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Expanded handling for protein strings #20

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Expanded handling for protein strings #20

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3a99f2d
added 1-letter amino acid codes
jeargle May 28, 2015
55b7541
added termination suffix to frameshift (fs)
jeargle May 28, 2015
bb86c03
Fix install error when PIP 10 is installed
tskir May 11, 2018
b587284
Merge pull request #1 from tskir/patch-1
chenghlee Jul 30, 2018
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4 changes: 2 additions & 2 deletions pyhgvs/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -170,12 +170,12 @@ 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 + ")"

PEP_EXTRA = "(?P<extra>(|=|\?)(|fs))"
PEP_EXTRA = "(?P<extra>(|=|\?)(|fs((Ter|\*)\d+)?))"

# Peptide allele syntax
PEP_ALLELE = [
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8 changes: 6 additions & 2 deletions setup.py
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Original file line number Diff line number Diff line change
@@ -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, "
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