Fix: run from self directory; all tissues from eQTL projects by default

codes3d/codes3d.py

@@ -82,8 +82,8 @@ def parse_tissues(user_tissues, match_tissues, eqtl_project, db):
             print(user_df[['name', 'project']].to_string(index=False))
             sys.exit()
         tissues = user_df[['name', 'project']]
-    else:  # Use GTEx database as default
-        tissues = df[df['project'] == 'GTEx'][[
+    else:  # Pull all tissues in eQTL project
+        tissues = df[df['project'] == eqtl_project][[
             'name', 'project']]
     return tissues
 
@@ -261,8 +261,8 @@ def parse_intermediate_files(inter_files, output_dir, file_type, multi_test=['al
         for chunk_df in pd.read_csv(inter_file, sep='\t', chunksize=1000000):
             df.append(chunk_df)
     df = pd.concat(df).drop_duplicates()
-    if file_type == 'eqtls':
-        df = multi_test_correction(df, multi_test)
+    #if file_type == 'eqtls':
+    #    df = multi_test_correction(df, multi_test)
     return df
 
 def multi_test_correction(eqtl_df, multi_test):
@@ -840,7 +840,6 @@ def log_settings(args, logger):
             sys.exit('Exiting.')
 
     log_settings(args, logger)
-
     eqtl_project = tissues['project'].tolist()[0]
     config = configparser.ConfigParser()
     config.read(args.config)

codes3d/eqtls.py

@@ -263,6 +263,8 @@ def fetch_phenotypes(
         return
     covariates_df = pd.read_csv(covariates_fp, sep='\t', index_col=0).T
     phenotype_df, pos_df = tensorqtl.read_phenotype_bed(phenotype_fp)
+    if gene_list is None:
+        gene_list = []
     if len(gene_list) > 0:
         phenotype_df = phenotype_df[
             phenotype_df.index.isin(gene_list)]
@@ -289,7 +291,10 @@ def fetch_genotypes(snps, geno, plink_prefix, C):
                 .sort_values(by=['snp'])
     )['snp'].drop_duplicates().tolist()
     filtering = time.time()
-    cmd = f'''{C.plink} \
+    plink = C.plink
+    if os.path.dirname(plink) == '':
+        plink = f'./{plink}'
+    cmd = f'''{plink} \
     --bfile {geno} \
     --snps {', '.join(snp_list)} \
     --out {plink_prefix} \