python-pfb-sdk 0.0.1

Python SDK for PFB format

# python-pfb-sdk Python scripts used to modify PFB files ## PFB Editing Scripts

### Add Field Adds a new field to the specified node for the specified pfb file as of right now this is only limited to string and int with enum supported later This writes to a new file new.pfb

usage: addField.py [-h] PFB_file parentField field fieldType fieldDefault

Add a new field to PFB schema

positional arguments:

PFB_file pfb file to add record to. Default = test.pfb parentField parent of field wanting to add to schema field field to add to the schema fieldType type for new field fieldDefault default value for new field

optional arguments:

-h, --help

show this help message and exit

Example usage

command line usage:

python reader.py test.pfb

python usage:

import reader reader.read(“test.pfb”)

### Remove Field removes a field from pfb file to a new file (rm.pfb)

usage: removeField.py [-h] PFB_file parentField field

Remove a field from PFB schema and output to new file “rm.pfb”

positional arguments:

PFB_file pfb file to remove field from. Default = test.pfb parentField parent of field wanting to remove from schema field field to remove to the schema

optional arguments:

-h, --help

show this help message and exit

Example usage

command line usage:

python removeField.py test.pfb demographic gender

python usage:

import removeField removeField.remove(“test.pfb”, “simple_germline_variation”, “data_category”)

### Add Record Adds new record(s) to the pfb file from a json file

usage: addRecord.py [-h] PFB_file JSON_file

Add a record to PFB file from a minified JSON file

positional arguments:

PFB_file pfb file to add record to. Default = test.pfb JSON_file JSON file to add into the pfb file. Default = test.json

optional arguments:

-h, --help

show this help message and exit

Exapmle Usage

command line usage:

python addRecord.py test.pfb test.json

python usage

import addRecord addRecord.add(“test.pfb”, “test.json”)

### Reader Used to read the records from pfb file records]

usage: reader.py [-h] PFB_file

Read a PFB file in json format

positional arguments:

PFB_file pfb file to add record to. Default = test.pfb

optional arguments:

-h, --help

show this help message and exit

Example Usage

command line usage:

python reader.py test.pfb

python usage:

import reader reader.read(“test.pfb”)

### Make Blank Record Make a blank json record for specific pfb schema to blank.json files

usage: makeBlankRecord.py [-h] PFB_file node

Create a blank record from a pfb schema

positional arguments:

PFB_file pfb file to read schema from node Node to add record to

optional arguments:

-h, --help

show this help message and exit

Example Usage

command line usage:

python makeBlankRecord.py test.pfb demographic

python usage:

import makeBlankRecord makeBlankRecord.makeRecord(“test.pfb”, “simple_germline_variation”)