Maf

genie_registry.maf

Attributes

logger = logging.getLogger(__name__) module-attribute

Classes

FileTypeFormat

Functions

__init__(syn, center, genie_config=None, ancillary_files=None)

A validator helper class for a center's files.

PARAMETER	DESCRIPTION
syn	a synapseclient.Synapse object TYPE: Synapse
center	The participating center name. TYPE: str
genie_config	The configurations needed for the GENIE codebase. GENIE table type/name to Synapse Id. Defaults to None. TYPE: dict DEFAULT: None
ancillary_files	all files downloaded for validation. Defaults to None. TYPE: List[List[Entity]] DEFAULT: None

read_file(filePathList)

Each file is to be read in for validation and processing. This is not to be changed in any functions.

PARAMETER	DESCRIPTION
filePathList	A list of file paths (Max is 2 for the two clinical files)

RETURNS	DESCRIPTION
df	Pandas dataframe of file

validateFilename(filePath)

Validation of file name. The filename is what maps the file to its validation and processing.

PARAMETER	DESCRIPTION
filePath	Path to file

RETURNS	DESCRIPTION
str	file type defined by self._fileType

process_steps(df, **kwargs)

This function is modified for every single file. It reformats the file and stores the file into database and Synapse.

preprocess(newpath)

This is for any preprocessing that has to occur to the entity name to add to kwargs for processing. entity name is included in the new path

PARAMETER	DESCRIPTION
newpath	Path to file

process(filePath, **kwargs)

This is the main processing function.

PARAMETER	DESCRIPTION
filePath	Path to file
kwargs	The kwargs are determined by self._process_kwargs DEFAULT: {}

RETURNS	DESCRIPTION
str	file path of processed file

validate(filePathList, **kwargs)

This is the main validation function. Every file type calls self._validate, which is different.

PARAMETER	DESCRIPTION
filePathList	A list of file paths.
kwargs	The kwargs are determined by self._validation_kwargs DEFAULT: {}

RETURNS	DESCRIPTION
tuple	The errors and warnings as a file from validation. TYPE: ValidationResults

maf

Bases: FileTypeFormat

MAF file format validation / processing

Functions

process_steps(df)

The processing of maf files is specific to GENIE, so not included in this function

Functions

_check_allele_col_validity(df)

This function checks specific columns in a MAF (Mutation Annotation Format) file for certain conditions.

The following conditions must be met

If the MAF file has all three of these columns

- TUMOR_SEQ_ALLELE1 (TSA1)
- TUMOR_SEQ_ALLELE2 (TSA2)
- REFERENCE_ALLELE (REF)

Then, one of the following must be true

- Every value in TSA1 must be the same as the value in REF
- Every value in TSA1 must be the same as the value in TSA2

Additionally, if the MAF file has at least these two columns

- REFERENCE_ALLELE (REF)
- TUMOR_SEQ_ALLELE2 (TSA2)

Then

NO values in REF can match TSA2

These rules are important because Genome Nexus (GN) uses TSA1 to annotate data when it's not clear which variant to use. So, there can't be a mix of rows where some have TSA1 equal to REF and some have TSA1 equal to TSA2.

Valid Examples

| REFERENCE_ALLELE | TUMOR_SEQ_ALLELE1 | TUMOR_SEQ_ALLELE2 |
| ---------------- | ----------------- | ----------------- |
| C                | C                 | A                 |
| T                | T                 | C                 |

| REFERENCE_ALLELE | TUMOR_SEQ_ALLELE1 | TUMOR_SEQ_ALLELE2 |
| ---------------- | ----------------- | ----------------- |
| C                | A                 | A                 |
| T                | C                 | C                 |

| REFERENCE_ALLELE | TUMOR_SEQ_ALLELE2 |
| ---------------- | ----------------- |
| C                | A                 |
| T                | C                 |

Invalid Examples

| REFERENCE_ALLELE | TUMOR_SEQ_ALLELE1 | TUMOR_SEQ_ALLELE2 |
| ---------------- | ----------------- | ----------------- |
| C                | C                 | A                 |
| C                | A                 | A                 |

| REFERENCE_ALLELE | TUMOR_SEQ_ALLELE1 | TUMOR_SEQ_ALLELE2 |
| ---------------- | ----------------- | ----------------- |
| A                | C                 | A                 |
| T                | C                 | T                 |

| REFERENCE_ALLELE | TUMOR_SEQ_ALLELE2 |
| ---------------- | ----------------- |
| C                | C                 |
| T                | C                 |

See this Genome Nexus issue for more background regarding why this validation rule was implemented.

PARAMETER	DESCRIPTION
df	input mutation dataframe TYPE: DataFrame

RETURNS	DESCRIPTION
str	the error message TYPE: str

_check_allele_col(df, col)

Check the Allele column is correctly formatted.

PARAMETER	DESCRIPTION
df	mutation dataframe
col	Column header name

RETURNS	DESCRIPTION
	error, warning