Last minute save of new pcr parser.
This commit is contained in:
lwark
@@ -735,20 +735,46 @@ class BasicSubmission(BaseClass):
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return re.sub(rf"{abb}(\d)", rf"{abb}-\1", outstr)
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# return outstr
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# @classmethod
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# def parse_pcr(cls, xl: pd.DataFrame, rsl_number: str) -> list:
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# """
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# Perform custom parsing of pcr info.
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#
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# Args:
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# xl (pd.DataFrame): pcr info form
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# rsl_number (str): rsl plate num of interest
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#
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# Returns:
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# list: _description_
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# """
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# logger.debug(f"Hello from {cls.__mapper_args__['polymorphic_identity']} PCR parser!")
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# return []
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@classmethod
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def parse_pcr(cls, xl: pd.DataFrame, rsl_number: str) -> list:
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def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> list:
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"""
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Perform custom parsing of pcr info.
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Args:
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xl (pd.DataFrame): pcr info form
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rsl_number (str): rsl plate num of interest
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rsl_plate_number (str): rsl plate num of interest
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Returns:
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list: _description_
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"""
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logger.debug(f"Hello from {cls.__mapper_args__['polymorphic_identity']} PCR parser!")
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return []
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pcr_sample_map = cls.get_submission_type().sample_map['pcr_samples']
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logger.debug(f'sample map: {pcr_sample_map}')
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main_sheet = xl[pcr_sample_map['main_sheet']]
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samples = []
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fields = {k: v for k, v in pcr_sample_map.items() if k not in ['main_sheet', 'start_row']}
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for row in main_sheet.iter_rows(min_row=pcr_sample_map['start_row']):
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idx = row[0].row
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sample = {}
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for k, v in fields.items():
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sheet = xl[v['sheet']]
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sample[k] = sheet.cell(row=idx, column=v['column']).value
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samples.append(sample)
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return samples
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@classmethod
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def filename_template(cls) -> str:
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@@ -1314,46 +1340,74 @@ class Wastewater(BasicSubmission):
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input_dict['csv'] = xl["Copy to import file"]
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return input_dict
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# @classmethod
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# def parse_pcr(cls, xl: pd.ExcelFile, rsl_number: str) -> list:
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# """
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# Parse specific to wastewater samples.
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# """
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# samples = super().parse_pcr(xl=xl, rsl_number=rsl_number)
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# df = xl.parse(sheet_name="Results", dtype=object).fillna("")
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# column_names = ["Well", "Well Position", "Omit", "Sample", "Target", "Task", " Reporter", "Quencher",
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# "Amp Status", "Amp Score", "Curve Quality", "Result Quality Issues", "Cq", "Cq Confidence",
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# "Cq Mean", "Cq SD", "Auto Threshold", "Threshold", "Auto Baseline", "Baseline Start",
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# "Baseline End"]
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# samples_df = df.iloc[23:][0:]
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# logger.debug(f"Dataframe of PCR results:\n\t{samples_df}")
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# samples_df.columns = column_names
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# logger.debug(f"Samples columns: {samples_df.columns}")
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# well_call_df = xl.parse(sheet_name="Well Call").iloc[24:][0:].iloc[:, -1:]
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# try:
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# samples_df['Assessment'] = well_call_df.values
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# except ValueError:
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# logger.error("Well call number doesn't match sample number")
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# logger.debug(f"Well call df: {well_call_df}")
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# for _, row in samples_df.iterrows():
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# try:
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# sample_obj = [sample for sample in samples if sample['sample'] == row[3]][0]
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# except IndexError:
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# sample_obj = dict(
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# sample=row['Sample'],
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# plate_rsl=rsl_number,
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# )
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# logger.debug(f"Got sample obj: {sample_obj}")
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# if isinstance(row['Cq'], float):
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# sample_obj[f"ct_{row['Target'].lower()}"] = row['Cq']
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# else:
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# sample_obj[f"ct_{row['Target'].lower()}"] = 0.0
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# try:
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# sample_obj[f"{row['Target'].lower()}_status"] = row['Assessment']
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# except KeyError:
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# logger.error(f"No assessment for {sample_obj['sample']}")
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# samples.append(sample_obj)
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# return samples
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@classmethod
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def parse_pcr(cls, xl: pd.ExcelFile, rsl_number: str) -> list:
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def parse_pcr(cls, xl: Workbook, rsl_plate_num: str) -> list:
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"""
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Parse specific to wastewater samples.
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"""
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samples = super().parse_pcr(xl=xl, rsl_number=rsl_number)
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df = xl.parse(sheet_name="Results", dtype=object).fillna("")
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column_names = ["Well", "Well Position", "Omit", "Sample", "Target", "Task", " Reporter", "Quencher",
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"Amp Status", "Amp Score", "Curve Quality", "Result Quality Issues", "Cq", "Cq Confidence",
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"Cq Mean", "Cq SD", "Auto Threshold", "Threshold", "Auto Baseline", "Baseline Start",
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"Baseline End"]
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samples_df = df.iloc[23:][0:]
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logger.debug(f"Dataframe of PCR results:\n\t{samples_df}")
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samples_df.columns = column_names
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logger.debug(f"Samples columns: {samples_df.columns}")
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well_call_df = xl.parse(sheet_name="Well Call").iloc[24:][0:].iloc[:, -1:]
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try:
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samples_df['Assessment'] = well_call_df.values
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except ValueError:
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logger.error("Well call number doesn't match sample number")
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logger.debug(f"Well call df: {well_call_df}")
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for _, row in samples_df.iterrows():
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samples = super().parse_pcr(xl=xl, rsl_plate_num=rsl_plate_num)
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logger.debug(f'Samples from parent pcr parser: {pformat(samples)}')
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output = []
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for sample in samples:
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sample['sample'] = re.sub('-N\\d$', '', sample['sample'])
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if sample['sample'] in [item['sample'] for item in output]:
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continue
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sample[f"ct_{sample['target'].lower()}"] = sample['ct'] if isinstance(sample['ct'], float) else 0.0
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sample[f"{sample['target'].lower()}_status"] = sample['assessment']
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other_targets = [s for s in samples if re.sub('-N\\d$', '', s['sample']) == sample['sample']]
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for s in other_targets:
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sample[f"ct_{s['target'].lower()}"] = s['ct'] if isinstance(s['ct'], float) else 0.0
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sample[f"{s['target'].lower()}_status"] = s['assessment']
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try:
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sample_obj = [sample for sample in samples if sample['sample'] == row[3]][0]
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except IndexError:
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sample_obj = dict(
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sample=row['Sample'],
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plate_rsl=rsl_number,
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)
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logger.debug(f"Got sample obj: {sample_obj}")
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if isinstance(row['Cq'], float):
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sample_obj[f"ct_{row['Target'].lower()}"] = row['Cq']
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else:
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sample_obj[f"ct_{row['Target'].lower()}"] = 0.0
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try:
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sample_obj[f"{row['Target'].lower()}_status"] = row['Assessment']
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del sample['ct']
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except KeyError:
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logger.error(f"No assessment for {sample_obj['sample']}")
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samples.append(sample_obj)
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return samples
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pass
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try:
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del sample['assessment']
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except KeyError:
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pass
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output.append(sample)
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return output
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@classmethod
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def enforce_name(cls, instr: str, data: dict | None = {}) -> str:
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