diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py index 7b5d636ea746c06072e746f605235b821e5d9024..f879681e77375f912dfb0de6a499a8f3c1a0be4d 100644 --- a/workflow/scripts/pool_and_psuedoreplicate.py +++ b/workflow/scripts/pool_and_psuedoreplicate.py @@ -124,13 +124,14 @@ def self_psuedoreplication(tag_file, prefix, paired): # Convert read pairs to reads into standard tagAlign file - for i, string(index) in enumerate([0, 1]): - steps = ['cat %s' % (splits_prefix + index)] + for i, index in enumerate([0, 1]): + string_index = str(index) + steps = ['cat %s' % (splits_prefix + string_index)] if paired: steps.extend([r"""awk 'BEGIN{OFS="\t"}{printf "%s\t%s\t%s\tN\t1000\t%s\n%s\t%s\t%s\tN\t1000\t%s\n",$1,$2,$3,$9,$4,$5,$6,$10}'"""]) steps.extend(['gzip -cn']) out, err = utils.run_pipe(steps, outfile=pseudoreplicate_dict[i]) - os.remove(splits_prefix + index) + os.remove(splits_prefix + string_index) return pseudoreplicate_dict