From c5e2cb268bcd8518e6da730dfefe37e4f570487b Mon Sep 17 00:00:00 2001
From: Peter Kruczkiewicz <peter.kruczkiewicz@gmail.com>
Date: Tue, 30 Mar 2021 04:28:43 -0500
Subject: [PATCH 1/2] Fix SnpEff/SnpSift parsing

---
 xlavir/tools/variants.py | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/xlavir/tools/variants.py b/xlavir/tools/variants.py
index 2596f90..f29fe26 100644
--- a/xlavir/tools/variants.py
+++ b/xlavir/tools/variants.py
@@ -194,21 +194,26 @@ def parse_aa(gene: str,
 
     if effect == 'stop_lost':
         alt_aa = get_aa(alt_aa.replace('ext', ''))
-        return f'{ref}{nt_pos}{alt}({gene}:{ref_aa}{aa_pos}{alt_aa}[stop_lost])'
+        return f'{ref}{nt_pos}{alt}({gene}:{ref_aa}{aa_pos_str}{alt_aa}[stop_lost])'
     if effect == 'frameshift_variant':
-        return f'{ref}{nt_pos}{alt}({gene}:{ref_aa}{aa_pos}[FRAMESHIFT])'
+        return f'{ref}{nt_pos}{alt}({gene}:{ref_aa}{aa_pos_str}[FRAMESHIFT])'
     if effect == 'conservative_inframe_deletion':
-        return f'{ref}{nt_pos}{alt}({gene}:{ref_aa}{aa_pos}{alt_aa})'
+        return f'{ref}{nt_pos}{alt}({gene}:{ref_aa}{aa_pos_str}{alt_aa})'
+    if effect == 'disruptive_inframe_deletion':
+        return f'{ref}{nt_pos}{alt}({gene}:{ref_aa}{aa_pos_str}{alt_aa}[disruptive_inframe_deletion])'
 
     alt_aa = get_aa(alt_aa)
-    return f'{ref}{nt_pos}{alt}({gene}:{ref_aa}{aa_pos}{alt_aa})'
+    return f'{ref}{nt_pos}{alt}({gene}:{ref_aa}{aa_pos_str}{alt_aa})'
 
 
 def get_aa(s: str) -> str:
     out = ''
     for i in range(0, len(s), 3):
         aa = s[i: i + 3]
-        aa_code = aa_codes[aa.upper()]
+        try:
+            aa_code = aa_codes[aa.upper()]
+        except KeyError:
+            aa_code = aa
         out += aa_code
     return out
 

From 958513391f40192c4b96f38dd24db84eeb05cb20 Mon Sep 17 00:00:00 2001
From: Peter Kruczkiewicz <peter.kruczkiewicz@gmail.com>
Date: Tue, 30 Mar 2021 04:28:55 -0500
Subject: [PATCH 2/2] =?UTF-8?q?Bump=20version:=200.2.1=20=E2=86=92=200.2.2?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 setup.cfg          | 2 +-
 setup.py           | 2 +-
 xlavir/__init__.py | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index fd09a8e..b96fd27 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.1
+current_version = 0.2.2
 commit = True
 tag = True
 
diff --git a/setup.py b/setup.py
index 904e9ce..369a267 100644
--- a/setup.py
+++ b/setup.py
@@ -58,6 +58,6 @@
     test_suite='tests',
     tests_require=test_requirements,
     url='https://github.com/peterk87/xlavir',
-    version='0.2.1',
+    version='0.2.2',
     zip_safe=False,
 )
diff --git a/xlavir/__init__.py b/xlavir/__init__.py
index cc7b867..04db824 100644
--- a/xlavir/__init__.py
+++ b/xlavir/__init__.py
@@ -2,4 +2,4 @@
 
 __author__ = """Peter Kruczkiewicz"""
 __email__ = 'peter.kruczkiewicz@gmail.com'
-__version__ = '0.2.1'
+__version__ = '0.2.2'