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”)
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