hlatypingtools 1.0.4

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HLATypingTools

Getting Started

Install from PyPI (recommended)

To use HLATypingTools, run pip install HLATypingTools in your terminal. All python packages necessary for HLATypingTools will automatically be downloaded.

Usage

If you haven't decrypted the data yet (first time you are using the package and you did request access to the product), run:

from hlatypingtools.decrypt_file import decrypt_file

password: str = "___"   # Replace with password provided by the author 
decrypt_file(password)

It should print File decrypted successfully.

Then you can use the package as follows:

from hlatypingtools.get_info import get_allele_info

allele: str = "A*01:01"
print(get_allele_info(allele, "Broad"))  # will output A1
print(get_allele_info(allele, "G Group"))  # will output A*01:01:01G
print(get_allele_info(allele, "P Group"))  # will output A*01:01P
print(get_allele_info(allele, "% locus"))  # will output 11.906

Or as follows:

from hlatypingtools.get_info import get_locus
print(get_locus("A*01:01"))  # will output HLA_A

Or as follows to output all possible high-resolution alleles for a given low-resolution typing:

from hlatypingtools.get_info import get_same_low_res_broad, get_same_low_res_assigned_type
broad = "DQ3"
print("DQB1*03:01" in get_same_low_res_broad(broad))  # will output True
print("DQB1*03:02" in get_same_low_res_broad(broad))  # will output True

assigned_type = "DQ7"
print("DQB1*03:01" in get_same_low_res_assigned_type(assigned_type))  # will output True
print("DQB1*03:02" in get_same_low_res_assigned_type(assigned_type))  # will output False

Note:

• Broad = something like A1, B7, Cw1, DR1, DQ3 (!!!), DQA1*01, DR52, DPB1*01, or DPA1*01
• Assigned Type = something like A1, B7, Cw1, DR1, DQ7 (!!!), DQA1*01, DR52, DPB1*01, or DPA1*01

Exit codes

0: Wrong password.
1: Tried to acess the functions of the package without decrypting the data first.
2: type_info requested is not available.
3: wrong format for a low-resolution input. Has to be of the form A1, B7, Cw1, DR1, DQ3, DQA1*01, DR52, DPB1*01, or 
DPA1*01.

About the source code

• Follows PEP8 Style Guidelines.
• All functions are unit-tested with pytest.
• All variables are correctly type-hinted, reviewed with static type checker mypy.
• All functions are documented with docstrings.

Useful links:

• Corresponding GitHub repository
• Corresponding PyPI page