scout/build/individual.py
def build_individual(ind):
    """Build a Individual object

        Args:
            ind (dict): A dictionary with individual information

        Returns:
            ind_obj (dict): A Individual object

        dict(
            individual_id = str, # required
            display_name = str,
            sex = str,
            phenotype = int,
            father = str, # Individual id of father
            mother = str, # Individual id of mother
            capture_kits = list, # List of names of capture kits
            bam_file = str, # Path to bam file
            vcf2cytosure = str, # Path to CGH file
            analysis_type = str, # choices=ANALYSIS_TYPES
        )

    """

    try:
        ind_obj = dict(
            individual_id=ind['individual_id']
        )
        log.info("Building Individual with id:{0}".format(ind['individual_id']))
    except KeyError as err:
        raise PedigreeError("Individual is missing individual_id")

    ind_obj['display_name'] = ind.get('display_name', ind_obj['individual_id'])

    sex = ind.get('sex', 'unknown')
    # Convert sex to .ped
    try:
        # Check if sex is coded as an integer
        int(sex)
        ind_obj['sex'] = str(sex)
    except ValueError as err:
        try:
            # Sex are numbers in the database
            ind_obj['sex'] = REV_SEX_MAP[sex]
        except KeyError as err:
            raise(PedigreeError("Unknown sex: %s" % sex))

    phenotype = ind.get('phenotype', 'unknown')
    # Make the phenotype integers
    try:
        ped_phenotype = REV_PHENOTYPE_MAP[phenotype]
        if ped_phenotype == -9:
            ped_phenotype = 0
        ind_obj['phenotype'] = ped_phenotype
    except KeyError as err:
        raise(PedigreeError("Unknown phenotype: %s" % phenotype))

    ind_obj['father'] = ind.get('father')
    ind_obj['mother'] = ind.get('mother')
    ind_obj['capture_kits'] = ind.get('capture_kits', [])
    ind_obj['bam_file'] = ind.get('bam_file')
    ind_obj['mt_bam'] = ind.get('mt_bam')
    ind_obj['vcf2cytosure'] = ind.get('vcf2cytosure')
    ind_obj['confirmed_sex'] = ind.get('confirmed_sex')
    ind_obj['confirmed_parent'] = ind.get('confirmed_parent')
    ind_obj['predicted_ancestry'] = ind.get('predicted_ancestry')

    # Check if the analysis type is ok
    # Can be anyone of ('wgs', 'wes', 'mixed', 'unknown')
    analysis_type = ind.get('analysis_type', 'unknown')
    if not analysis_type in ANALYSIS_TYPES:
        raise PedigreeError("Analysis type %s not allowed", analysis_type)
    ind_obj['analysis_type'] = analysis_type
    
    if 'tmb' in ind:
        ind_obj['tmb'] = ind['tmb']

    if 'msi' in ind:
        ind_obj['msi'] = ind['msi']

    if 'tumor_purity' in ind:
        ind_obj['tumor_purity'] = ind['tumor_purity']

    if 'tumor_type' in ind:
        ind_obj['tumor_type'] = ind['tumor_type']

    return ind_obj
def build_individual(ind):
    """Build a Individual object

        Args:
            ind (dict): A dictionary with individual information

        Returns:
            ind_obj (dict): A Individual object

        dict(
            individual_id = str, # required
            display_name = str,
            sex = str,
            phenotype = int,
            father = str, # Individual id of father
            mother = str, # Individual id of mother
            capture_kits = list, # List of names of capture kits
            bam_file = str, # Path to bam file
            vcf2cytosure = str, # Path to CGH file
            analysis_type = str, # choices=ANALYSIS_TYPES
        )

    """

    try:
        ind_obj = dict(
            individual_id=ind['individual_id']
        )
        log.info("Building Individual with id:{0}".format(ind['individual_id']))
    except KeyError as err:
        raise PedigreeError("Individual is missing individual_id")

    ind_obj['display_name'] = ind.get('display_name', ind_obj['individual_id'])

    sex = ind.get('sex', 'unknown')
    # Convert sex to .ped
    try:
        # Check if sex is coded as an integer
        int(sex)
        ind_obj['sex'] = str(sex)
    except ValueError as err:
        try:
            # Sex are numbers in the database
            ind_obj['sex'] = REV_SEX_MAP[sex]
        except KeyError as err:
            raise(PedigreeError("Unknown sex: %s" % sex))

    phenotype = ind.get('phenotype', 'unknown')
    # Make the phenotype integers
    try:
        ped_phenotype = REV_PHENOTYPE_MAP[phenotype]
        if ped_phenotype == -9:
            ped_phenotype = 0
        ind_obj['phenotype'] = ped_phenotype
    except KeyError as err:
        raise(PedigreeError("Unknown phenotype: %s" % phenotype))

    ind_obj['father'] = ind.get('father')
    ind_obj['mother'] = ind.get('mother')
    ind_obj['capture_kits'] = ind.get('capture_kits', [])
    ind_obj['bam_file'] = ind.get('bam_file')
    ind_obj['mt_bam'] = ind.get('mt_bam')
    ind_obj['vcf2cytosure'] = ind.get('vcf2cytosure')
    ind_obj['confirmed_sex'] = ind.get('confirmed_sex')
    ind_obj['confirmed_parent'] = ind.get('confirmed_parent')
    ind_obj['predicted_ancestry'] = ind.get('predicted_ancestry')

    # Check if the analysis type is ok
    # Can be anyone of ('wgs', 'wes', 'mixed', 'unknown')
    analysis_type = ind.get('analysis_type', 'unknown')
    if not analysis_type in ANALYSIS_TYPES:
        raise PedigreeError("Analysis type %s not allowed", analysis_type)
    ind_obj['analysis_type'] = analysis_type
    
    if 'tmb' in ind:
        ind_obj['tmb'] = ind['tmb']

    if 'msi' in ind:
        ind_obj['msi'] = ind['msi']

    if 'tumor_purity' in ind:
        ind_obj['tumor_purity'] = ind['tumor_purity']

    if 'tumor_type' in ind:
        ind_obj['tumor_type'] = ind['tumor_type']

    return ind_obj
Build a Individual object

        Args:
            ind (dict): A dictionary with individual information

        Returns:
            ind_obj (dict): A Individual object

        dict(
            individual_id = str, # required
            display_name = str,
            sex = str,
            phenotype = int,
            father = str, # Individual id of father
            mother = str, # Individual id of mother
            capture_kits = list, # List of names of capture kits
            bam_file = str, # Path to bam file
            vcf2cytosure = str, # Path to CGH file
            analysis_type = str, # choices=ANALYSIS_TYPES
        )