Annotation parsers

AnnotationMatrixParser

Bases: object

A generic annotation matrix parser class.

Source code in magenpy/parsers/annotation_parsers.py

class AnnotationMatrixParser(object):
    """
    A generic annotation matrix parser class.
    """

    def __init__(self, col_name_converter=None, **read_csv_kwargs):
        """
        :param col_name_converter: A dictionary mapping column names
        in the original table to magenpy's column names for the various
        SNP features in the annotation matrix.
        :param read_csv_kwargs: Keyword arguments to pass to pandas' `read_csv`.
        """

        self.col_name_converter = col_name_converter
        self.read_csv_kwargs = read_csv_kwargs

        # If the delimiter is not specified, assume whitespace by default:
        if 'sep' not in self.read_csv_kwargs and 'delimiter' not in self.read_csv_kwargs:
            self.read_csv_kwargs['sep'] = r'\s+'

    def parse(self, annotation_file, drop_na=True):
        """
        Parse the annotation matrix file
        :param annotation_file: The path to the annotation file.
        :param drop_na: Drop any entries with missing values.
        """

        try:
            df = pd.read_csv(annotation_file, **self.read_csv_kwargs)
        except Exception as e:
            raise e

        if drop_na:
            df = df.dropna()

        if self.col_name_converter is not None:
            df.rename(columns=self.col_name_converter, inplace=True)

        df.sort_values(['CHR', 'POS'], inplace=True)

        annotations = [ann for ann in df.columns if ann not in ('CHR', 'SNP', 'POS')]

        return df, annotations

__init__(col_name_converter=None, **read_csv_kwargs)

Parameters:

Name	Type	Description	Default
col_name_converter		A dictionary mapping column names in the original table to magenpy's column names for the various SNP features in the annotation matrix.	None
read_csv_kwargs		Keyword arguments to pass to pandas' read_csv.	{}

Source code in magenpy/parsers/annotation_parsers.py

def __init__(self, col_name_converter=None, **read_csv_kwargs):
    """
    :param col_name_converter: A dictionary mapping column names
    in the original table to magenpy's column names for the various
    SNP features in the annotation matrix.
    :param read_csv_kwargs: Keyword arguments to pass to pandas' `read_csv`.
    """

    self.col_name_converter = col_name_converter
    self.read_csv_kwargs = read_csv_kwargs

    # If the delimiter is not specified, assume whitespace by default:
    if 'sep' not in self.read_csv_kwargs and 'delimiter' not in self.read_csv_kwargs:
        self.read_csv_kwargs['sep'] = r'\s+'

parse(annotation_file, drop_na=True)

Parse the annotation matrix file

Parameters:

Name	Type	Description	Default
annotation_file		The path to the annotation file.	required
drop_na		Drop any entries with missing values.	True

Source code in magenpy/parsers/annotation_parsers.py

def parse(self, annotation_file, drop_na=True):
    """
    Parse the annotation matrix file
    :param annotation_file: The path to the annotation file.
    :param drop_na: Drop any entries with missing values.
    """

    try:
        df = pd.read_csv(annotation_file, **self.read_csv_kwargs)
    except Exception as e:
        raise e

    if drop_na:
        df = df.dropna()

    if self.col_name_converter is not None:
        df.rename(columns=self.col_name_converter, inplace=True)

    df.sort_values(['CHR', 'POS'], inplace=True)

    annotations = [ann for ann in df.columns if ann not in ('CHR', 'SNP', 'POS')]

    return df, annotations

LDSCAnnotationMatrixParser

Bases: AnnotationMatrixParser

Source code in magenpy/parsers/annotation_parsers.py

class LDSCAnnotationMatrixParser(AnnotationMatrixParser):

    def __init__(self, col_name_converter=None, **read_csv_kwargs):
        """
        :param col_name_converter: A dictionary mapping column names
        in the original table to magenpy's column names for the various
        SNP features in the annotation matrix.
        :param read_csv_kwargs: Keyword arguments to pass to pandas' read_csv
        """

        super().__init__(col_name_converter, **read_csv_kwargs)
        self.col_name_converter = self.col_name_converter or {}
        self.col_name_converter.update(
            {
                'BP': 'POS'
            }
        )

    def parse(self, annotation_file, drop_na=True):
        """
        Parse the annotation matrix file
        :param annotation_file: The path to the annotation file.
        :param drop_na: Drop any entries with missing values.
        """

        df, annotations = super().parse(annotation_file, drop_na=drop_na)

        df = df.drop(['CM', 'base'], axis=1)
        annotations = [ann for ann in annotations if ann not in ('CM', 'base')]

        return df, annotations

__init__(col_name_converter=None, **read_csv_kwargs)

Parameters:

Name	Type	Description	Default
col_name_converter		A dictionary mapping column names in the original table to magenpy's column names for the various SNP features in the annotation matrix.	None
read_csv_kwargs		Keyword arguments to pass to pandas' read_csv	{}

Source code in magenpy/parsers/annotation_parsers.py

def __init__(self, col_name_converter=None, **read_csv_kwargs):
    """
    :param col_name_converter: A dictionary mapping column names
    in the original table to magenpy's column names for the various
    SNP features in the annotation matrix.
    :param read_csv_kwargs: Keyword arguments to pass to pandas' read_csv
    """

    super().__init__(col_name_converter, **read_csv_kwargs)
    self.col_name_converter = self.col_name_converter or {}
    self.col_name_converter.update(
        {
            'BP': 'POS'
        }
    )

parse(annotation_file, drop_na=True)

Parse the annotation matrix file

Parameters:

Name	Type	Description	Default
annotation_file		The path to the annotation file.	required
drop_na		Drop any entries with missing values.	True

Source code in magenpy/parsers/annotation_parsers.py

def parse(self, annotation_file, drop_na=True):
    """
    Parse the annotation matrix file
    :param annotation_file: The path to the annotation file.
    :param drop_na: Drop any entries with missing values.
    """

    df, annotations = super().parse(annotation_file, drop_na=drop_na)

    df = df.drop(['CM', 'base'], axis=1)
    annotations = [ann for ann in annotations if ann not in ('CM', 'base')]

    return df, annotations

parse_annotation_bed_file(annot_bed_file)

Parse an annotation bed file in the format specified by Ensemble: https://uswest.ensembl.org/info/website/upload/bed.html

The file contains 3-12 columns, starting with Chromosome, start_coordinate, end_coordinate, etc. After reading the raw file, we let pandas infer whether the file has a header or not and we standardize the names of the first 3 columns and convert the chromosome column into an integer.

Parameters:

Name	Type	Description	Default
annot_bed_file	str	The path to the annotation BED file.	required

Source code in magenpy/parsers/annotation_parsers.py

def parse_annotation_bed_file(annot_bed_file):
    """
    Parse an annotation bed file in the format specified by Ensemble:
    https://uswest.ensembl.org/info/website/upload/bed.html

    The file contains 3-12 columns, starting with Chromosome, start_coordinate, end_coordinate, etc.
    After reading the raw file, we let pandas infer whether the file has a header or not and we
    standardize the names of the first 3 columns and convert the chromosome column into an integer.

    :param annot_bed_file: The path to the annotation BED file.
    :type annot_bed_file: str
    """

    try:
        annot_bed = pd.read_csv(annot_bed_file, usecols=[0, 1, 2],
                                sep=r'\s+',
                                names=['CHR', 'Start', 'End'])
    except Exception as e:
        raise e

    annot_bed['CHR'] = annot_bed['CHR'].str.replace('chr', '').astype(int)

    return annot_bed