Save and Load the Sumstats Object

GWASLab provides functions to save and load unfinished gl.Sumstats objects. This is useful for: - Saving intermediate results during long processing pipelines - Resuming work on partially processed sumstats - Sharing processed sumstats objects with others

Methods

`mysumstats.to_pickle()`

Save a Sumstats object to a pickle file. This is the recommended method as it's called directly on the Sumstats object.

mysumstats.to_pickle(path="~/mysumstats.pickle", 
                     overwrite=False)

Parameters:

Parameter	DataType	Description	Default
`path`	`str`	File path for the pickle file. Supports `~` for home directory expansion.	`"~/mysumstats.pickle"`
`overwrite`	`bool`	If `True`, overwrite the file if it already exists. If `False`, skip saving if file exists.	`False`

Returns: None (saves the object to disk)

`gl.dump_pickle()`

Alternative function-based approach to save a Sumstats object.

gl.dump_pickle(SumstatsObject, 
                path, 
                overwrite=False)

Parameters:

Parameter	DataType	Description	Default
`SumstatsObject`	`gl.Sumstats`	GWASLab Sumstats Object to save.	Required
`path`	`str`	File path for the pickle file.	Required
`overwrite`	`bool`	If `True`, overwrite the file if it already exists. If `False`, skip saving if file exists.	`False`

Returns: None (saves the object to disk)

`gl.load_pickle()`

Load a previously saved Sumstats object from a pickle file.

gl.load_pickle(path)

Parameters:

Parameter	DataType	Description	Default
`path`	`str`	File path to the pickle file.	Required

Returns: gl.Sumstats object

Examples

Using to_pickle() method (recommended)

import gwaslab as gl

# Load and process sumstats
mysumstats = gl.Sumstats("sumstats.txt.gz", fmt="plink2")
mysumstats.basic_check()
mysumstats.fix_chr()
mysumstats.fix_pos()

# Save the processed object
mysumstats.to_pickle("./processed_sumstats.pickle", overwrite=True)

# Later, load it back
mysumstats2 = gl.load_pickle("./processed_sumstats.pickle")

Using dump_pickle() function

import gwaslab as gl

# Process sumstats
mysumstats = gl.Sumstats("sumstats.txt.gz", fmt="plink2")
mysumstats.basic_check()

# Save using function
gl.dump_pickle(mysumstats, "./first.pickle", overwrite=True)

# Load it back
mysumstats2 = gl.load_pickle("./first.pickle")

Save with custom path

# Save to home directory
mysumstats.to_pickle("~/my_analysis/sumstats.pickle")

# Save to current directory
mysumstats.to_pickle("./sumstats.pickle", overwrite=True)

# Save with absolute path
mysumstats.to_pickle("/data/analysis/sumstats.pickle")

Notes

File format: The objects are saved using Python's pickle module in binary format (.pickle extension recommended)
Compatibility: Pickled objects are generally compatible across GWASLab versions, but may require the same Python version
What's saved: The entire Sumstats object is saved, including:
The data DataFrame
Metadata
Log history
All processed results (clumps, associations, etc.)
File existence: By default, if a file already exists at the specified path, it will not be overwritten unless overwrite=True
Home directory: The ~ symbol in paths is automatically expanded to your home directory