Skip to main content
Join the official 2020 Python Developers SurveyStart the survey!

Python SDK for PFB format

Project description

# 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”)

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for python-pfb-sdk, version 0.0.1
Filename, size File type Python version Upload date Hashes
Filename, size python_pfb_sdk-0.0.1-py2-none-any.whl (30.0 kB) File type Wheel Python version py2 Upload date Hashes View
Filename, size python_pfb_sdk-0.0.1.tar.gz (6.7 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page