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' 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