fixed stage for deletion of concordace method

tbrunetti · Oct 26, 2018 · 5a101c8 · 5a101c8
1 parent 185a81d
commit 5a101c8
Showing 1 changed file with 5 additions and 5 deletions.
diff --git a/run_GWAS_QC_filtering_pipeline.py b/run_GWAS_QC_filtering_pipeline.py
@@ -261,11 +261,11 @@ def concordance(qcPassPLINK, plink, hapmap, tgp, outdir):
 
 				indConc.append(round(float(concordant_rate.group(1)) * 100, 2))
 
-				stage_for_deletion.append(line.split('\t')[1].rstrip() + '.bed')
-				stage_for_deletion.append(line.split('\t')[1].rstrip() + '.bim')
-				stage_for_deletion.append(line.split('\t')[1].rstrip() + '.fam')
-				stage_for_deletion.append(line.split('\t')[1].rstrip() + '.hh')
-				stage_for_deletion.append(line.split('\t')[1].rstrip() + '.log')
+				stage_for_deletion.append(os.path.join(outdir, line.split('\t')[1].rstrip() + '.bed'))
+				stage_for_deletion.append(os.path.join(outdir, line.split('\t')[1].rstrip() + '.bim'))
+				stage_for_deletion.append(os.path.join(outdir, line.split('\t')[1].rstrip() + '.fam'))
+				stage_for_deletion.append(os.path.join(outdir, line.split('\t')[1].rstrip() + '.hh'))
+				stage_for_deletion.append(os.path.join(outdir, line.split('\t')[1].rstrip() + '.log'))
 
 		concordanceResults.flush()
 		concordanceResults.close()