Merge 8bf8e94 into c7a580b

openvax · Feb 22, 2018 · 3c5a84c · 3c5a84c
2 parents c7a580b + 8bf8e94
commit 3c5a84c
Show file tree

Hide file tree

Showing 3 changed files with 27 additions and 6 deletions.
diff --git a/mhcnames/__init__.py b/mhcnames/__init__.py
@@ -7,7 +7,7 @@
 )
 from .allele_parse_error import AlleleParseError
 
-__version__ = "0.4.4"
+__version__ = "0.4.5"
 
 __all__ = [
     "AlleleName",

diff --git a/mhcnames/allele_name.py b/mhcnames/allele_name.py
@@ -104,15 +104,15 @@ def parse_allele_name(name, species_prefix=None):
         if gene.isalpha():
             # expand e.g. DRA -> DRA1, DQB -> DQB1
             gene = gene + "1"
+    elif len(name) == 5:
+        # example: SLA-30101
+        gene, name = name[0], name[1:]
     elif name[0].isalpha():
         # if there are more separators to come, then assume the gene names
         # can have the form "DQA1"
         gene, name = parse_letters(name)
     elif name[0].isdigit():
         gene, name = parse_numbers(name)
-    elif len(name) == 5:
-        # example: SLA-30101
-        gene, name = name[0], name[1:]
     elif len(name) in (6, 7) and ("*" in name or "-" in name or ":" in name):
         # example: SLA-3*0101 or SLA-3*01:01
         gene, name = parse_alphanum(name)
@@ -127,7 +127,6 @@ def parse_allele_name(name, species_prefix=None):
         raise AlleleParseError("Malformed MHC type %s" % original)
 
     gene = gene.upper()
-
     # skip initial separator
     sep, name = parse_separator(name)
 

diff --git a/test/test_swine.py b/test/test_swine.py
@@ -1,11 +1,16 @@
+"""
+Pig allele names from:
+    Analyzing the genetic characteristics and function of the swine
+    leukocyte antigen 2 gene in a Chinese inbreed of pigs
+"""
 
 from mhcnames import (
     parse_allele_name,
     AlleleName,
 )
 from nose.tools import eq_
 
-def test_SLA_1_0101():
+def test_SLA_1_0101_with_seps():
     eq_(
         parse_allele_name("SLA-1*01:01"),
         AlleleName("SLA", "1", "01", "01"))
@@ -14,3 +19,20 @@ def test_SLA_1_HB01():
     eq_(
         parse_allele_name("SLA-1-HB01"),
         AlleleName("SLA", "1", "HB", "01"))
+
+def test_SLA_1_0101_no_seps():
+    eq_(
+        parse_allele_name("SLA-10101"),
+        AlleleName("SLA", "1", "01", "01"))
+
+def test_SLA_2_07we01():
+    eq_(parse_allele_name("SLA-2*07we01"),
+        AlleleName("SLA", "2", "07we", "01"))
+
+def test_SLA_2_jh01():
+    eq_(parse_allele_name("SLA-2*jh01"),
+        AlleleName("SLA", "2", "jh", "01"))
+
+def test_SLA_2_w09pt22():
+    eq_(parse_allele_name("SLA-2*w09pt22"),
+        AlleleName("SLA", "2", "w09pt", "22"))