.loc[:,cov_range[0]:cov_range[1]])

temp_cov_range = None
# Total coverage should be calculated after per sample normalization
if add_total_coverage:
cov['total_coverage'] = cov.ix[:,cov_range[0]:cov_range[1]].sum(axis=1)
cov['total_coverage'] = cov.loc[:,cov_range[0]:cov_range[1]].sum(axis=1)
temp_cov_range = (cov_range[0],'total_coverage')

if not no_cov_normalization:
# Normalize contigs next
cov.ix[:,cov_range[0]:cov_range[1]] = \
_normalize_per_contig(cov.ix[:,cov_range[0]:cov_range[1]])
cov.loc[:,cov_range[0]:cov_range[1]] = \
_normalize_per_contig(cov.loc[:,cov_range[0]:cov_range[1]])

if temp_cov_range:
cov_range = temp_cov_range

# Log transform
cov.ix[:,cov_range[0]:cov_range[1]] = np.log(
cov.ix[:,cov_range[0]:cov_range[1]])
cov.loc[:,cov_range[0]:cov_range[1]] = np.log(
cov.loc[:,cov_range[0]:cov_range[1]])

logging.info('Successfully loaded coverage data.')
return cov, cov_range
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16 changes: 8 additions & 8 deletions tests/test_gen_input_table.py
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Expand Up @@ -90,10 +90,10 @@ def test_with_bamfiles(self):

new_output = os.path.join(tmp_dir_path, 'inputtable.tsv')
df = pd.read_csv(new_output, sep='\t', index_col=0)
assert_almost_equal(df['cov_mean_sample_ten_reads'].ix['contig-75000034'], 10*100.0/1615, 5)
assert_almost_equal(df['cov_mean_sample_ten_reads'].ix['contig-21000001'], 10*100.0/9998, 5)
assert_almost_equal(df['cov_mean_sample_twenty_reads'].ix['contig-75000034'], 20*100.0/1615, 5)
assert_almost_equal(df['cov_mean_sample_twenty_reads'].ix['contig-21000001'], 20*100.0/9998, 5)
assert_almost_equal(df['cov_mean_sample_ten_reads'].loc['contig-75000034'], 10*100.0/1615, 5)
assert_almost_equal(df['cov_mean_sample_ten_reads'].loc['contig-21000001'], 10*100.0/9998, 5)
assert_almost_equal(df['cov_mean_sample_twenty_reads'].loc['contig-75000034'], 20*100.0/1615, 5)
assert_almost_equal(df['cov_mean_sample_twenty_reads'].loc['contig-21000001'], 20*100.0/9998, 5)


#assert_equal(new_output, old_output,
Expand All @@ -111,8 +111,8 @@ def test_with_bedfiles(self):

new_output = os.path.join(tmp_dir_path, 'inputtable.tsv')
df = pd.read_csv(new_output, sep='\t', index_col=0)
assert_almost_equal(df['cov_mean_sample_ten_reads'].ix['contig-75000034'], 10*100.0/1615, 5)
assert_almost_equal(df['cov_mean_sample_ten_reads'].ix['contig-21000001'], 10*100.0/9998, 5)
assert_almost_equal(df['cov_mean_sample_twenty_reads'].ix['contig-75000034'], 20*100.0/1615, 5)
assert_almost_equal(df['cov_mean_sample_twenty_reads'].ix['contig-21000001'], 20*100.0/9998, 5)
assert_almost_equal(df['cov_mean_sample_ten_reads'].loc['contig-75000034'], 10*100.0/1615, 5)
assert_almost_equal(df['cov_mean_sample_ten_reads'].loc['contig-21000001'], 10*100.0/9998, 5)
assert_almost_equal(df['cov_mean_sample_twenty_reads'].loc['contig-75000034'], 20*100.0/1615, 5)
assert_almost_equal(df['cov_mean_sample_twenty_reads'].loc['contig-21000001'], 20*100.0/9998, 5)

6 changes: 3 additions & 3 deletions tests/test_unittest_input.py
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Expand Up @@ -46,7 +46,7 @@ def test_load_composition(self):
assert_equal(len(c_len), len(contig_lengths))
# All equal
for ix in ids:
assert_equal(c_len.ix[ix], contig_lengths.ix[ix])
assert_equal(c_len.loc[ix], contig_lengths.loc[ix])


def test__calculate_composition(self):
Expand All @@ -67,15 +67,15 @@ def test__calculate_composition(self):

for seq_id, s in seq_strings.items():
c = count_substrings(s, "".join(kmer_s))
assert_equal(composition.ix[seq_id, feature_mapping[kmer_s]], c+1)
assert_equal(composition.loc[seq_id, feature_mapping[kmer_s]], c+1)

# Check that non palindromic kmers works as well:
kmer_s = ('A', 'G', 'G', 'G')
reverse_kmer_s = ('C', 'C', 'C', 'T')
for seq_id, s in seq_strings.items():
c_1 = count_substrings(s, "".join(kmer_s))
c_2 = count_substrings(s, "".join(reverse_kmer_s))
assert_equal(composition.ix[seq_id, feature_mapping[kmer_s]], c_1 + c_2 + 1)
assert_equal(composition.loc[seq_id, feature_mapping[kmer_s]], c_1 + c_2 + 1)


def count_substrings(s, subs):
Expand Down