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Fixing errors in the repo setup #3

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Fixing errors in the repo setup #3

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9e38946
fix naming issue deep_ancestry, redirecting to flan
TheVidz Mar 30, 2026
242990b
error in qc.py file causing issue on "prepare"
TheVidz Mar 30, 2026
e9e9d8a
fix num folds error in sample_splitter
TheVidz Mar 30, 2026
a339c66
Fixing Error: --read-freq variant ID '.' appears multiple times
TheVidz Mar 31, 2026
e0d0bd1
revert commit a339c66
TheVidz May 24, 2026
ffa8170
coment-out commit e9e9d8a
TheVidz May 24, 2026
2de0dc6
revert commit 242990b
TheVidz May 24, 2026
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1 change: 1 addition & 0 deletions deep_ancestry/__init__.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
from flan import *
2 changes: 0 additions & 2 deletions flan/preprocess/qc.py
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Expand Up @@ -14,14 +14,12 @@ class QCArgs:
class QC:
def __init__(self, qc_config: Dict) -> None:
self.qc_config = qc_config

def fit_transform(self, cache: FileCache) -> None:
run_plink(args_list=['--pfile', str(cache.pfile_path()), 'vzs', '--make-pgen'],
args_dict={**{'--out': str(cache.pfile_path()), # Merging dicts here
'--set-missing-var-ids': '@:#'},
**self.qc_config})


def transform(self, source_path: str, dest_path: str) -> None:
run_plink(args_list=['--make-pgen', '--pfile', str(source_path)],
args_dict={**{'--out': str(dest_path),
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8 changes: 6 additions & 2 deletions flan/preprocess/sample_splitter.py
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Expand Up @@ -29,6 +29,10 @@ def _split_ids(self,
y: y can be passed to trigger StratifiedKFold instead of KFold
random_state (int): Fixed random_state for train_test_split sklearn function
"""
# adding min 5 folds
# num_folds = getattr(self.args, "num_folds", 5)
# self.args.num_folds = num_folds

ids = pandas.read_table(cache.ids_path()).rename(columns={'#IID': 'IID'}).filter(['FID', 'IID'])
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indices = numpy.arange(ids.shape[0])
if self.args.num_folds == 1:
Expand Down Expand Up @@ -75,7 +79,7 @@ def _split_genotypes(self, cache: FileCache) -> None:
'--out': str(cache.pfile_path(fold_index, part))
},
args_list=['--make-pgen']
)
)

def _split_phenotypes(self, cache: FileCache) -> None:
phenotype = pandas.read_table(cache.phenotype_path(), names=['IID', 'ancestry', 'in_phase3'])
Expand All @@ -89,7 +93,7 @@ def _split_phenotypes(self, cache: FileCache) -> None:
)

def fit_transform(self, cache: FileCache) -> None:

self._split_ids(cache)
self._split_genotypes(cache)
self._split_phenotypes(cache)
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