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Feature/v1.5.2 #89

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merged 4 commits into from
Jul 19, 2021
Merged

Feature/v1.5.2 #89

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27beeff
v1.5.2 bug fixes, improved test coverage; all tests passing and sesam…
marcmaxson Jul 14, 2021
1c3cbfe
minor bug fixes; methylcheck.plot_controls works again
marcmaxson Jul 19, 2021
8b5754e
removed debug print/logging lines
marcmaxson Jul 19, 2021
cb891bb
one ref value for M was wrong in test_pipeline.py
marcmaxson Jul 19, 2021
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removed debug print/logging lines
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@marcmaxson
marcmaxson committed Jul 19, 2021
commit 8b5754e435910010bf56071daaf771e66caed30d
2 changes: 1 addition & 1 deletion methylprep/cli.py
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Expand Up @@ -255,7 +255,7 @@ def cli_process(cmd_args):
args.export_poobah = True
args.no_quality_mask = False

print(vars(args).items())
#print(vars(args).items())

run_pipeline(
args.data_dir,
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24 changes: 12 additions & 12 deletions methylprep/processing/pipeline.py
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Expand Up @@ -630,18 +630,18 @@ def __init__(self, idat_dataset_pair, manifest, retain_uncorrected_probe_intensi
if self.data_type not in ('float64','float32','float16'):
raise ValueError(f"invalid data_type: {self.data_type} should be one of ('float64','float32','float16')")

#if self.debug:
print(f"DEBUG SDC params:")
exclude = ['data_channel', 'man', 'snp_man', 'ctl_man', 'address_code', 'ctrl_green', 'ctrl_red', 'II',
'IG', 'IR', 'oobG', 'oobR', 'methylated', 'unmethylated', 'snp_methylated', 'snp_unmethylated', 'ibG', 'ibR']
for key,value in self.__dict__.items():
if key in exclude:
try:
print(f"-- {key}: {value.shape}")
except:
print(f"-- skipping {key}")
else:
print(f"-- {key}: {value}")
if self.debug:
print(f"DEBUG SDC params:")
exclude = ['data_channel', 'man', 'snp_man', 'ctl_man', 'address_code', 'ctrl_green', 'ctrl_red', 'II',
'IG', 'IR', 'oobG', 'oobR', 'methylated', 'unmethylated', 'snp_methylated', 'snp_unmethylated', 'ibG', 'ibR']
for key,value in self.__dict__.items():
if key in exclude:
try:
print(f"-- {key}: {value.shape}")
except:
print(f"-- skipping {key}")
else:
print(f"-- {key}: {value}")

def process_all(self):
"""Runs all pre and post-processing calculations for the dataset."""
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4 changes: 2 additions & 2 deletions methylprep/processing/postprocess.py
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Expand Up @@ -84,7 +84,7 @@ def consolidate_values_for_sheet(data_containers, postprocess_func_colname='beta
# remove all failed probes by replacing with NaN before building DF.
sample._SampleDataContainer__data_frame.loc[sample._SampleDataContainer__data_frame[poobah_column] >= poobah_sig, postprocess_func_colname] = np.nan
elif poobah == True and poobah_column not in sample._SampleDataContainer__data_frame.columns:
print('DEBUG: missing poobah')
LOGGER.warning('DEBUG: missing poobah')

if sample.quality_mask == True and mask_column in sample._SampleDataContainer__data_frame.columns:
sample._SampleDataContainer__data_frame.loc[sample._SampleDataContainer__data_frame[mask_column].isna(), postprocess_func_colname] = np.nan
Expand Down Expand Up @@ -216,7 +216,7 @@ def merge_batches(num_batches, data_dir, filepattern):
if dfs: # pipeline passes in all filenames, but not all exist
dfs = pd.concat(dfs, axis='columns', join='inner') #.progress_apply(lambda x: x)
outfile_name = Path(data_dir, f"{filepattern}.pkl")
print(f"{filepattern}: {dfs.shape}")
LOGGER.info(f"{filepattern}: {dfs.shape}")
dfs.to_pickle(str(outfile_name))
del dfs # save memory.

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2 changes: 1 addition & 1 deletion methylprep/processing/preprocess.py
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Expand Up @@ -19,7 +19,7 @@
LOGGER = logging.getLogger(__name__)


def preprocess_noob(container, offset=15, pval_probes_df=None, quality_mask_df=None, nonlinear_dye_correction=True, debug=True, unit_test_oob=False): # v1.4.5+
def preprocess_noob(container, offset=15, pval_probes_df=None, quality_mask_df=None, nonlinear_dye_correction=True, debug=False, unit_test_oob=False): # v1.4.5+
""" NOOB pythonized copy of https://github.com/zwdzwd/sesame/blob/master/R/background_correction.R
- The function takes a SigSet and returns a modified SigSet with the background subtracted.
- Background is modelled in a normal distribution and true signal in an exponential distribution.
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