Description:
pythonpfbsdk 0.0.1
# 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”)
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
Customer Reviews
There are no reviews.
