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Plink parsers

From the plink documentation: https://www.cog-genomics.org/plink/1.9/formats#bim

A text file with no header line, and one line per variant with the following six fields:

- Chromosome code (either an integer, or 'X'/'Y'/'XY'/'MT'; '0' indicates unknown) or name
- Variant identifier
- Position in morgans or centimorgans (safe to use dummy value of '0')
- Base-pair coordinate (1-based; limited to 231-2)
- Allele 1 (corresponding to clear bits in .bed; usually minor)
- Allele 2 (corresponding to set bits in .bed; usually major)

Parameters:

Name Type Description Default
plink_bfile str

The path to the plink bfile (with or without the extension).

 required
Source code in magenpy/parsers/plink_parsers.py 
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def parse_bim_file(plink_bfile):
    """
    From the plink documentation:
    https://www.cog-genomics.org/plink/1.9/formats#bim

        A text file with no header line, and one line per variant with the following six fields:

        - Chromosome code (either an integer, or 'X'/'Y'/'XY'/'MT'; '0' indicates unknown) or name
        - Variant identifier
        - Position in morgans or centimorgans (safe to use dummy value of '0')
        - Base-pair coordinate (1-based; limited to 231-2)
        - Allele 1 (corresponding to clear bits in .bed; usually minor)
        - Allele 2 (corresponding to set bits in .bed; usually major)

    :param plink_bfile: The path to the plink bfile (with or without the extension).
    :type plink_bfile: str
    """

    if '.bim' not in plink_bfile:
        if '.bed' in plink_bfile:
            plink_bfile = plink_bfile.replace('.bed', '.bim')
        else:
            plink_bfile = plink_bfile + '.bim'

    bim_df = pd.read_csv(plink_bfile,
                         sep=r'\s+',
                         names=['CHR', 'SNP', 'cM', 'POS', 'A1', 'A2'],
                         dtype={
                             'CHR': int,
                             'SNP': str,
                             'cM': np.float32,
                             'POS': np.int32,
                             'A1': str,
                             'A2': str
                         })

    return bim_df

From the plink documentation: https://www.cog-genomics.org/plink/1.9/formats#fam

A text file with no header line, and one line per sample with the following six fields:

- Family ID ('FID')
- Within-family ID ('IID'; cannot be '0')
- Within-family ID of father ('0' if father isn't in dataset)
- Within-family ID of mother ('0' if mother isn't in dataset)
- Sex code ('1' = male, '2' = female, '0' = unknown)
- Phenotype value ('1' = control, '2' = case, '-9'/'0'/non-numeric = missing data if case/control)

Parameters:

Name Type Description Default
plink_bfile str

The path to the plink bfile (with or without the extension).

 required
Source code in magenpy/parsers/plink_parsers.py 
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def parse_fam_file(plink_bfile):
    """
    From the plink documentation:
    https://www.cog-genomics.org/plink/1.9/formats#fam

        A text file with no header line, and one line per sample with the following six fields:

        - Family ID ('FID')
        - Within-family ID ('IID'; cannot be '0')
        - Within-family ID of father ('0' if father isn't in dataset)
        - Within-family ID of mother ('0' if mother isn't in dataset)
        - Sex code ('1' = male, '2' = female, '0' = unknown)
        - Phenotype value ('1' = control, '2' = case, '-9'/'0'/non-numeric = missing data if case/control)

    :param plink_bfile: The path to the plink bfile (with or without the extension).
    :type plink_bfile: str
    """

    if '.fam' not in plink_bfile:
        if '.bed' in plink_bfile:
            plink_bfile = plink_bfile.replace('.bed', '.fam')
        else:
            plink_bfile = plink_bfile + '.fam'

    fam_df = pd.read_csv(plink_bfile,
                         sep=r'\s+',
                         usecols=list(range(6)),
                         names=['FID', 'IID', 'fatherID', 'motherID', 'sex', 'phenotype'],
                         dtype={'FID': str,
                                'IID': str,
                                'fatherID': str,
                                'motherID': str,
                                'sex': np.float32,
                                'phenotype': np.float32
                                },
                         na_values={
                             'phenotype': [-9.],
                             'sex': [0]
                         })

    # If the phenotype is all null or unknown, drop the column:
    if fam_df['phenotype'].isnull().all():
        fam_df.drop('phenotype', axis=1, inplace=True)

    # If the sex column is all null or unknown, drop the column:
    if fam_df['sex'].isnull().all():
        fam_df.drop('sex', axis=1, inplace=True)

    return fam_df