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| Original file line number | Diff line number | Diff line change |
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| #!/bin/python | ||
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| import argparse | ||
| import re | ||
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| """ | ||
| Summary: Validates a PED file for use with GATK-SV. Performs some sample ID validations as well. | ||
| Usage: python validate_ped.py -p pedigree.ped -s samples.list | ||
| Outputs: The script will write to stdout "PED file passes validation!" if successful, and | ||
| otherwise it will print an error message to stderr describing the PED file format violation. | ||
| """ | ||
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| FIELD_NUMBER_ID = 1 | ||
| FIELD_NUMBER_SEX = 4 | ||
| ILLEGAL_ID_SUBSTRINGS = ["chr", "name", "DEL", "DUP", "CPX", "CHROM"] | ||
| ID_TYPE_SAMPLE, ID_TYPE_FAMILY, ID_TYPE_PARENT = "sample", "family", "parent" | ||
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| def validate_id(identifier, id_set, id_type, source_file): | ||
| # check for empty IDs | ||
| if identifier is None or identifier == "": | ||
| raise ValueError(f"Empty {id_type} ID in {source_file}") | ||
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| # check all characters are alphanumeric or underscore | ||
| if not re.match(r'^\w+$', identifier): | ||
| raise ValueError(f"Invalid {id_type} ID in {source_file}: '{identifier}'. " + | ||
| "IDs should only contain alphanumeric and underscore characters.") | ||
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| # check for all-numeric IDs | ||
| # except: allow maternal and paternal ID to be 0 | ||
| # except: allow all-numeric family IDs (as in current ref panel PED file) | ||
| if id_type != ID_TYPE_FAMILY and not (id_type == ID_TYPE_PARENT and identifier == "0") and identifier.isdigit(): | ||
| raise ValueError(f"Invalid {id_type} ID in {source_file}: {identifier}. " + | ||
| "IDs should not contain only numeric characters.") | ||
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| # check for illegal substrings | ||
| for sub in ILLEGAL_ID_SUBSTRINGS: | ||
| if sub in identifier: | ||
| raise ValueError(f"Invalid {id_type} ID in {source_file}: {identifier}. " + | ||
| f"IDs cannot contain the following substrings: {', '.join(ILLEGAL_ID_SUBSTRINGS)}.") | ||
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| # check for duplicate IDs | ||
| if id_set is not None: | ||
| if identifier in id_set: | ||
| raise ValueError(f"Duplicate {id_type} ID in {source_file}: {identifier}") | ||
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| def get_samples(samples_file): | ||
| # Note that this sample ID validation is incomplete: | ||
| # * It does not check if sample IDs are substrings of other sample IDs | ||
| # * It only checks the provided sample list for duplicates, which is not the full cohort in GatherBatchEvidence | ||
| samples = set() | ||
| with open(samples_file, 'r') as samp: | ||
| for line in samp: | ||
| sample = line.strip() | ||
| validate_id(sample, samples, ID_TYPE_SAMPLE, "sample list") | ||
| samples.add(sample) | ||
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| if len(samples) < 1: | ||
| raise ValueError("Empty samples list provided") | ||
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| return samples | ||
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| def validate_ped(ped_file, samples): | ||
| seen_sex_1 = False | ||
| seen_sex_2 = False | ||
| samples_found = set() | ||
| with open(ped_file, 'r') as ped: | ||
| for line in ped: | ||
| # specification allows commented lines, which should be removed by SubsetPedFile and CleanVcfPart1 | ||
| if line.startswith("#"): | ||
| continue | ||
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| # we require tab-delimited PED files although the specification does not | ||
| fields = line.strip().split("\t") | ||
| if len(fields) != 6: | ||
| raise ValueError("Invalid PED file. PED file must be tab-delimited and have 6 columns: " + | ||
| "family_ID, sample_ID, paternal_ID, maternal_ID, sex, phenotype.") | ||
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| # validate IDs | ||
| # don't check for duplicates here: | ||
| # family and parent IDs may appear multiple times, and sample IDs checked elsewhere | ||
| for identifier, id_type in zip(fields[:FIELD_NUMBER_SEX], | ||
| [ID_TYPE_FAMILY, ID_TYPE_SAMPLE, ID_TYPE_PARENT, ID_TYPE_PARENT]): | ||
| validate_id(identifier, None, id_type, "PED file") | ||
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| # check for at least one appearance each of 1 and 2 in sex column | ||
| # this check is to ensure M/F are coded as 1 and 2 (not 0 and 1) | ||
| # and both M and F are present (for sex-specific steps) | ||
| sample_id = fields[FIELD_NUMBER_ID] | ||
| sex = fields[FIELD_NUMBER_SEX] | ||
| if sex == "1": | ||
| seen_sex_1 = True | ||
| elif sex == "2": | ||
| seen_sex_2 = True | ||
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| # require sex = 0, 1, or 2 | ||
| elif sex != "0": | ||
| raise ValueError(f"Sample {sample_id} has an invalid value for sex: {sex}. " + | ||
| "PED file must use the following values for sex: 1=Male, 2=Female, 0=Unknown/Other.") | ||
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| # check all samples in samples list are present in PED file exactly once | ||
| # no duplicate sample IDs | ||
| if sample_id in samples_found: | ||
| raise ValueError(f"Invalid PED file. PED file has duplicate entries for sample {sample_id}.") | ||
| elif sample_id in samples: | ||
| samples_found.add(sample_id) | ||
| # if not in samples list, ignore: ok for PED file to contain samples not in sample list | ||
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| # check if all samples in sample list are present in PED file | ||
| if len(samples_found) < len(samples): | ||
| missing = samples - samples_found | ||
| raise ValueError(f"Invalid PED file. PED file is missing sample(s): {','.join(missing)}.") | ||
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| if not (seen_sex_2 and seen_sex_1): | ||
| raise ValueError("Invalid PED file. PED file must use the following values for sex: " + | ||
| "1=Male, 2=Female, 0=Unknown/Other. PED file must contain at least " + | ||
| "one sample with sex=1 and one with sex=2.") | ||
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| # passed validation tests | ||
| print("PED file passes validation!") | ||
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| def main(): | ||
| parser = argparse.ArgumentParser() | ||
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| parser.add_argument("-p", "--ped-file", required=True, help="PED file to validate") | ||
| parser.add_argument("-s", "--samples-file", required=True, | ||
| help="File containing samples (one per line) that should be in PED file") | ||
| args = parser.parse_args() | ||
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| samples = get_samples(args.samples_file) | ||
| validate_ped(args.ped_file, samples) | ||
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| if __name__ == "__main__": | ||
| main() |
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