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bugfix: Convert missing ancestry to Other category for grafpop output (Issue 326) #331

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merged 2 commits into from
Sep 26, 2024
Merged

bugfix: Convert missing ancestry to Other category for grafpop output (Issue 326) #331

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03770cf
Reformat missing ancestry to Other
Sep 26, 2024
eec673b
Merge pull request #330 from NCI-CGR/default
carynwillis Sep 26, 2024
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46 changes: 28 additions & 18 deletions src/cgr_gwas_qc/workflow/scripts/sample_qc_table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -192,7 +192,9 @@ def main(
)

add_qc_columns(
sample_qc, remove_contam, remove_rep_discordant,
sample_qc,
remove_contam,
remove_rep_discordant,
)

sample_qc = sample_qc.rename(
Expand Down Expand Up @@ -328,19 +330,20 @@ def _read_GRAF(file_name: Path, Sample_IDs: pd.Index) -> pd.DataFrame:
.. _manuscript: https://pubmed.ncbi.nlm.nih.gov/31151998/

"""
return (
pd.read_csv(file_name, sep="\t")
.assign(
Sample_ID=lambda x: x["Subject"].astype(str)
) # Issue 216: When subject IDs are numeric reindex fails. This makes sure index Sample_ID will always be as a character
.assign(Ancestry=lambda x: x["Computed population"].str.replace(" ", "_"))
.assign(AFR=lambda x: x["P_f (%)"] / 100)
.assign(EUR=lambda x: x["P_e (%)"] / 100)
.assign(ASN=lambda x: x["P_a (%)"] / 100)
.set_index("Sample_ID")
.loc[:, ("AFR", "EUR", "ASN", "Ancestry")]
.reindex(Sample_IDs)
)

graf = pd.read_csv(file_name, sep="\t")
graf = graf.assign(
Sample_ID=lambda x: x["Subject"].astype(str)
) # Issue 216: When subject IDs are numeric reindex fails. This makes sure index Sample_ID will always be as a character
graf = graf.assign(Ancestry=lambda x: x["Computed population"].str.replace(" ", "_"))
graf = graf.assign(AFR=lambda x: x["P_f (%)"] / 100)
graf = graf.assign(EUR=lambda x: x["P_e (%)"] / 100)
graf = graf.assign(ASN=lambda x: x["P_a (%)"] / 100)
graf = graf.set_index("Sample_ID")
graf = graf.loc[:, ("AFR", "EUR", "ASN", "Ancestry")]
graf["Ancestry"] = graf["Ancestry"].fillna("Other")
graf = graf.reindex(Sample_IDs)
return graf


def _read_SNPweights(file_name: Path, Sample_IDs: pd.Index) -> pd.DataFrame:
Expand Down Expand Up @@ -411,7 +414,8 @@ def _read_contam(file_name: Optional[Path], Sample_IDs: pd.Index) -> pd.DataFram

if file_name is None:
return pd.DataFrame(
index=Sample_IDs, columns=["Contamination_Rate", "is_contaminated"],
index=Sample_IDs,
columns=["Contamination_Rate", "is_contaminated"],
).astype({"Contamination_Rate": "float", "is_contaminated": "boolean"})

return (
Expand Down Expand Up @@ -454,12 +458,16 @@ def _read_intensity(file_name: Optional[Path], Sample_IDs: pd.Index) -> pd.Serie


def add_qc_columns(
sample_qc: pd.DataFrame, remove_contam: bool, remove_rep_discordant: bool,
sample_qc: pd.DataFrame,
remove_contam: bool,
remove_rep_discordant: bool,
) -> pd.DataFrame:
add_call_rate_flags(sample_qc)
_add_identifiler(sample_qc)
_add_analytic_exclusion(
sample_qc, remove_contam, remove_rep_discordant,
sample_qc,
remove_contam,
remove_rep_discordant,
)
_add_subject_representative(sample_qc)
_add_subject_dropped_from_study(sample_qc)
Expand Down Expand Up @@ -505,7 +513,9 @@ def reason_string(row: pd.Series) -> str:


def _add_analytic_exclusion(
sample_qc: pd.DataFrame, remove_contam: bool, remove_rep_discordant: bool,
sample_qc: pd.DataFrame,
remove_contam: bool,
remove_rep_discordant: bool,
) -> pd.DataFrame:
"""Adds a flag to remove samples based on provided conditions.

Expand Down
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