diff options
| -rw-r--r-- | pyhegp/pyhegp.py | 9 |
1 files changed, 5 insertions, 4 deletions
diff --git a/pyhegp/pyhegp.py b/pyhegp/pyhegp.py index ef18ede..48d0ea2 100644 --- a/pyhegp/pyhegp.py +++ b/pyhegp/pyhegp.py @@ -210,7 +210,7 @@ def pool_command(pooled_summary_file, summary_files): max_snps = max(len(summary.data) for summary in summaries) if len(pooled_summary.data) < max_snps: dropped_snps = max_snps - len(pooled_summary.data) - print(f"Dropped {dropped_snps} SNP(s)") + print(f"Dropped {dropped_snps} SNP(s) that were not present in all datasets") write_summary(pooled_summary_file, pooled_summary) @main.command("encrypt") @@ -266,20 +266,21 @@ def encrypt_command(genotype_file, phenotype_file, summary_file, # discriminatory power in the analysis and mess with our # standardization by causing a division by zero. summary_subset = drop_zero_stddev_snps(summary) + if (dropped_zero_stddev_snps := len(summary.data) - len(summary_subset.data)) > 0: + print(f"Dropped {dropped_zero_stddev_snps} SNP(s) with zero standard deviation") # Drop any SNPs that are not in both genotype and summary. Some # SNPs may have been dropped from the summary because they had a # zero standard deviation. Others may have been dropped because # they were not present in all datasets. common_genotype = drop_uncommon_snps(genotype, summary_subset) + if (dropped_uncommon_snps := len(genotype) - len(common_genotype) - dropped_zero_stddev_snps) > 0: + print(f"Dropped {dropped_uncommon_snps} SNP(s) that were not present in all datasets") encrypted_genotype = encrypt_genotype(common_genotype, key, summary_subset, only_center) - if len(encrypted_genotype) < len(genotype): - dropped_snps = len(genotype) - len(encrypted_genotype) - print(f"Dropped {dropped_snps} SNP(s)") write_ciphertext(genotype_file.name, lambda file: write_genotype(file, encrypted_genotype)) |