0.7.0 Version: Stricter Validation

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
+```
+

pyard/__init__.py

@@ -24,4 +24,4 @@
 from .pyard import ARD
 
 __author__ = """NMDP Bioinformatics"""
-__version__ = '0.6.9'
+__version__ = '0.7.0'

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,