From d33615fd1c9c2d0df2c341d583d35032fb0fc63c Mon Sep 17 00:00:00 2001 From: Cole Lyman Date: Fri, 24 May 2024 11:06:54 -0600 Subject: [PATCH] Fix typo and move flexiguide to debug (#77) * Change flexiguide output to debug level * Fix typo in fastp merged output file name --- CRISPResso2/CRISPRessoCORE.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py index 45ec50c1..10980b0c 100644 --- a/CRISPResso2/CRISPRessoCORE.py +++ b/CRISPResso2/CRISPRessoCORE.py @@ -1914,7 +1914,7 @@ def get_prime_editing_guides(this_amp_seq, this_amp_name, ref0_seq, prime_edited this_guide_plot_cut_points.append(False) else: this_guide_plot_cut_points.append(True) - info('Added %d guides with flexible matching\n\tOriginal flexiguides: %s\n\tFound guides: %s\n\tMismatch locations: %s'%(flexi_guide_count, str(args.flexiguide_seq.split(",")), str(flexi_guides), str(flexi_guide_mismatches)), {'percent_complete': 7}) + debug('Added %d guides with flexible matching\n\tOriginal flexiguides: %s\n\tFound guides: %s\n\tMismatch locations: %s'%(flexi_guide_count, str(args.flexiguide_seq.split(",")), str(flexi_guides), str(flexi_guide_mismatches)), {'percent_complete': 7}) if args.prime_editing_pegRNA_extension_seq: nicking_qw_center = int(args.quantification_window_center.split(",")[0]) @@ -2382,7 +2382,7 @@ def get_prime_editing_guides(this_amp_seq, this_amp_name, ref0_seq, prime_edited processed_output_filename = output_forward_filename elif args.fastq_r1 != '' and args.fastq_r2 != '':#paired end reads - processed_output_filename = _jp('oet.extendedFrags.fastq.gz') + processed_output_filename = _jp('out.extendedFrags.fastq.gz') not_combined_1_filename = _jp('out.notCombined_1.fastq.gz') not_combined_2_filename = _jp('out.notCombined_2.fastq.gz') check_fastp()