diff --git a/LICENSE b/LICENSE index 94a9ed0..0a04128 100644 --- a/LICENSE +++ b/LICENSE @@ -1,674 +1,165 @@ - GNU GENERAL PUBLIC LICENSE + GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 - Copyright (C) 2007 Free Software Foundation, Inc. + Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. By contrast, -the GNU General Public License is intended to guarantee your freedom to -share and change all versions of a program--to make sure it remains free -software for all its users. 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Combined Libraries. + + You may place library facilities that are a work based on the +Library side by side in a single library together with other library +facilities that are not Applications and are not covered by this +License, and convey such a combined library under terms of your +choice, if you do both of the following: + + a) Accompany the combined library with a copy of the same work based + on the Library, uncombined with any other library facilities, + conveyed under the terms of this License. + + b) Give prominent notice with the combined library that part of it + is a work based on the Library, and explaining where to find the + accompanying uncombined form of the same work. + + 6. Revised Versions of the GNU Lesser General Public License. + + The Free Software Foundation may publish revised and/or new versions +of the GNU Lesser General Public License from time to time. Such new +versions will be similar in spirit to the present version, but may +differ in detail to address new problems or concerns. + + Each version is given a distinguishing version number. If the +Library as you received it specifies that a certain numbered version +of the GNU Lesser General Public License "or any later version" +applies to it, you have the option of following the terms and +conditions either of that published version or of any later version +published by the Free Software Foundation. If the Library as you +received it does not specify a version number of the GNU Lesser +General Public License, you may choose any version of the GNU Lesser +General Public License ever published by the Free Software Foundation. + + If the Library as you received it specifies that a proxy can decide +whether future versions of the GNU Lesser General Public License shall +apply, that proxy's public statement of acceptance of any version is +permanent authorization for you to choose that version for the +Library. diff --git a/README.md b/README.md new file mode 100644 index 0000000..e8de5a3 --- /dev/null +++ b/README.md @@ -0,0 +1,181 @@ +# py-ard +[![PyPi Version](https://img.shields.io/pypi/v/py-ard.svg)](https://pypi.python.org/pypi/py-ard) + +ARD reduction for HLA with Python + +## Install from source + +```shell +python3 -m venv venv +source venv/bin/activate + +python setup.py install +``` + +## Install from PyPi + +```shell +pip install py-ard +``` + +## Testing + +To run behavior-driven development (BDD) tests locally via the behave framework, you'll need to set up a virtual +environment. See Install from source. + +```shell +# Install test dependencies +pip install --upgrade pip +pip install -r test-requirements.txt + +# Running Behave and all BDD tests +behave +``` + +## Using `py-ard` from Python code + +### Initialize `py-ard` + +Import `pyard` package. + +```python +import pyard +``` + +The cache size of pre-computed reductions can be changed from the default of 1000 + +```python +pyard.max_cache_size = 1_000_000 +``` + +Initialize `ARD` object with a version of IMGT HLA database + +```python +ard = pyard.ARD(3290) +``` + +You can specify a different directory for the cached data. + +```python +ard = pyard.ARD('3290', data_dir='/tmp/py-ard') +``` + +You can choose to refresh the MAC code for current IMGT HLA database version + +```python +ard.refresh_mac_codes() +``` + +The default initialization is to use the latest IMGT HLA database + +```python +ard = pyard.ARD() +``` + +### Reduce Typings + +Reduce a single locus HLA Typing + +```python +allele = "A*01:01:01" + +ard.redux_gl(allele, 'G') +# >>> 'A*01:01:01G' + +ard.redux_gl(allele, 'lg') +# >>> 'A*01:01g' + +ard.redux_gl(allele, 'lgx') +# >>> 'A*01:01' +``` + +Reduce an ambiguous GL String + +```python +# Reduce GL String +# +ard.redux_gl("A*01:01/A*01:01N+A*02:AB^B*07:02+B*07:AB", "G") +# 'B*07:02:01G+B*07:02:01G^A*01:01:01G+A*02:01:01G/A*02:02' +``` + +You can also reduce serology based typings. + +```python +ard.redux_gl('B14', 'lg') +# >>> 'B*14:01g/B*14:02g/B*14:03g/B*14:04g/B*14:05g/B*14:06g/B*14:08g/B*14:09g/B*14:10g/B*14:11g/B*14:12g/B*14:13g/B*14:14g/B*14:15g/B*14:16g/B*14:17g/B*14:18g/B*14:19g/B*14:20g/B*14:21g/B*14:22g/B*14:23g/B*14:24g/B*14:25g/B*14:26g/B*14:27g/B*14:28g/B*14:29g/B*14:30g/B*14:31g/B*14:32g/B*14:33g/B*14:34g/B*14:35g/B*14:36g/B*14:37g/B*14:38g/B*14:39g/B*14:40g/B*14:42g/B*14:43g/B*14:44g/B*14:45g/B*14:46g/B*14:47g/B*14:48g/B*14:49g/B*14:50g/B*14:51g/B*14:52g/B*14:53g/B*14:54g/B*14:55g/B*14:56g/B*14:57g/B*14:58g/B*14:59g/B*14:60g/B*14:62g/B*14:63g/B*14:65g/B*14:66g/B*14:68g/B*14:70Qg/B*14:71g/B*14:73g/B*14:74g/B*14:75g/B*14:77g/B*14:82g/B*14:83g/B*14:86g/B*14:87g/B*14:88g/B*14:90g/B*14:93g/B*14:94g/B*14:95g/B*14:96g/B*14:97g/B*14:99g/B*14:102g' +``` + +## Valid Reduction Types + +|Reduction Type | Description | +|-------------- |-------------| +| `G` | Reduce to G Group Level | +| `lg` | Reduce to 2 field ARD level (append `g`) | +| `lgx` | Reduce to 2 field ARD level | +| `W` | Reduce/Expand to 3 field WHO nomenclature level| +| `exon` | Reduce/Expand to exon level | + +# Command Line Tools + +## Using `py-ard` from the command line + +### Import the latest IMGT database + +```shell +$ pyard-import +Created Latest py-ard database +``` + +### Import particular version of IMGT database + +```shell +$ pyard-import --db-version 3.29.0 +Created py-ard version 3290 database +``` + +Import particular version of IMGT database and replace the v2 to v3 mapping +table from a CSV file. + +```shell +$ pyard-import --db-version 3.29.0 --v2-to-v3-mapping map2to3.csv +Created py-ard version 3290 database +Updated v2_mapping table with 'map2to3.csv' mapping file. +``` + +### Reinstall a particular IMGT database + +```shell +pyard-import --db-version 3340 --re-install +``` + +### Replace the Latest IMGT database with V2 mappings + +```shell +$ pyard-import --v2-to-v3-mapping map2to3.csv +``` + +### Refresh the MAC for the specified version + +```shell +$ pyard-import --db-version 3450 --refresh-mac +``` + +### Reduce a GL String from command line + +```shell +$ pyard --gl 'A*01:AB' -r lgx +A*01:01/A*01:02 + +$ pyard --gl 'DRB1*08:XX' -r G +DRB1*08:01:01G/DRB1*08:02:01G/DRB1*08:03:02G/DRB1*08:04:01G/DRB1*08:05/ ... + +$ pyard -v 3290 --gl 'A1' -r lgx # For a particular version of DB +A*01:01/A*01:02/A*01:03/A*01:06/A*01:07/A*01:08/A*01:09/A*01:10/A*01:12/ ... +``` + +### Show the status of all `py-ard` databases + +```shell +$ pyard-status +``` + diff --git a/README.rst b/README.rst deleted file mode 100644 index a76a7bc..0000000 --- a/README.rst +++ /dev/null @@ -1,141 +0,0 @@ -=============================== -py-ard -=============================== - - -.. image:: https://img.shields.io/pypi/v/py-ard.svg - :target: https://pypi.python.org/pypi/py-ard - -.. image:: https://readthedocs.org/projects/pyars/badge/?version=latest - :target: https://pyard.readthedocs.io/en/latest/?badge=latest - :alt: Documentation Status - - -ARD reduction for HLA with Python - -* Free software: LGPL 3.0 -* Documentation: https://pyard.readthedocs.io. - - -Install from source -------------------- - -.. code-block:: - - python3 -m venv venv - source venv/bin/activate - - python setup.py install - -Install from PyPi ------------------ - -.. code-block:: - - pip install py-ard - -Testing -------- - -To run behavior-driven development (BDD) tests locally via the behave framework, -you'll need to set up a virtual environment. See Install from source - -.. code-block:: - - # Install test dependencies - pip install --upgrade pip - pip install -r test-requirements.txt - - # Running Behave and all BDD tests - behave - -Example -------- - -.. code-block:: python3 - - import pyard - - # The cache size of pre-computed reductions can be changed - # from the default of 1000 - pyard.max_cache_size = 1_000_000 - - # Initialize ARD object with a version of IMGT HLA database - ard = pyard.ARD(3290) - - # You can specify a data directory for temp files - # ard = pyard.ARD('3290', data_dir='/tmp/py-ard') - - - # Initialize with latest IMGT HLA database - ard = pyard.ARD() - - # You can choose to refresh the MAC code for current ARD db version - # ard.refresh_mac_codes() - - # You can reinstall a particular IMGT database - # pyard-import --db-version 3340 --re-install - # - # Reduce Allele - # - allele = "A*01:01:01" - - ard.redux(allele, 'G') - # >>> 'A*01:01:01G' - - ard.redux(allele, 'lg') - # >>> 'A*01:01g' - - ard.redux(allele, 'lgx') - # >>> 'A*01:01' - - # - # Reduce GL String - # - ard.redux_gl("A*01:01/A*01:01N+A*02:AB^B*07:02+B*07:AB", "G") - # 'B*07:02:01G+B*07:02:01G^A*01:01:01G+A*02:01:01G/A*02:02' - - # py-ard can also reduce serology based typings - ard.redux_gl('B14', 'lg') - # >>> 'B*14:01g/B*14:02g/B*14:03g/B*14:04g/B*14:05g/B*14:06g/B*14:08g/B*14:09g/B*14:10g/B*14:11g/B*14:12g/B*14:13g/B*14:14g/B*14:15g/B*14:16g/B*14:17g/B*14:18g/B*14:19g/B*14:20g/B*14:21g/B*14:22g/B*14:23g/B*14:24g/B*14:25g/B*14:26g/B*14:27g/B*14:28g/B*14:29g/B*14:30g/B*14:31g/B*14:32g/B*14:33g/B*14:34g/B*14:35g/B*14:36g/B*14:37g/B*14:38g/B*14:39g/B*14:40g/B*14:42g/B*14:43g/B*14:44g/B*14:45g/B*14:46g/B*14:47g/B*14:48g/B*14:49g/B*14:50g/B*14:51g/B*14:52g/B*14:53g/B*14:54g/B*14:55g/B*14:56g/B*14:57g/B*14:58g/B*14:59g/B*14:60g/B*14:62g/B*14:63g/B*14:65g/B*14:66g/B*14:68g/B*14:70Qg/B*14:71g/B*14:73g/B*14:74g/B*14:75g/B*14:77g/B*14:82g/B*14:83g/B*14:86g/B*14:87g/B*14:88g/B*14:90g/B*14:93g/B*14:94g/B*14:95g/B*14:96g/B*14:97g/B*14:99g/B*14:102g' - - - -Command Line Tools ------------------- - -.. code-block:: bash - - # Import the latest IMGT database - $ pyard-import - Created Latest py-ard database - - # Import particular version of IMGT database - $ pyard-import --db-version 3.29.0 - Created py-ard version 3290 database - - # Import particular version of IMGT database and - # replace the v2 to v3 mapping table - $ pyard-import --db-version 3.29.0 --v2-to-v3-mapping map2to3.csv - Created py-ard version 3290 database - Updated v2_mapping table with 'map2to3.csv' mapping file. - - # Replace the Latest IMGT database with V2 mappings - $ pyard-import --v2-to-v3-mapping map2to3.csv - - # Refresh the MAC for the specified version - $ pyard-import --db-version 3450 --refresh-mac - - # Reduce a gl string from command line - $ pyard --gl 'A*01:AB' -r lgx - A*01:01/A*01:02 - - $ pyard --gl 'DRB1*08:XX' -r G - DRB1*08:01:01G/DRB1*08:02:01G/DRB1*08:03:02G/DRB1*08:04:01G/DRB1*08:05/ ... - - $ pyard -v 3290 --gl 'A1' -r lgx - A*01:01/A*01:02/A*01:03/A*01:06/A*01:07/A*01:08/A*01:09/A*01:10/A*01:12/ ... - - # Show the status of all py-ard databases - $ pyard-status - diff --git a/pyard/__init__.py b/pyard/__init__.py index a419903..dd1b611 100644 --- a/pyard/__init__.py +++ b/pyard/__init__.py @@ -24,4 +24,4 @@ from .pyard import ARD __author__ = """NMDP Bioinformatics""" -__version__ = '0.6.9' +__version__ = '0.7.0' diff --git a/pyard/db.py b/pyard/db.py index aa88b7a..2a5fa4c 100644 --- a/pyard/db.py +++ b/pyard/db.py @@ -124,6 +124,20 @@ def mac_code_to_alleles(connection: sqlite3.Connection, code: str) -> List[str]: return alleles +def is_valid_mac_code(connection: sqlite3.Connection, code: str) -> bool: + """ + Check db if the MAC code exists. + + :param connection: db connection of type sqlite.Connection + :param code: MAC code + :return: code is MAC code ? + """ + mac_query = "SELECT count(alleles) from mac_codes where code = ?" + cursor = connection.execute(mac_query, (code,)) + result = cursor.fetchone() + cursor.close() + return result[0] > 0 + def serology_to_alleles(connection: sqlite3.Connection, serology: str) -> List[str]: """ Look up Serology in the database and return corresponding list of alleles. @@ -142,6 +156,20 @@ def serology_to_alleles(connection: sqlite3.Connection, serology: str) -> List[s alleles = [] return alleles +def is_valid_serology(connection: sqlite3.Connection, serology: str) -> bool: + """ + Check db if the serology exists + + :param connection: db connection of type sqlite.Connection + :param serology: serology to test + :return: is it serology ? + """ + serology_query = "SELECT count(allele_list) from serology_mapping where serology = ?" + cursor = connection.execute(serology_query, (serology,)) + result = cursor.fetchone() + cursor.close() + return result[0] > 0 + def v2_to_v3_allele(connection: sqlite3.Connection, v2_allele: str) -> str: """ @@ -157,22 +185,7 @@ def v2_to_v3_allele(connection: sqlite3.Connection, v2_allele: str) -> str: cursor.close() if result: return result[0] - return '' - - -def is_valid_mac_code(connection: sqlite3.Connection, code: str) -> bool: - """ - Check db if the MAC code exists. - - :param connection: db connection of type sqlite.Connection - :param code: MAC code - :return: code is MAC code ? - """ - mac_query = "SELECT count(alleles) from mac_codes where code = ?" - cursor = connection.execute(mac_query, (code,)) - result = cursor.fetchone() - cursor.close() - return result[0] > 0 + return None def save_dict(connection: sqlite3.Connection, table_name: str, diff --git a/pyard/exceptions.py b/pyard/exceptions.py new file mode 100644 index 0000000..793199f --- /dev/null +++ b/pyard/exceptions.py @@ -0,0 +1,29 @@ +class PyArdError(Exception): + """ + Base Class for All py-ard Errors + """ + pass + + +class InvalidAlleleError(PyArdError): + def __init__(self, message: str) -> None: + self.message = message + + def __str__(self) -> str: + return f"Invalid Allele: {self.message}" + + +class InvalidMACError(PyArdError): + def __init__(self, message: str) -> None: + self.message = message + + def __str__(self) -> str: + return f"Invalid MAC Code: {self.message}" + + +class InvalidTypingError(PyArdError): + def __init__(self, message: str) -> None: + self.message = message + + def __str__(self) -> str: + return f"Invalid HLA Typing: {self.message}" diff --git a/pyard/pyard.py b/pyard/pyard.py index 76db46f..0ce7721 100644 --- a/pyard/pyard.py +++ b/pyard/pyard.py @@ -24,14 +24,12 @@ import functools import sys import re -from typing import Iterable +from typing import Iterable, Literal from . import db -from .data_repository import generate_ars_mapping, \ - generate_mac_codes, generate_alleles_and_xx_codes_and_who, \ - generate_serology_mapping, generate_v2_to_v3_mapping -from .db import is_valid_mac_code, mac_code_to_alleles, v2_to_v3_allele +from . import data_repository as dr from .smart_sort import smart_sort_comparator +from .exceptions import InvalidAlleleError, InvalidMACError, InvalidTypingError HLA_regex = re.compile("^HLA-") @@ -49,7 +47,25 @@ "reduce_XX": True, "reduce_MAC": True, "map_drb345_to_drbx": True, - "verbose_log": True} + "verbose_log": True +} + +reduction_types = ( + 'G', + 'lg', + 'lgx', + 'W', + 'exon' +) + +# Typing information +VALID_REDUCTION_TYPES = Literal['G', 'lg', 'lgx', 'W', 'exon'] + + +def validate_reduction_type(ars_type): + if ars_type not in reduction_types: + raise ValueError(f'Reduction type needs to be one of {reduction_types}') + class ARD(object): """ @@ -57,7 +73,7 @@ class ARD(object): Allows reducing alleles and allele code(MAC) to G, lg and lgx levels. """ - def __init__(self, imgt_version: str = 'Latest', data_dir : str = None, config: dict = None): + def __init__(self, imgt_version: str = 'Latest', data_dir: str = None, config: dict = None): """ ARD will load valid alleles, xx codes and MAC mappings for the given @@ -77,20 +93,17 @@ def __init__(self, imgt_version: str = 'Latest', data_dir : str = None, config: self.db_connection = db.create_db_connection(data_dir, imgt_version) # Load MAC codes - generate_mac_codes(self.db_connection, False) + dr.generate_mac_codes(self.db_connection, False) # Load ARS mappings - self.ars_mappings = generate_ars_mapping(self.db_connection, imgt_version) + self.ars_mappings = dr.generate_ars_mapping(self.db_connection, imgt_version) # Load Alleles and XX Codes self.valid_alleles, self.who_alleles, self.xx_codes, self.who_group = \ - generate_alleles_and_xx_codes_and_who(self.db_connection, imgt_version, self.ars_mappings ) - # Load Alleles and XX Codes - self.valid_alleles, self.who_alleles, self.xx_codes, self.who_group = generate_alleles_and_xx_codes_and_who(self.db_connection, imgt_version, self.ars_mappings) + dr.generate_alleles_and_xx_codes_and_who(self.db_connection, imgt_version, self.ars_mappings) - # Load Serology mappings - generate_serology_mapping(self.db_connection, imgt_version) + dr.generate_serology_mapping(self.db_connection, imgt_version) # Load V2 to V3 mappings - generate_v2_to_v3_mapping(self.db_connection, imgt_version) + dr.generate_v2_to_v3_mapping(self.db_connection, imgt_version) # Close the current read-write db connection self.db_connection.close() @@ -112,21 +125,24 @@ def __del__(self): self.db_connection.close() @functools.lru_cache(maxsize=max_cache_size) - def redux(self, allele: str, ars_type: str) -> str: + def redux(self, allele: str, redux_type: VALID_REDUCTION_TYPES) -> str: """ Does ARS reduction with allele and ARS type :param allele: An HLA allele. :type: str - :param ars_type: The ARS ars_type. + :param redux_type: The ARS ars_type. :type: str :return: ARS reduced allele :rtype: str """ + + validate_reduction_type(redux_type) + # deal with leading 'HLA-' if HLA_regex.search(allele): hla, allele_name = allele.split("-") - redux_allele = self.redux(allele_name, ars_type) + redux_allele = self.redux(allele_name, redux_type) if redux_allele: return "HLA-" + redux_allele else: @@ -139,14 +155,14 @@ def redux(self, allele: str, ars_type: str) -> str: # C*12:02 => C*12:02:01G if allele.endswith(('P', 'G')): - if ars_type in ["lg", "lgx", "G"]: - allele = allele[:-1] - if ars_type == "G" and allele in self.ars_mappings.g_group: + if redux_type in ["lg", "lgx", "G"]: + allele = allele[:-1] + if redux_type == "G" and allele in self.ars_mappings.g_group: if allele in self.ars_mappings.dup_g: return self.ars_mappings.dup_g[allele] else: return self.ars_mappings.g_group[allele] - elif ars_type == "lg": + elif redux_type == "lg": if allele in self.ars_mappings.dup_lg: return self.ars_mappings.dup_lg[allele] elif allele in self.ars_mappings.lg_group: @@ -155,7 +171,7 @@ def redux(self, allele: str, ars_type: str) -> str: # for 'lg' when allele is not in G group, # return allele with only first 2 field return ':'.join(allele.split(':')[0:2]) + 'g' - elif ars_type == "lgx": + elif redux_type == "lgx": if allele in self.ars_mappings.dup_lgx: return self.ars_mappings.dup_lgx[allele] elif allele in self.ars_mappings.lgx_group: @@ -164,15 +180,15 @@ def redux(self, allele: str, ars_type: str) -> str: # for 'lgx' when allele is not in G group, # return allele with only first 2 field return ':'.join(allele.split(':')[0:2]) - elif ars_type == "W": - # new ars_type which is full WHO expansion + elif redux_type == "W": + # new redux_type which is full WHO expansion if self._is_who_allele(allele): return allele if allele in self.who_group: - return self.redux_gl("/".join(self.who_group[allele]), ars_type) + return self.redux_gl("/".join(self.who_group[allele]), redux_type) else: return allele - elif ars_type == "exon": + elif redux_type == "exon": if allele in self.ars_mappings.exon_group: return self.ars_mappings.exon_group[allele] else: @@ -180,28 +196,29 @@ def redux(self, allele: str, ars_type: str) -> str: return ':'.join(allele.split(':')[0:3]) else: if allele.endswith(('P', 'G')): - allele = allele[:-1] + allele = allele[:-1] if self._is_valid_allele(allele): return allele else: - # TODO: raise error - return '' + raise InvalidAlleleError(f"{allele} is an invalid allele.") @functools.lru_cache(maxsize=max_cache_size) - def redux_gl(self, glstring: str, redux_type: str) -> str: + def redux_gl(self, glstring: str, redux_type: VALID_REDUCTION_TYPES) -> str: """ Does ARS reduction with gl string and ARS type :param glstring: A GL String :type: str - :param redux_type: The ARS ars_type. + :param redux_type: The ARS redux_type. :type: str :return: ARS reduced allele :rtype: str """ + validate_reduction_type(redux_type) + if not self.isvalid_gl(glstring): - return "" + raise InvalidTypingError(f"{glstring} is not a valid typing.") if re.search(r"\^", glstring): return "^".join(sorted(set([self.redux_gl(a, redux_type) for a in glstring.split("^")]), @@ -223,7 +240,7 @@ def redux_gl(self, glstring: str, redux_type: str) -> str: key=functools.cmp_to_key(smart_sort_comparator))) # Handle V2 to V3 mapping - if self._config["reduce_v2"] and self.is_v2(glstring): + if self.is_v2(glstring): glstring = self._map_v2_to_v3(glstring) return self.redux_gl(glstring, redux_type) @@ -232,12 +249,11 @@ def redux_gl(self, glstring: str, redux_type: str) -> str: alleles = self._get_alleles_from_serology(glstring) return self.redux_gl("/".join(alleles), redux_type) - if ":" in glstring: + if ":" in glstring: loc_allele = glstring.split(":") loc_antigen, code = loc_allele[0], loc_allele[1] else: - # TODO: raise error - return '' + raise InvalidTypingError(f"{glstring} is not a valid V2 or Serology typing.") # Handle XX codes if self._config["reduce_XX"] and self.is_XX(glstring, loc_antigen, code): @@ -245,7 +261,7 @@ def redux_gl(self, glstring: str, redux_type: str) -> str: # Handle MAC if self._config["reduce_MAC"] and self.is_mac(glstring): - if is_valid_mac_code(self.db_connection, code): + if db.is_valid_mac_code(self.db_connection, code): if HLA_regex.search(glstring): # Remove HLA- prefix allele_name = glstring.split("-")[1] @@ -256,19 +272,26 @@ def redux_gl(self, glstring: str, redux_type: str) -> str: alleles = self._get_alleles(code, loc_antigen) return self.redux_gl("/".join(alleles), redux_type) else: - # future: raise ValueError - return '' + raise InvalidMACError(f"{glstring} is an invalid MAC.") + return self.redux(glstring, redux_type) def is_XX(self, glstring: str, loc_antigen: str = None, code: str = None) -> bool: if loc_antigen is None or code is None: - loc_allele = glstring.split(":") - loc_antigen, code = loc_allele[0], loc_allele[1] - return self.is_mac(glstring) and code == "XX" and loc_antigen in self.xx_codes + if ':' in glstring: + loc_allele = glstring.split(":") + loc_antigen, code = loc_allele[0], loc_allele[1] + else: + return False + return code == "XX" and loc_antigen in self.xx_codes - @staticmethod - def is_serology(allele: str) -> bool: + def is_serology(self, allele: str) -> bool: """ + + Strict validation of serology: + Does not have * or : in serology. + If it exists in the database, it's serology otherwise it's not serology. + A serology has the locus name (first 2 letters for DRB1, DQB1) of the allele followed by numerical antigen. Cw is the serological designation for HLA-C @@ -279,45 +302,43 @@ def is_serology(allele: str) -> bool: if '*' in allele or ':' in allele: return False - locus = allele[0:2] - if locus in ['DR', 'DP', 'DQ', 'Cw']: - antigen = allele[2:] - return antigen.isdigit() - - locus = allele[0:1] - if locus in ['A', 'B']: - antigen = allele[1:] - return antigen.isdigit() + return db.is_valid_serology(self.db_connection, allele) - return False - - @staticmethod - def is_mac(gl: str) -> bool: - # TODO: need a more stringent test here - # not all strings are MACs e.g. ":THISISNOTAMAC" + def is_mac(self, allele: str) -> bool: """ MAC has non-digit characters after the : character. - :param gl: glstring to test if it has a MAC code + Strict validation of MAC. + The allele is a MAC code if it exists in the database. + Not all strings are MACs e.g. ":THISISNOTAMAC" + + :param allele: test if it is a MAC code :return: True if MAC """ - return re.search(r":\D+", gl) is not None + if ':' in allele: + code = allele.split(":")[1] + return db.is_valid_mac_code(self.db_connection, code) + return False - @staticmethod - def is_v2(allele: str) -> bool: - # TODO: need a more stringent test here - # not all strings with "*" but not ":" are v2 nomenclature e.g. "this s*it" + def is_v2(self, allele: str) -> bool: """ Version 2 of the nomenclature is a single field. It does not have any ':' field separator. Eg: A*0104 Exceptions: + Not all strings with "*" but not ":" are v2 nomenclature DRB3*NNNN is not v2 allele + Stricter Check: + if the conversion of v2 to v3 is the same, then + it's not a V2 typing + Set 'reduce_v2' option to False to skip the check for V2. + :param allele: Possible allele :return: Is the allele in V2 nomenclature """ - return '*' in allele and ':' not in allele \ - and not allele.endswith('*NNNN') + return self._config["reduce_v2"] \ + and '*' in allele and ':' not in allele \ + and allele != self._map_v2_to_v3(allele) def _is_who_allele(self, allele): """ @@ -342,7 +363,7 @@ def _get_alleles(self, code, locus_antigen) -> Iterable[str]: :param locus_antigen: locus name for alleles :return: valid alleles corresponding to allele code """ - alleles = mac_code_to_alleles(self.db_connection, code) + alleles = db.mac_code_to_alleles(self.db_connection, code) # It's an allelic expansion if any of the alleles have a `:` # else it's a group expansion @@ -402,7 +423,7 @@ def _map_v2_to_v3(self, v2_allele): :return: V3 versioned allele """ # Check if it's in the exception case mapping - v3_allele = v2_to_v3_allele(self.db_connection, v2_allele) + v3_allele = db.v2_to_v3_allele(self.db_connection, v2_allele) if not v3_allele: # Try and predict V3 v3_allele = self._predict_v3(v2_allele) @@ -431,6 +452,7 @@ def isvalid(self, allele: str) -> bool: return False if not self.is_mac(allele) and \ + not self.is_XX(allele) and \ not self.is_serology(allele) and \ not self.is_v2(allele): # Alleles ending with P or G are valid_alleles @@ -440,7 +462,7 @@ def isvalid(self, allele: str) -> bool: if self._is_valid_allele(allele): return True else: - # reduce to 2 field for things like DPB1*28:01:01G + # reduce to 2 field for things like DPB1*28:01:01G allele = ':'.join(allele.split(':')[0:2]) return self._is_valid_allele(allele) return True @@ -481,15 +503,15 @@ def mac_toG(self, allele: str) -> str: locus_antigen, code = allele.split(":") if HLA_regex.search(allele): locus_antigen = locus_antigen.split("-")[1] # Remove HLA- prefix - if is_valid_mac_code(self.db_connection, code): + if db.is_valid_mac_code(self.db_connection, code): alleles = self._get_alleles(code, locus_antigen) group = [self.toG(a) for a in alleles] if "X" in group: - return '' + raise InvalidMACError(f"{allele} is an invalid MAC.") else: return "/".join(group) else: - return '' + raise InvalidMACError(f"{allele} is an invalid MAC.") def toG(self, allele: str) -> str: """ @@ -518,14 +540,14 @@ def expand_mac(self, mac_code: str): :rtype: List """ locus_antigen, code = mac_code.split(":") - if is_valid_mac_code(self.db_connection, code): + if db.is_valid_mac_code(self.db_connection, code): if HLA_regex.search(mac_code): locus_antigen = locus_antigen.split("-")[1] # Remove HLA- prefix return ['HLA-' + a for a in self._get_alleles(code, locus_antigen)] else: return list(self._get_alleles(code, locus_antigen)) - return '' + raise InvalidMACError(f"{mac_code} is an invalid MAC.") def v2_to_v3(self, v2_allele) -> str: """ @@ -543,4 +565,4 @@ def refresh_mac_codes(self) -> None: Refreshes MAC code for the current IMGT db version. :return: None """ - generate_mac_codes(self.db_connection, True) + dr.generate_mac_codes(self.db_connection, True) diff --git a/scripts/pyard-reduce-csv b/scripts/pyard-reduce-csv index 59e453c..8f0eddf 100755 --- a/scripts/pyard-reduce-csv +++ b/scripts/pyard-reduce-csv @@ -37,6 +37,7 @@ import pandas as pd import pyard import pyard.drbx as drbx +from pyard.exceptions import PyArdError def is_serology(allele: str) -> bool: @@ -99,7 +100,7 @@ def reduce(allele, locus, column_name): # print(f"reducing '{locus_allele}'") try: reduced_allele = ard.redux_gl(locus_allele, ard_config["redux_type"]) - except RuntimeError as e: + except PyArdError as e: if verbose: print(e) message = f"Failed reducing '{locus_allele}' in column {column_name}" @@ -170,7 +171,7 @@ if __name__ == '__main__': sys.exit(1) # Instantiate py-ard object with the latest - ard = pyard.ARD(remove_invalid=False) + ard = pyard.ARD() # Read the Input File # Read only the columns to be saved. diff --git a/setup.cfg b/setup.cfg index 9917d39..f921a1e 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.6.9 +current_version = 0.7.0 commit = True tag = True diff --git a/setup.py b/setup.py index f3cc342..e8fb423 100644 --- a/setup.py +++ b/setup.py @@ -25,7 +25,7 @@ from setuptools import setup -with open('README.rst') as readme_file: +with open('README.md') as readme_file: readme = readme_file.read() with open('HISTORY.rst') as history_file: @@ -42,7 +42,7 @@ setup( name='py-ard', - version='0.6.9', + version='0.7.0', description="ARD reduction for HLA with Python", long_description=readme + '\n\n' + history, author="CIBMTR", diff --git a/tests/steps/redux_allele.py b/tests/steps/redux_allele.py index a997971..409f5e8 100644 --- a/tests/steps/redux_allele.py +++ b/tests/steps/redux_allele.py @@ -1,6 +1,8 @@ from behave import given, when, then from hamcrest import assert_that, is_ +from pyard.exceptions import PyArdError + @given('the allele as {allele}') def step_impl(context, allele): @@ -16,13 +18,14 @@ def step_impl(context, level): @when('reducing on the {level} level (ambiguous)') def step_impl(context, level): context.level = level - context.redux_allele = context.ard.redux_gl(context.allele, level) + try: + context.redux_allele = context.ard.redux_gl(context.allele, level) + except PyArdError: + context.redux_allele = 'X' @then('the reduced allele is found to be {redux_allele}') def step_impl(context, redux_allele): - if redux_allele == 'X': - redux_allele = '' assert_that(context.redux_allele, is_(redux_allele)) @@ -45,9 +48,10 @@ def step_impl(context, allele): def step_impl(context, level): context.expanded_alleles = context.ard.redux_gl(context.allele, level) + @when("expanding to WHO then reducing to the {level} level") def step_impl(context, level): - context.expanded_alleles = context.ard.redux_gl(context.ard.redux_gl(context.allele,"W"), level) + context.expanded_alleles = context.ard.redux_gl(context.ard.redux_gl(context.allele, "W"), level) @then("the expanded allele is found to be {expanded_alleles}") diff --git a/tests/test_pyard.py b/tests/test_pyard.py index 425c4f6..7e124a7 100644 --- a/tests/test_pyard.py +++ b/tests/test_pyard.py @@ -32,7 +32,9 @@ import os import unittest +import pyard.pyard from pyard import ARD +from pyard.exceptions import InvalidAlleleError, InvalidMACError, InvalidTypingError class TestPyArd(unittest.TestCase): @@ -85,7 +87,8 @@ def test_serology(self): def test_mac_G(self): self.assertEqual(self.ard.redux("A*01:01:01", 'G'), "A*01:01:01G") self.assertEqual(self.ard.redux_gl("HLA-A*01:AB", "G"), "HLA-A*01:01:01G/HLA-A*01:02") - self.assertEqual(self.ard.redux("HLA-A*01:AB", "G"), "") + with self.assertRaises(InvalidAlleleError): + self.ard.redux("HLA-A*01:AB", "G") def test_xx_code(self): expanded_string = """ @@ -110,4 +113,30 @@ def test_expand_mac(self): def test_mac_toG(self): g_alleles = 'A*01:01:01G/A*01:03:01G' self.assertEqual(self.ard.mac_toG('A*01:AC'), g_alleles) - self.assertEqual(self.ard.mac_toG('A*01:AB'), '') + with self.assertRaises(InvalidMACError): + self.ard.mac_toG('A*01:AB') + + def test_redux_types(self): + self.assertIsNone(pyard.pyard.validate_reduction_type('G')) + self.assertIsNone(pyard.pyard.validate_reduction_type('lg')) + self.assertIsNone(pyard.pyard.validate_reduction_type('lgx')) + self.assertIsNone(pyard.pyard.validate_reduction_type('W')) + self.assertIsNone(pyard.pyard.validate_reduction_type('exon')) + with self.assertRaises(ValueError): + pyard.pyard.validate_reduction_type('XX') + + def test_empty_allele(self): + with self.assertRaises(InvalidTypingError): + self.ard.redux_gl('A*', 'lgx') + + def test_fp_allele(self): + with self.assertRaises(InvalidTypingError): + self.ard.redux_gl('A*0.123', 'lgx') + + def test_invalid_serology(self): + # Test that A10 works and the first one is 'A*25:01' + serology_a10 = self.ard.redux_gl('A10', 'lgx') + self.assertEqual(serology_a10.split('/')[0], 'A*25:01') + # And A100 isn't a valid typing + with self.assertRaises(InvalidTypingError): + self.ard.redux_gl('A100', 'lgx') \ No newline at end of file