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| author | zsloan | 2021-10-12 18:56:34 +0000 |
|---|---|---|
| committer | zsloan | 2021-10-12 18:56:34 +0000 |
| commit | 0f396f4a1a753d449cf2975fc425d587d9350689 (patch) | |
| tree | c9dac243dc05e5cb90ccb7f1d96fd599986bf60a /gn3/computations/parsers.py | |
| parent | 976660ce9ef915426c7ce5ff9077b439e4102a2c (diff) | |
| parent | 77c274b79c3ec01de60e90db3299763cb58f715b (diff) | |
| download | genenetwork3-0f396f4a1a753d449cf2975fc425d587d9350689.tar.gz | |
Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into feature/add_rqtl_pairscan
Diffstat (limited to 'gn3/computations/parsers.py')
| -rw-r--r-- | gn3/computations/parsers.py | 10 |
1 files changed, 5 insertions, 5 deletions
diff --git a/gn3/computations/parsers.py b/gn3/computations/parsers.py index 94387ff..1af35d6 100644 --- a/gn3/computations/parsers.py +++ b/gn3/computations/parsers.py @@ -14,7 +14,7 @@ def parse_genofile(file_path: str) -> Tuple[List[str], 'h': 0, 'u': None, } - genotypes, strains = [], [] + genotypes, samples = [], [] with open(file_path, "r") as _genofile: for line in _genofile: line = line.strip() @@ -22,8 +22,8 @@ def parse_genofile(file_path: str) -> Tuple[List[str], continue cells = line.split() if line.startswith("Chr"): - strains = cells[4:] - strains = [strain.lower() for strain in strains] + samples = cells[4:] + samples = [sample.lower() for sample in samples] continue values = [__map.get(value.lower(), None) for value in cells[4:]] genotype = { @@ -32,7 +32,7 @@ def parse_genofile(file_path: str) -> Tuple[List[str], "cm": cells[2], "mb": cells[3], "values": values, - "dicvalues": dict(zip(strains, values)), + "dicvalues": dict(zip(samples, values)), } genotypes.append(genotype) - return strains, genotypes + return samples, genotypes |