Understanding Filtering: Learn to harness FAT's DSL to Power Filtering Schemes

Introduction

Filtering Analysis Tool (FAT) uses a DSL to define the filtering scheme to apply to the input tab-delimited (tsv) file.

Operations

The DSL FAT uses to apply filtering is made up of several operators.

Arithmetic Operators

The following arithmetic operators are supported by the DSL:

• + : Addition
• - : Subtraction
• / : Division
• | : Null (do nothing)

A multiplication operator is slated to be added in the next release.

Relational Operators

The following relational operators are supported by the DSL:

• >= : Greater than or equal to
• <= : Less than or equal to
• == : Equal to
• /= : Not equal to
• =~ : Regex

Strict less than and greater than operators are slated to be added in the next release.

Supported Types of Data

Data in the following structures are supported by the DSL:

• x,y : This structure should be used for two-piece data (i.e. 32,54)
• y,x : This structure should be used for two-piece data, but will treat the second element first. (i.e. 54,32)
• x,_ : This structure should be used for two-piece data, but will ignore the second element. (i.e. 32,54 -> 32)
• _,y : This structure should be used for two-piece data, but will ignore the first element. (i.e. 32,54 -> 54)
• x : This structure should be used for one-piece data (2.241 or missense)

Other structures can be added and supported, please create an issue for this request.

Defining Filtering Schemes in the Configuration YAML

The configuration YAML is allows for a modular and extensible way to power the filtering schemes and customization of the resultant XLSX file.

The filtering schemes are defined using the filters associative array.

For example,

filters:
   - filtering_type: 'BINARY'
     filtering_column: 'tumor_exome_day0_var_count'
     filtering_column_type: 'x'
     filtering_operator: '|'
     filtering_string:
       bfs_numeric_operator: '>='
       bfs_numeric_number: '5'
   - filtering_type: 'BINARY'
     filtering_column: 'normal_exome_day0_VAF'
     filtering_column_type: 'x'
     filtering_operator: '|'
     filtering_string:
       bfs_numeric_operator: '<='
       bfs_numeric_number: '4.99'