From 5a101c811895321339b5103f4f3709b314ab4bcc Mon Sep 17 00:00:00 2001 From: tbrunetti Date: Fri, 26 Oct 2018 16:45:32 -0600 Subject: [PATCH] fixed stage for deletion of concordace method --- run_GWAS_QC_filtering_pipeline.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/run_GWAS_QC_filtering_pipeline.py b/run_GWAS_QC_filtering_pipeline.py index 7793948..cab271b 100644 --- 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()