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
def build_individual ( ind ) : 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
        )
Build a Individual object