Merge pull request #98 from EBISPOT/ci_from_master

1. Chang the output of ci_upper and ci_lower 2. Cancel the variant_id check using the sql
EBISPOT · Jul 16, 2024 · db70e5d · db70e5d
2 parents 89441e3 + 46f2f4d
commit db70e5d
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/bin/basic_qc_nf.py b/bin/basic_qc_nf.py
@@ -237,8 +237,8 @@ def main():
             else:
                 # First try to replace an invalid variant_id with the hm_rsid
                 # Checks for blanks, integers and floats:
-                sql_client = sqlClient(db) if db else None
-                ensembl_client = EnsemblRestClient() if not db else None
+                #sql_client = sqlClient(db) if db else None
+                #ensembl_client = EnsemblRestClient() if not db else None
                 #row = resolve_invalid_rsids(row, header, ensembl_client, sql_client)
                 row = blanks_to_NA(row)
                 row = map_chr_values_to_numbers(row, header)

diff --git a/bin/main_pysam.py b/bin/main_pysam.py
@@ -157,8 +157,8 @@ def main():
             out_raw["other_allele"] = ss_rec.hm_other_al.str() if vcf_rec and ss_rec.is_harmonised else args.na_rep_out
             out_raw["beta"] = ss_rec.beta if ss_rec.beta is not None and ss_rec.is_harmonised else args.na_rep_out
             out_raw["odds_ratio"] = ss_rec.oddsr if ss_rec.oddsr is not None and ss_rec.is_harmonised else args.na_rep_out
-            out_raw["ci_lower"] = ss_rec.oddsr_lower is not None if ss_rec.oddsr_lower and ss_rec.is_harmonised else args.na_rep_out
-            out_raw["ci_upper"] = ss_rec.oddsr_upper is not None if ss_rec.oddsr_upper and ss_rec.is_harmonised else args.na_rep_out
+            out_raw["ci_lower"] = ss_rec.oddsr_lower if ss_rec.oddsr_lower is not None and ss_rec.is_harmonised else args.na_rep_out
+            out_raw["ci_upper"] = ss_rec.oddsr_upper if ss_rec.oddsr_upper is not None and ss_rec.is_harmonised else args.na_rep_out
             out_raw["effect_allele_frequency"] = ss_rec.eaf if ss_rec.eaf is not None and ss_rec.is_harmonised else args.na_rep_out
             # Process the neg_log_10_p_value
             if "neg_log_10_p_value" in out_header: