unit testing

methylprep/__init__.py

@@ -7,8 +7,6 @@
     get_raw_datasets,
     run_pipeline,
     consolidate_values_for_sheet,
-    load,
-    load_both,
     read_geo,
     )
 from .download import run_series, run_series_list, convert_miniml
@@ -26,8 +24,6 @@
     'run_series',
     'run_series_list',
     'convert_miniml',
-    'load',
-    'load_both',
     'read_geo',
     'build_composite_dataset',
 ]

methylprep/processing/__init__.py

@@ -2,7 +2,6 @@
 from .preprocess import preprocess_noob
 from .raw_dataset import RawDataset, get_raw_datasets, get_array_type
 from .postprocess import consolidate_values_for_sheet
-from .load_processed import load, load_both
 from .read_geo_processed import read_geo
 
 __all__ = [
@@ -14,7 +13,5 @@
     'run_pipeline',
     'consolidate_values_for_sheet',
     'get_array_type',
-    'load',
-    'load_both',
     'read_geo',
 ]

methylprep/processing/pipeline.py

@@ -340,7 +340,7 @@ def run_pipeline(data_dir, array_type=None, export=False, manifest_filepath=None
         LOGGER.info(f"Exported control probes to {control_filename}")
         consolidate_control_snp(data_containers, Path(data_dir,control_filename))
 
-    elif betas:
+    if betas:
         return consolidate_values_for_sheet(data_containers, postprocess_func_colname='beta_value')
     elif m_value:
         return consolidate_values_for_sheet(data_containers, postprocess_func_colname='m_value')

tests/download/test_geo_alert.py

@@ -0,0 +1,12 @@
+import methylprep
+import pandas as pd
+from pathlib import Path
+
+def test_geo_alert(keys="blood spleen"):
+    df = methylprep.download.geo_alert.search(keys)
+    if type(df) is not type(pd.DataFrame()):
+        raise AssertionError()
+    if Path(f'geo_alert {keys}.csv').exists():
+        Path(f'geo_alert {keys}.csv').unlink()
+    else:
+        print(f'file not found')

tests/processing/test_compare_to_minfi.r

@@ -0,0 +1,25 @@
+library(minfi)
+# specify directory
+minfi_baseDir = paste0("/Users/nrigby/Desktop/idats_standard/batch_1052641/")
+# read samplesheet
+minfi_targets = read.metharray.sheet(minfi_baseDir)
+# read IDAT's into RGChannelSet
+rgSet <- read.metharray.exp(targets = minfi_targets1,verbose = TRUE)
+# preprocessRaw
+mSet.raw = preprocessRaw(rgSet)
+# make files
+meth.raw = getMeth(mSet.raw)
+write.csv(file='~/Desktop/idats_standard/minfi_raw_meth.csv',x=meth.raw1,row.names=TRUE,col.names=TRUE)
+unmeth.raw = getUnmeth(mSet.raw)
+write.csv(file='~/Desktop/idats_standard/minfi_raw_unmeth.csv',x=unmeth.raw1,row.names=TRUE,col.names=TRUE)
+betas.raw = getBeta(mSet.raw)
+write.csv(file='~/Desktop/idats_standard/minfi_raw_betas.csv',x=betas.raw1,row.names=TRUE,col.names=TRUE)
+# preprocessNoob
+mSet.noob = preprocessNoob(rgSet)
+# make files
+meth.noob = getMeth(mSet.noob)
+write.csv(file='~/Desktop/idats_standard/minfi_noob_meth.csv',x=meth.noob,row.names=TRUE,col.names=TRUE)
+unmeth.noob = getUnmeth(mSet.noob)
+write.csv(file='~/Desktop/idats_standard/minfi_noob_unmeth.csv',x=unmeth.noob,row.names=TRUE,col.names=TRUE)
+betas.noob = getBeta(mSet.noob)
+write.csv(file='~/Desktop/idats_standard/minfi_noob_betas.csv',x=betas.noob,row.names=TRUE,col.names=TRUE)