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Merge branch 'CW-2063-samplesheet' into 'dev'
add sample_sheet test Closes CW-2063 See merge request epi2melabs/workflows/wf-bacterial-genomes!61
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,93 @@ | ||
| """Script to check that sample sheet is well-formatted.""" | ||
| """Check if a sample sheet is valid.""" | ||
| import csv | ||
| import sys | ||
|
|
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| import pandas as pd | ||
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| from .util import get_named_logger, wf_parser # noqa: ABS101 | ||
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| def main(args): | ||
| """Run entry point.""" | ||
| logger = get_named_logger("check-sheet") | ||
| """Run the entry point.""" | ||
| logger = get_named_logger("checkSheet") | ||
|
|
||
| barcodes = [] | ||
| aliases = [] | ||
| sample_types = [] | ||
| allowed_sample_types = [ | ||
| "test_sample", "positive_control", "negative_control", "no_template_control" | ||
| ] | ||
|
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||
| try: | ||
| logger.info(f"Reading {args.sample_sheet}.") | ||
| samples = pd.read_csv(args.sample_sheet, sep=None) | ||
| if 'alias' in samples.columns: | ||
| if 'sample_id' in samples.columns: | ||
| sys.stderr.write( | ||
| "Warning: sample sheet contains both 'alias' and " | ||
| 'sample_id, using the former.') | ||
| samples['sample_id'] = samples['alias'] | ||
| if not set(['sample_id', 'barcode']).intersection(samples.columns): | ||
| raise IOError() | ||
| except Exception: | ||
| raise IOError( | ||
| "Could not parse sample sheet, it must contain two columns " | ||
| "named 'barcode' and 'sample_id' or 'alias'.") | ||
| # check duplicates | ||
| dup_bc = samples['barcode'].duplicated() | ||
| dup_sample = samples['sample_id'].duplicated() | ||
| if any(dup_bc) or any(dup_sample): | ||
| raise IOError( | ||
| "Sample sheet contains duplicate values.") | ||
| samples.to_csv(args.output, sep=",", index=False) | ||
| logger.info(f"Written cleaned-up sheet to {args.output}.") | ||
| with open(args.sample_sheet, "r") as f: | ||
| csv_reader = csv.DictReader(f) | ||
| n_row = 0 | ||
| for row in csv_reader: | ||
| n_row += 1 | ||
| if n_row == 1: | ||
| n_cols = len(row) | ||
| else: | ||
| # check we got the same number of fields | ||
| if len(row) != n_cols: | ||
| raise ValueError( | ||
| f"Unexpected number of cells in row number {n_row}." | ||
| ) | ||
| try: | ||
| barcodes.append(row["barcode"]) | ||
| except KeyError: | ||
| sys.stdout.write("'barcode' column missing") | ||
| sys.exit() | ||
| try: | ||
| aliases.append(row["alias"]) | ||
| except KeyError: | ||
| sys.stdout.write("'alias' column missing") | ||
| sys.exit() | ||
| try: | ||
| sample_types.append(row["type"]) | ||
| except KeyError: | ||
| pass | ||
| except Exception as e: | ||
| sys.stdout.write(f"Parsing error: {e}") | ||
| sys.exit() | ||
|
|
||
| # check barcode and alias values are unique | ||
| if len(barcodes) > len(set(barcodes)): | ||
| sys.stdout.write("values in 'barcode' column not unique") | ||
| sys.exit() | ||
| if len(aliases) > len(set(aliases)): | ||
| sys.stdout.write("values in 'alias' column not unique") | ||
| sys.exit() | ||
|
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| if sample_types: | ||
| # check if "type" column has unexpected values | ||
| unexp_type_vals = set(sample_types) - set(allowed_sample_types) | ||
|
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||
| if unexp_type_vals: | ||
| sys.stdout.write( | ||
| f"found unexpected values in 'type' column: {unexp_type_vals}. " | ||
| f"Allowed values are: {allowed_sample_types}" | ||
| ) | ||
| sys.exit() | ||
|
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| if args.required_sample_types: | ||
| for required_type in args.required_sample_types: | ||
| if required_type not in allowed_sample_types: | ||
| sys.stdout.write(f"Not an allowed sample type: {required_type}") | ||
| sys.exit() | ||
| if sample_types.count(required_type) < 1: | ||
| sys.stdout.write( | ||
| f"Sample sheet requires at least 1 of {required_type}") | ||
| sys.exit() | ||
|
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| logger.info(f"Checked sample sheet {args.sample_sheet}.") | ||
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| def argparser(): | ||
| """Argument parser for entrypoint.""" | ||
| parser = wf_parser("check-sample-sheet") | ||
| parser.add_argument('sample_sheet') | ||
| parser.add_argument('output') | ||
| parser = wf_parser("check_sample_sheet") | ||
| parser.add_argument("sample_sheet", help="Sample sheet to check") | ||
| parser.add_argument( | ||
| "--required_sample_types", | ||
| help="List of required sample types. Each sample type provided must " | ||
| "appear at least once in the sample sheet", | ||
| nargs="*" | ||
| ) | ||
| return parser |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| barcode,alias,type | ||
| barcode01,sample1,test_sample | ||
| barcode02,sample2,test_sample |