41 lines
1.3 KiB
Python
Executable File
41 lines
1.3 KiB
Python
Executable File
#!/usr/bin/env python
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"""Script to check that sample sheet is well-formatted."""
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import argparse
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import sys
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import pandas as pd
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def main():
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"""Run entry point."""
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parser = argparse.ArgumentParser()
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parser.add_argument('sample_sheet')
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parser.add_argument('output')
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args = parser.parse_args()
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try:
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samples = pd.read_csv(args.sample_sheet, sep=None)
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if 'alias' in samples.columns:
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if 'sample_id' in samples.columns:
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sys.stderr.write(
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"Warning: sample sheet contains both 'alias' and "
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'sample_id, using the former.')
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samples['sample_id'] = samples['alias']
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if not set(['sample_id', 'barcode']).intersection(samples.columns):
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raise IOError()
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except Exception:
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raise IOError(
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"Could not parse sample sheet, it must contain two columns "
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"named 'barcode' and 'sample_id' or 'alias'.")
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# check duplicates
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dup_bc = samples['barcode'].duplicated()
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dup_sample = samples['sample_id'].duplicated()
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if any(dup_bc) or any(dup_sample):
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raise IOError(
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"Sample sheet contains duplicate values.")
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samples.to_csv(args.output, sep=",", index=False)
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if __name__ == '__main__':
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main()
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