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adapted code for pandas2.0 #127

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adapted code for pandas2.0 #127

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d764fd6
adapted code for pandas2.0, where append is deprecated and replaced b…
jwuillou8 Aug 13, 2023
a0ca704
removed ug
jwuillou8 Aug 17, 2023
146173e
simpler row handling
jwuillou8 Aug 17, 2023
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6 changes: 5 additions & 1 deletion methylprep/files/sample_sheets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -499,6 +499,7 @@ def build_meta_data(self, samples = None):
cols = list(self.fields.values()) + ['Sample_ID']
meta_frame = pd.DataFrame(columns=cols)
# row contains the renamed fields, and pulls in the original data from sample_sheet
rows = []
for sample in samples:
row = {}
for field in self.fields.keys():
Expand All @@ -511,5 +512,8 @@ def build_meta_data(self, samples = None):
# add the UID that matches m_value/beta value pickles
#... unless there's a GSM_ID too
row['Sample_ID'] = f"{row['Sentrix_ID']}_{row['Sentrix_Position']}"
meta_frame = meta_frame.append(row, ignore_index=True)
rows.append(row)

meta_frame = pd.DataFrame(columns=cols, data=rows)

return meta_frame
7 changes: 4 additions & 3 deletions methylprep/processing/infer_channel_switch.py
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Expand Up @@ -168,8 +168,8 @@ def get_infer_channel_probes(manifest, green_idat, red_idat, debug=False):
green_in_band['unmeth'] = oobR_meth

# next, add the green-in-band to oobG and red-in-band to oobR
oobG_IG = oobG.append(green_in_band).sort_index()
oobR_IR = oobR.append(red_in_band).sort_index()
oobG_IG = pd.concat([oobG, green_in_band]).sort_index()
oobR_IR = pd.concat([oobR, red_in_band]).sort_index()

# channel swap requires a way to update idats with illumina_ids
lookupIR = probe_details_IR.merge(
Expand All @@ -186,7 +186,8 @@ def get_infer_channel_probes(manifest, green_idat, red_idat, debug=False):
right_index=True,
suffixes=(False, False),
)[['AddressA_ID','AddressB_ID']]
lookup = lookupIG.append(lookupIR).sort_index()
#lookup = lookupIG.append(lookupIR).sort_index()
lookup = pd.concat([lookupIG, lookupIR]).sort_index()

if debug:
return {'green': oobG_IG, 'red': oobR_IR, 'oobG': oobG, 'oobR':oobR, 'IG': green_in_band, 'IR': red_in_band, 'lookup': lookup}
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