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Build fail: KeyError 'MIM Number' #106

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merged 1 commit into from
Oct 15, 2023
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Build fail: KeyError 'MIM Number' #106

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20 changes: 17 additions & 3 deletions omim2obo/parsers/omim_txt_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -224,8 +224,22 @@ def get_hgnc_map(filename, symbol_col, mim_col='MIM Number') -> Dict:
"""Get HGNC Map"""
map = {}
input_path = os.path.join(DATA_DIR, filename)
df = pd.read_csv(input_path, delimiter='\t', comment='#').fillna('')
df[mim_col] = df[mim_col].astype(int) # these were being read as floats
try:
df = pd.read_csv(input_path, delimiter='\t', comment='#').fillna('')
df[mim_col] = df[mim_col].astype(int) # these were being read as floats
# TODO: Need a better solution than this. Which should be: When these files are downloaded, should uncomment header
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The issue

I'm not sure why this suddenly started happening, where the header is missing from the files. This is what is causing the KeyError causing the action to fail.

The solution

The best way to fix this would be to do things at download time for all the files. But in the interest of time, I fixed it at the point of failure.
Need a better solution than this. Which should be: When these files are downloaded, should uncomment header

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What issue is this solving? Sorry I was in a big hole, but getting back to life now!

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That's all right. Thanks for checking in on this. I wanted more time to look more deeply into the root cause and fix the issue upstream in a better way, but basically I did a quick fix.

Basically what's happening is that when the TSVs are downloaded, there are a few comment lines, including the header is commented out. So we do a special operation to uncomment that header . For some reason it suddenly it wasn't getting uncommented

except KeyError:
with open(input_path, 'r') as f:
lines = f.readlines()
header = lines[3]
if not header.startswith('# Chromosome'):
raise RuntimeError(f'Error parsing header for: {input_path}')
lines[3] = header[2:]
with open(input_path, 'w') as f:
f.writelines(lines)
finally:
df = pd.read_csv(input_path, delimiter='\t', comment='#').fillna('')
df[mim_col] = df[mim_col].astype(int) # these were being read as floats

for index, row in df.iterrows():
symbol = row[symbol_col]
Expand All @@ -237,7 +251,7 @@ def get_hgnc_map(filename, symbol_col, mim_col='MIM Number') -> Dict:
return map


def parse_mim2gene(lines, filename='mim2gene.tsv', filename2='genemap2.tsv') -> Tuple[Dict, Dict, Dict]:
def parse_mim2gene(lines: List[str], filename='mim2gene.tsv', filename2='genemap2.tsv') -> Tuple[Dict, Dict, Dict]:
"""Parse OMIM # 2 gene file
todo: ideally replace this whole thing with pandas
todo: How to reconcile inconsistent mim#::hgnc_symbol mappings?
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