From 3a99f2daab83198590130c18cc36eb58aba9b6f6 Mon Sep 17 00:00:00 2001
From: John Eargle <jeargle@gmail.com>
Date: Thu, 28 May 2015 14:23:55 -0500
Subject: [PATCH 1/3] added 1-letter amino acid codes

---
 pyhgvs/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyhgvs/__init__.py b/pyhgvs/__init__.py
index c9b2c1b..0a11c70 100644
--- a/pyhgvs/__init__.py
+++ b/pyhgvs/__init__.py
@@ -170,7 +170,7 @@ class HGVSRegex(object):
                            for regex in CDNA_ALLELE]
 
     # Peptide syntax
-    PEP = "([A-Z]([a-z]{2}))+"
+    PEP = "(([A-Z]([a-z]{2}))|([GAVLIMFWPSTCYNQDEKRH\*]))+"
     PEP_REF = "(?P<ref>" + PEP + ")"
     PEP_REF2 = "(?P<ref2>" + PEP + ")"
     PEP_ALT = "(?P<alt>" + PEP + ")"

From 55b7541a5df9c58b92c4459b279ccbdd027f6cdb Mon Sep 17 00:00:00 2001
From: John Eargle <jeargle@gmail.com>
Date: Thu, 28 May 2015 16:19:34 -0500
Subject: [PATCH 2/3] added termination suffix to frameshift (fs)

---
 pyhgvs/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyhgvs/__init__.py b/pyhgvs/__init__.py
index 0a11c70..663c154 100644
--- a/pyhgvs/__init__.py
+++ b/pyhgvs/__init__.py
@@ -175,7 +175,7 @@ class HGVSRegex(object):
     PEP_REF2 = "(?P<ref2>" + PEP + ")"
     PEP_ALT = "(?P<alt>" + PEP + ")"
 
-    PEP_EXTRA = "(?P<extra>(|=|\?)(|fs))"
+    PEP_EXTRA = "(?P<extra>(|=|\?)(|fs((Ter|\*)\d+)?))"
 
     # Peptide allele syntax
     PEP_ALLELE = [

From bb86c0372a21b313022b3e5d31c9e829a8389ec5 Mon Sep 17 00:00:00 2001
From: Kirill Tsukanov <tskir@users.noreply.github.com>
Date: Fri, 11 May 2018 12:01:02 +0300
Subject: [PATCH 3/3] Fix install error when PIP 10 is installed

Since PIP 10 has a different module structure, two import calls fail. This change fixes it, while stitll maintaining compatibility with PIP 9 or earlier.
---
 setup.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index ace27d1..3ca2cef 100644
--- a/setup.py
+++ b/setup.py
@@ -1,8 +1,12 @@
 #!/usr/bin/env python
 
 from setuptools import setup
-from pip.req import parse_requirements
-from pip.download import PipSession
+try:  # pip 9 or earlier
+    from pip.req import parse_requirements
+    from pip.download import PipSession
+except ImportError:  # pip 10 or later
+    from pip._internal.req import parse_requirements
+    from pip._internal.download import PipSession
 import sys
 
 description = ("This library provides a simple to use Python API for parsing, "