scout/parse/peddy.py
def parse_peddy_sex_check(lines):
    """Parse a .ped_check.csv file
    
    Args:
        lines(iterable(str))
    
    Returns:
        sex_check(list(dict))
    """
    sex_check = []
    header = []
    for i,line in enumerate(lines):
        line = line.rstrip()
        if i == 0:
            # Header line
            header = line.lstrip('#').split(',')
        else:
            ind_info = dict(zip(header, line.split(',')))

            # boolean indicating wether there is a mismatch between X 
            # genotypes and ped sex.
            ind_info['error'] = make_bool(ind_info.get('error'))

            # number of homozygous-alternate calls
            ind_info['hom_alt_count'] = convert_number(ind_info['hom_alt_count'])
            #number of homozygous-reference calls
            ind_info['hom_ref_count'] = convert_number(ind_info['hom_ref_count'])
            # number of heterozygote calls
            ind_info['het_count'] = convert_number(ind_info['het_count'])

            # ratio of het_count / hom_alt_count. Low for males, high for females
            ind_info['het_ratio'] = convert_number(ind_info['het_ratio'])

            sex_check.append(ind_info)

    return sex_check
def parse_peddy_sex_check(lines):
    """Parse a .ped_check.csv file
    
    Args:
        lines(iterable(str))
    
    Returns:
        sex_check(list(dict))
    """
    sex_check = []
    header = []
    for i,line in enumerate(lines):
        line = line.rstrip()
        if i == 0:
            # Header line
            header = line.lstrip('#').split(',')
        else:
            ind_info = dict(zip(header, line.split(',')))

            # boolean indicating wether there is a mismatch between X 
            # genotypes and ped sex.
            ind_info['error'] = make_bool(ind_info.get('error'))

            # number of homozygous-alternate calls
            ind_info['hom_alt_count'] = convert_number(ind_info['hom_alt_count'])
            #number of homozygous-reference calls
            ind_info['hom_ref_count'] = convert_number(ind_info['hom_ref_count'])
            # number of heterozygote calls
            ind_info['het_count'] = convert_number(ind_info['het_count'])

            # ratio of het_count / hom_alt_count. Low for males, high for females
            ind_info['het_ratio'] = convert_number(ind_info['het_ratio'])

            sex_check.append(ind_info)

    return sex_check
def parse_peddy_sex_check ( lines ) : sex_check = [ ] header = [ ] for i , line in enumerate ( lines ) : line = line . rstrip ( ) if i == 0 : # Header line header = line . lstrip ( '#' ) . split ( ',' ) else : ind_info = dict ( zip ( header , line . split ( ',' ) ) ) # boolean indicating wether there is a mismatch between X  # genotypes and ped sex. ind_info [ 'error' ] = make_bool ( ind_info . get ( 'error' ) ) # number of homozygous-alternate calls ind_info [ 'hom_alt_count' ] = convert_number ( ind_info [ 'hom_alt_count' ] ) #number of homozygous-reference calls ind_info [ 'hom_ref_count' ] = convert_number ( ind_info [ 'hom_ref_count' ] ) # number of heterozygote calls ind_info [ 'het_count' ] = convert_number ( ind_info [ 'het_count' ] ) # ratio of het_count / hom_alt_count. Low for males, high for females ind_info [ 'het_ratio' ] = convert_number ( ind_info [ 'het_ratio' ] ) sex_check . append ( ind_info ) return sex_check
Parse a .ped_check.csv file
    
    Args:
        lines(iterable(str))
    
    Returns:
        sex_check(list(dict))
Parse a . ped_check . csv file Args : lines ( iterable ( str )) Returns : sex_check ( list ( dict ))