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Replace .get_value() calls with .at[] and account for float32 issues
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@biologyguy
biologyguy committed Apr 4, 2018
1 parent fc0f363 commit 780fd7c
Showing 1 changed file with 45 additions and 45 deletions.
90 changes: 45 additions & 45 deletions rdmcl/tests/test_merge_orthogroups.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,26 +127,26 @@ def test_check_init(hf, monkeypatch):
assert check.rdmcl_dir == test_dir.path
assert check.clusters == clusters
assert check.master_clust.taxa == taxa
assert check.r_squares.get_value(37, 'seq1') == 'BOL-PanxαC'
assert check.r_squares.get_value(316, 'seq2') == 'Edu-PanxαC'
assert check.r_squares['r_square'].sum() == 455.83679143893914
assert check.fwd_scores.get_value(2636, 'hmm_id') == 'Bfo-PanxαA'
assert check.fwd_scores.get_value(2, 'rec_id') == 'Edu-PanxαC'
assert check.fwd_scores['fwd_raw'].sum() == 640373.9347999988
assert check.within_group_r2_df.get_value(1, 'seq1') == 'BOL-PanxαC'
assert check.within_group_r2_df.get_value(3, 'seq2') == 'Bch-PanxαE'
assert check.r_squares.at[37, 'seq1'] == 'BOL-PanxαC'
assert check.r_squares.at[316, 'seq2'] == 'Edu-PanxαC'
assert check.r_squares['r_square'].sum() == 455.83679143893875
assert check.fwd_scores.at[2636, 'hmm_id'] == 'Bfo-PanxαA'
assert check.fwd_scores.at[2, 'rec_id'] == 'Edu-PanxαC'
assert check.fwd_scores['fwd_raw'].sum() == 640373.9347999999
assert check.within_group_r2_df.at[1, 'seq1'] == 'BOL-PanxαC'
assert check.within_group_r2_df.at[3, 'seq2'] == 'Bch-PanxαE'
assert check.within_group_r2_df['r_square'].sum() == 4.978079
assert check.within_group_r2_dist is True
assert check.within_group_fwd_df.get_value(1, 'hmm_id') == 'Cfu-PanxαC'
assert check.within_group_fwd_df.get_value(3, 'rec_id') == 'Bch-PanxαE'
assert check.within_group_fwd_df.at[1, 'hmm_id'] == 'Cfu-PanxαC'
assert check.within_group_fwd_df.at[3, 'rec_id'] == 'Bch-PanxαE'
assert check.within_group_fwd_df['fwd_raw'].sum() == 3116.2209
assert type(check.within_group_fwd_dist) is scipy.stats.kde.gaussian_kde
assert check.btw_group_r2_df.get_value(1, 'seq1') == 'BOL-PanxαC'
assert check.btw_group_r2_df.get_value(3, 'seq2') == 'Bab-PanxαD'
assert check.btw_group_r2_df.at[1, 'seq1'] == 'BOL-PanxαC'
assert check.btw_group_r2_df.at[3, 'seq2'] == 'Bab-PanxαD'
assert check.btw_group_r2_df['r_square'].sum() == 2.758417
assert check.btw_group_r2_dist is True
assert check.btw_group_fwd_df.get_value(1, 'hmm_id') == 'Bch-PanxαC'
assert check.btw_group_fwd_df.get_value(3, 'rec_id') == 'Bch-PanxαE'
assert check.btw_group_fwd_df.at[1, 'hmm_id'] == 'Bch-PanxαC'
assert check.btw_group_fwd_df.at[3, 'rec_id'] == 'Bch-PanxαE'
assert check.btw_group_fwd_df['fwd_raw'].sum() == 1566.3966
assert type(check.btw_group_fwd_dist) is scipy.stats.kde.gaussian_kde

Expand Down Expand Up @@ -192,8 +192,8 @@ def test_prepare_within_group_r2_df(capsys, hf):
merge = merge_orthogroups.Check._prepare_within_group_r2_df(check, force=False)
out, err = capsys.readouterr()
assert err == "Preparing hmm/within_group_rsquares.csv...\n"
assert merge.get_value(1, 'seq1') == 'BOL-PanxαC'
assert merge.get_value(3, 'seq2') == 'Bch-PanxαE'
assert merge.at[1, 'seq1'] == 'BOL-PanxαC'
assert merge.at[3, 'seq2'] == 'Bch-PanxαE'
assert merge['r_square'].sum() == 124.34523271531056
os.remove(join(test_dir.path, "hmm", "within_group_rsquares.csv"))

Expand All @@ -202,8 +202,8 @@ def test_prepare_within_group_r2_df(capsys, hf):
merge = merge_orthogroups.Check._prepare_within_group_r2_df(check, force=True)
assert err == "Preparing hmm/within_group_rsquares.csv...\n"
assert type(merge) is pd.DataFrame
assert merge.get_value(1, 'seq1') == 'BOL-PanxαC'
assert merge.get_value(3, 'seq2') == 'Bch-PanxαE'
assert merge.at[1, 'seq1'] == 'BOL-PanxαC'
assert merge.at[3, 'seq2'] == 'Bch-PanxαE'
assert merge['r_square'].sum() == 124.34523271531056
assert os.path.isfile(join(test_dir.path, "hmm", "within_group_rsquares.csv")) is True

Expand Down Expand Up @@ -241,25 +241,25 @@ def test_prepare_within_group_fwd_df(capsys, hf):
merge = merge_orthogroups.Check._prepare_within_group_fwd_df(check, force=False)
out, err = capsys.readouterr()
assert err == "Preparing hmm/within_group_fwd.csv...\n"
assert merge.get_value(1, 'hmm_id') == 'Cfu-PanxαC'
assert merge.get_value(329, 'rec_id') == 'BOL-PanxαH'
assert merge['fwd_raw'].sum() == 177372.92289999998
assert merge.at[1, 'hmm_id'] == 'Cfu-PanxαC'
assert merge.at[329, 'rec_id'] == 'BOL-PanxαH'
assert merge['fwd_raw'].sum() == 177372.9229

# File "within_group_fwd.csv" already exists, run method again
assert os.path.isfile(join(test_dir.path, "hmm", "within_group_fwd.csv")) is True
check = SimpleNamespace(rdmcl_dir=test_dir.path, clusters=clusters, r_squares=r_squares, fwd_scores=fwd_scores)
merge = merge_orthogroups.Check._prepare_within_group_fwd_df(check, force=False)
assert merge.get_value(1, 'hmm_id') == 'Cfu-PanxαC'
assert merge.get_value(329, 'rec_id') == 'BOL-PanxαH'
assert merge['fwd_raw'].sum() == 177372.92289999998
assert merge.at[1, 'hmm_id'] == 'Cfu-PanxαC'
assert merge.at[329, 'rec_id'] == 'BOL-PanxαH'
assert merge['fwd_raw'].sum() == 177372.9229
os.remove(join(test_dir.path, "hmm", "within_group_fwd.csv"))

# force=True
check = SimpleNamespace(rdmcl_dir=test_dir.path, clusters=clusters, r_squares=r_squares, fwd_scores=fwd_scores)
merge = merge_orthogroups.Check._prepare_within_group_fwd_df(check, force=True)
assert merge.get_value(1, 'hmm_id') == 'Cfu-PanxαC'
assert merge.get_value(329, 'rec_id') == 'BOL-PanxαH'
assert merge['fwd_raw'].sum() == 177372.92289999998
assert merge.at[1, 'hmm_id'] == 'Cfu-PanxαC'
assert merge.at[329, 'rec_id'] == 'BOL-PanxαH'
assert merge['fwd_raw'].sum() == 177372.9229


def test_prepare_between_group_r2_df(capsys, hf):
Expand Down Expand Up @@ -292,27 +292,27 @@ def test_prepare_between_group_r2_df(capsys, hf):
merge = merge_orthogroups.Check._prepare_between_group_r2_df(check, force=False)
out, err = capsys.readouterr()
assert err == "Preparing hmm/between_group_rsquares.csv...\n"
assert merge.get_value(1, 'seq1') == 'BOL-PanxαC'
assert merge.get_value(978, 'seq2') == 'Dgl-PanxαA'
assert merge['r_square'].sum() == 250.8266601079159
assert merge.at[1, 'seq1'] == 'BOL-PanxαC'
assert merge.at[978, 'seq2'] == 'Dgl-PanxαA'
assert merge['r_square'].sum() == 250.82666010791604

# Skip the main loop when file already exists
check = SimpleNamespace(rdmcl_dir=test_dir.path, clusters=clusters, r_squares=r_squares)
merge = merge_orthogroups.Check._prepare_between_group_r2_df(check, force=False)
out, err = capsys.readouterr()
assert err == ""
assert merge.get_value(1, 'seq1') == 'BOL-PanxαC'
assert merge.get_value(978, 'seq2') == 'Dgl-PanxαA'
assert merge['r_square'].sum() == 250.8266601079159
assert merge.at[1, 'seq1'] == 'BOL-PanxαC'
assert merge.at[978, 'seq2'] == 'Dgl-PanxαA'
assert merge['r_square'].sum() == 250.82666010791604

# force=True
check = SimpleNamespace(rdmcl_dir=test_dir.path, clusters=clusters, r_squares=r_squares)
merge = merge_orthogroups.Check._prepare_between_group_r2_df(check, force=True)
out, err = capsys.readouterr()
assert err == "Preparing hmm/between_group_rsquares.csv...\n"
assert merge.get_value(1, 'seq1') == 'BOL-PanxαC'
assert merge.get_value(978, 'seq2') == 'Dgl-PanxαA'
assert merge['r_square'].sum() == 250.8266601079159
assert merge.at[1, 'seq1'] == 'BOL-PanxαC'
assert merge.at[978, 'seq2'] == 'Dgl-PanxαA'
assert merge['r_square'].sum() == 250.82666010791604


def test_prepare_between_group_fwd_df(capsys, hf):
Expand Down Expand Up @@ -346,28 +346,28 @@ def test_prepare_between_group_fwd_df(capsys, hf):
merge = merge_orthogroups.Check._prepare_between_group_fwd_df(check, force=False)
out, err = capsys.readouterr()
assert err == "Preparing hmm/between_group_fwd.csv...\n"
assert merge.get_value(1, 'hmm_id') == 'Bch-PanxαC'
assert merge.get_value(1959, 'rec_id') == 'Bfo-PanxαG'
assert merge['fwd_raw'].sum() == 384849.1751999998
assert merge.at[1, 'hmm_id'] == 'Bch-PanxαC'
assert merge.at[1959, 'rec_id'] == 'Bfo-PanxαG'
assert merge['fwd_raw'].sum() == 384849.17520000006

# File "between_group_fwd.csv" already exists
assert os.path.isfile(join(test_dir.path, "hmm", "between_group_fwd.csv")) is True
check = SimpleNamespace(rdmcl_dir=test_dir.path, clusters=clusters, fwd_scores=fwd_scores)
merge = merge_orthogroups.Check._prepare_between_group_fwd_df(check, force=False)
out, err = capsys.readouterr()
assert err == ""
assert merge.get_value(1, 'hmm_id') == 'Bch-PanxαC'
assert merge.get_value(1959, 'rec_id') == 'Bfo-PanxαG'
assert merge['fwd_raw'].sum() == 384849.1751999998
assert merge.at[1, 'hmm_id'] == 'Bch-PanxαC'
assert merge.at[1959, 'rec_id'] == 'Bfo-PanxαG'
assert merge['fwd_raw'].sum() == 384849.17520000006

# force=True
check = SimpleNamespace(rdmcl_dir=test_dir.path, clusters=clusters, fwd_scores=fwd_scores)
merge = merge_orthogroups.Check._prepare_between_group_fwd_df(check, force=True)
out, err = capsys.readouterr()
assert err == "Preparing hmm/between_group_fwd.csv...\n"
assert merge.get_value(1, 'hmm_id') == 'Bch-PanxαC'
assert merge.get_value(1959, 'rec_id') == 'Bfo-PanxαG'
assert merge['fwd_raw'].sum() == 384849.1751999998
assert merge.at[1, 'hmm_id'] == 'Bch-PanxαC'
assert merge.at[1959, 'rec_id'] == 'Bfo-PanxαG'
assert merge['fwd_raw'].sum() == 384849.17520000006


def test_check_existing_group(capsys, hf, monkeypatch):
Expand Down

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