INNER CODE UNIT · Python
in_vcf_not_in_ped
brentp/peddy · peddy/cli.py:186
in_vcf_not_in_ped = samples - set(ped_df.index)
in_ped_not_in_vcf = set(ped_df.index) - samples
if in_vcf_not_in_ped:
log.warning("%d samples in vcf not in ped:\n%s\n" %
(len(in_vcf_not_in_ped), ",".join(in_vcf_not_in_ped)))
if in_ped_not_in_vcf:
log.warning("%d samples in ped not in vcf:\n%s\n" %
(len(in_ped_not_in_vcf), ",".join(in_ped_not_in_vcf)))
# keep order.
samples = [s for s in ped_df['sample_id'] if s in samples]
ped_df = ped_df.loc[samples, :]
keep_cols = {"ped_check": [],
"het_check": ["call_rate", "het_ratio", "mean_depth", "idr_baf", "ancestry-prediction", "PC1", "PC2", "PC3"],
"sex_check": ["het_ratio", "error"]}