Check *.txt files for integration tests

.circleci/config.yml

@@ -49,37 +49,37 @@ jobs:
           name: test-crispresso
           command: |
                   CRISPResso -r1 tests/FANC.Cas9.fastq -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG -g GGAATCCCTTCTGCAGCACC --debug > test-crispresso.out 2>&1
-                  diff CRISPResso_on_FANC.Cas9/Nucleotide_frequency_table.txt tests/expectedResults/CRISPResso_on_FANC.Cas9/Nucleotide_frequency_table.txt >> test-crispresso.out 2>&1
-                  diff CRISPResso_on_FANC.Cas9/CRISPResso_quantification_of_editing_frequency.txt tests/expectedResults/CRISPResso_on_FANC.Cas9/CRISPResso_quantification_of_editing_frequency.txt >> test-crispresso.out 2>&1
+                  python tests/diff.py CRISPResso_on_FANC.Cas9 >> test-crispresso.out
 
       - run:
           name: test-crispresso-with-params
           command: |
                   CRISPResso -r1 tests/FANC.Cas9.fastq -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG -g GGAATCCCTTCTGCAGCACC -e CGGCCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCTGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG -c GGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTT --dump -qwc 20-30_45-50 -q 30 --default_min_aln_score 80 -an FANC -n params --base_edit -fg AGCCTTGCAGTGGGCGCGCTA,CCCACTGAAGGCCC --dsODN GCTAGATTTCCCAAGAAGA -gn hi -fgn dear --debug > test-crispresso-with-params.out 2>&1
-                  diff CRISPResso_on_params/FANC.Nucleotide_frequency_table.txt tests/expectedResults/CRISPResso_on_params/FANC.Nucleotide_frequency_table.txt >> test-crispresso-with-params.out 2>&1
-                  diff CRISPResso_on_params/CRISPResso_quantification_of_editing_frequency.txt tests/expectedResults/CRISPResso_on_params/CRISPResso_quantification_of_editing_frequency.txt >> test-crispresso-with-params.out 2>&1
+                  python tests/diff.py CRISPResso_on_params >> test-crispresso-with-params.out
 
       - run:
           name: test-crispresso-batch
           command: |
-                  CRISPRessoBatch -bs tests/FANC.batch -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG -g GGAATCCCTTCTGCAGCACC -p 2 --debug --base_editor --debug > test-crispresso-batch.out
-                  diff CRISPRessoBatch_on_FANC/MODIFICATION_FREQUENCY_SUMMARY.txt tests/expectedResults/CRISPRessoBatch_on_FANC/MODIFICATION_FREQUENCY_SUMMARY.txt >> test-crispresso-batch.out 2>&1
+                  cd tests && CRISPRessoBatch -bs FANC.batch -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG -g GGAATCCCTTCTGCAGCACC -p 2 --debug --base_editor --debug > ../test-crispresso-batch.out && cd ..
+                  python tests/diff.py CRISPRessoBatch_on_FANC >> test-crispresso-batch.out
 
       - run:
           name: test-crispresso-pooled
           command: |
                   CRISPRessoPooled -r1 tests/Both.Cas9.fastq -f tests/Cas9.amplicons.txt -p 2 --keep_intermediate --min_reads_to_use_region 100 --debug > test-crispresso-pooled.out
-                  diff CRISPRessoPooled_on_Both.Cas9/SAMPLES_QUANTIFICATION_SUMMARY.txt tests/expectedResults/CRISPRessoPooled_on_Both.Cas9/SAMPLES_QUANTIFICATION_SUMMARY.txt >> test-crispresso-pooled.out 2>&1
+                  python tests/diff.py CRISPRessoPooled_on_Both.Cas9 >> test-crispresso-pooled.out
 
       - run:
           name: test-crispresso-wgs
           command: |
                   CRISPRessoWGS -b tests/Both.Cas9.fastq.smallGenome.bam -r tests/smallGenome/smallGenome.fa -f tests/Cas9.regions.txt --debug > test-crispresso-wgs.out 2>&1
-                  diff CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome/SAMPLES_QUANTIFICATION_SUMMARY.txt tests/expectedResults/CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome/SAMPLES_QUANTIFICATION_SUMMARY.txt >> test-crispresso-wgs.out 2>&1
+                  python tests/diff.py CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome >> test-crispresso-wgs.out
+
       - run:
           name: test-crispresso-compare
           command: |
                   CRISPRessoCompare CRISPRessoBatch_on_FANC/CRISPResso_on_Cas9/ CRISPRessoBatch_on_FANC/CRISPResso_on_Untreated/ --debug > test-crispresso-compare.out 2>&1
+                  python tests/diff.py CRISPRessoCompare_on_Cas9_VS_Untreated >> test-crispresso-compare.out
 
       - store_artifacts:
           path: test-crispresso.out

CRISPResso2/CRISPRessoCompareCORE.py

@@ -108,16 +108,15 @@ def main():
         sample_1_name = args.sample_1_name
         if args.sample_1_name is None:
             sample_1_name = "Sample 1"
-            if 'name' in run_info_1 and run_info_1['running_info']['name'] != '':
+            if 'running_info' in run_info_1 and 'name' in run_info_1['running_info'] and run_info_1['running_info']['name']:
                 sample_1_name = run_info_1['running_info']['name']
 
         sample_2_name = args.sample_2_name
         if args.sample_2_name is None:
             sample_2_name = "Sample 2"
-            if 'name' in run_info_2 and run_info_2['running_info']['name'] != '':
+            if 'running_info' in run_info_2 and 'name' in run_info_2['running_info'] and run_info_2['running_info']['name']:
                 sample_2_name = run_info_2['running_info']['name']
 
-
         get_name_from_folder=lambda x: os.path.basename(os.path.abspath(x)).replace('CRISPResso_on_', '')
 
         if not args.name:

tests/FANC.batch

@@ -1,3 +1,3 @@
 n	r1
-Untreated	tests/FANC.Untreated.fastq
-Cas9	tests/FANC.Cas9.fastq
+Untreated	FANC.Untreated.fastq
+Cas9	FANC.Cas9.fastq

tests/Makefile

@@ -1,15 +1,16 @@
-.PHONY: all install test
+.PHONY: all install test clean
 
 SOURCES := $(wildcard ../CRISPResso2/*.py*)
+TEST_DIRECTORIES := CRISPResso_on_FANC.Cas9 CRISPResso_on_params CRISPRessoBatch_on_FANC \
+CRISPRessoPooled_on_Both.Cas9 CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome \
+CRISPRessoCompare_on_Cas9_VS_Untreated
 
-all: install
+all: test
 
 install: $(SOURCES)
 	cd .. && pip install -e .
 
-test: CRISPResso_on_FANC.Cas9 CRISPResso_on_params CRISPRessoBatch_on_FANC \
-CRISPRessoPooled_on_Both.Cas9 CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome \
-CRISPRessoCompare_on_Cas9_VS_Untreated
+test: clean $(TEST_DIRECTORIES)
 
 clean:
 	rm -rf CRISPResso_on_FANC.Cas9* CRISPResso_on_params* CRISPRessoBatch_on_FANC* \
@@ -18,18 +19,24 @@ CRISPRessoCompare_on_Cas9_VS_Untreated*
 
 CRISPResso_on_FANC.Cas9: install
 	time CRISPResso -r1 FANC.Cas9.fastq -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG -g GGAATCCCTTCTGCAGCACC --debug
+	python diff.py $@
 
 CRISPResso_on_params: install
 	time CRISPResso -r1 FANC.Cas9.fastq -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG -g GGAATCCCTTCTGCAGCACC -e CGGCCGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCTGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG -c GGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTT --dump -qwc 20-30_45-50 -q 30 --default_min_aln_score 80 -an FANC -n params --base_edit -fg AGCCTTGCAGTGGGCGCGCTA,CCCACTGAAGGCCC --dsODN GCTAGATTTCCCAAGAAGA -gn hi -fgn dear --debug
+	python diff.py $@
 
 CRISPRessoBatch_on_FANC: install
 	time CRISPRessoBatch -bs FANC.batch -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG -g GGAATCCCTTCTGCAGCACC --debug --base_editor
+	python diff.py $@
 
 CRISPRessoPooled_on_Both.Cas9: install
 	time CRISPRessoPooled -r1 Both.Cas9.fastq -f Cas9.amplicons.txt --keep_intermediate --min_reads_to_use_region 100 -p 4 --debug
+	python diff.py $@
 
 CRISPRessoWGS_on_Both.Cas9.fastq.smallGenome: install
 	time CRISPRessoWGS -b Both.Cas9.fastq.smallGenome.bam -r smallGenome/smallGenome.fa -f Cas9.regions.txt --debug
+	python diff.py $@
 
 CRISPRessoCompare_on_Cas9_VS_Untreated: install
 	time CRISPRessoCompare CRISPRessoBatch_on_FANC/CRISPResso_on_Cas9/ CRISPRessoBatch_on_FANC/CRISPResso_on_Untreated/ --debug
+	python diff.py $@

tests/diff.py

@@ -0,0 +1,73 @@
+import argparse
+import re
+import sys
+from difflib import unified_diff
+from pathlib import Path
+from os.path import basename, join
+
+
+FLOAT_REGEXP = re.compile(r'\d+\.\d+')
+IGNORE_FILES = frozenset([
+    'CRISPResso_RUNNING_LOG.txt',
+    'CRISPRessoBatch_RUNNING_LOG.txt',
+    'CRISPRessoPooled_RUNNING_LOG.txt',
+    'CRISPRessoWGS_RUNNING_LOG.txt',
+    'CRISPRessoCompare_RUNNING_LOG.txt',
+])
+
+
+def round_float(f):
+    return str(round(float(f.group(0)), 3))
+
+
+def diff(file_a, file_b):
+    with open(file_a) as fh_a, open(file_b) as fh_b:
+        lines_a = [FLOAT_REGEXP.sub(round_float, line) for line in fh_a]
+        lines_b = [FLOAT_REGEXP.sub(round_float, line) for line in fh_b]
+        return list(unified_diff(lines_a, lines_b))
+
+
+def diff_dir(dir_a, dir_b):
+    files_a = {basename(f): f for f in Path(dir_a).rglob('*.txt')}
+    files_b = {basename(f): f for f in Path(dir_b).rglob('*.txt')}
+    diff_exists = False
+    for file_basename_a, file_path_a in files_a.items():
+        if file_basename_a in IGNORE_FILES:
+            continue
+        if file_basename_a in files_b:
+            diff_results = diff(file_path_a, files_b[file_basename_a])
+            if diff_results:
+                print('Comparing {0} to {1}'.format(
+                    file_path_a, files_b[file_basename_a],
+                ))
+                for result in diff_results:
+                    print(result, end='')
+                diff_exists |= True
+        else:
+            print('{0} is not in {1}'.format(file_basename_a, dir_b))
+            diff_exists |= True
+
+    for file_basename_b in files_b.keys():
+        if file_basename_b not in files_a:
+            print('{0} is not in {1}'.format(file_basename_b, dir_a))
+            diff_exists |= True
+
+    return diff_exists
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('dir_a', help='Directory of text files to compare.')
+    parser.add_argument('--dir_b', help='Other directory of text files to compare.')
+    parser.add_argument('--expected_prefix', default='expectedResults')
+
+    args = parser.parse_args()
+
+    if args.dir_b is None:
+        dir_b = join(args.expected_prefix, args.dir_a)
+    else:
+        dir_b = args.dir_b
+
+    if diff_dir(args.dir_a, dir_b):
+        sys.exit(1)
+    sys.exit(0)

tests/expectedResults/CRISPRessoBatch_on_FANC/CRISPResso2Batch_info.json

@@ -0,0 +1 @@
+{"running_info": {"version": "2.2.7", "args": {"_type": "argparse.Namespace", "value": {"fastq_r1": "", "fastq_r2": "", "amplicon_seq": "CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG", "amplicon_name": "Reference", "amplicon_min_alignment_score": "", "default_min_aln_score": 60, "expand_ambiguous_alignments": false, "assign_ambiguous_alignments_to_first_reference": false, "guide_seq": "GGAATCCCTTCTGCAGCACC", "guide_name": "", "flexiguide_seq": null, "flexiguide_homology": 80, "flexiguide_name": "", "discard_guide_positions_overhanging_amplicon_edge": false, "expected_hdr_amplicon_seq": "", "coding_seq": "", "min_average_read_quality": 0, "min_single_bp_quality": 0, "min_bp_quality_or_N": 0, "file_prefix": "", "name": "", "output_folder": "", "split_interleaved_input": false, "trim_sequences": false, "trimmomatic_command": "trimmomatic", "trimmomatic_options_string": "", "flash_command": "flash", "min_paired_end_reads_overlap": 10, "max_paired_end_reads_overlap": 100, "stringent_flash_merging": false, "force_merge_pairs": false, "quantification_window_size": "1", "quantification_window_center": "-3", "exclude_bp_from_left": 15, "exclude_bp_from_right": 15, "use_legacy_insertion_quantification": false, "ignore_substitutions": false, "ignore_insertions": false, "ignore_deletions": false, "discard_indel_reads": false, "needleman_wunsch_gap_open": -20, "needleman_wunsch_gap_extend": -2, "needleman_wunsch_gap_incentive": 1, "needleman_wunsch_aln_matrix_loc": "EDNAFULL", "aln_seed_count": 5, "aln_seed_len": 10, "aln_seed_min": 2, "plot_histogram_outliers": false, "plot_window_size": 20, "min_frequency_alleles_around_cut_to_plot": 0.2, "expand_allele_plots_by_quantification": false, "allele_plot_pcts_only_for_assigned_reference": false, "quantification_window_coordinates": null, "annotate_wildtype_allele": "", "keep_intermediate": false, "dump": false, "write_detailed_allele_table": false, "fastq_output": false, "max_rows_alleles_around_cut_to_plot": 50, "suppress_report": false, "place_report_in_output_folder": false, "suppress_plots": false, "write_cleaned_report": false, "base_editor_output": true, "conversion_nuc_from": "C", "conversion_nuc_to": "T", "prime_editing_pegRNA_spacer_seq": "", "prime_editing_pegRNA_extension_seq": "", "prime_editing_pegRNA_extension_quantification_window_size": 5, "prime_editing_pegRNA_scaffold_seq": "", "prime_editing_pegRNA_scaffold_min_match_length": 1, "prime_editing_nicking_guide_seq": "", "prime_editing_override_prime_edited_ref_seq": "", "crispresso1_mode": false, "dsODN": "", "auto": false, "debug": true, "no_rerun": false, "n_processes": "1", "bam_input": "", "bam_chr_loc": "", "save_also_png": false, "batch_settings": "FANC.batch", "skip_failed": false, "min_reads_for_inclusion": 0, "batch_output_folder": null, "crispresso_command": "CRISPResso"}}, "log_filename": "CRISPRessoBatch_RUNNING_LOG.txt", "command_used": "/Users/cole/miniconda3/envs/crispresso/bin/CRISPRessoBatch -bs FANC.batch -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG -g GGAATCCCTTCTGCAGCACC --debug --base_editor", "report_location": "/Users/cole/code/edylitics/CRISPResso/tests/CRISPRessoBatch_on_FANC.html", "report_filename": "CRISPRessoBatch_on_FANC.html", "end_time": {"_type": "datetime.datetime", "value": "2021-12-09 10:13:03.843678"}, "end_time_string": "2021-12-09 10:13:03", "running_time": {"_type": "datetime.timedelta", "value": {"days": 0, "seconds": 58, "microseconds": 341340}}, "running_time_string": "0:00:58.341340"}, "results": {"alignment_stats": {}, "general_plots": {"summary_plot_titles": {"Nucleotide_percentage_quilt_around_sgRNA_GGAATCCCTTCTGCAGCACC": "", "Nucleotide_conversion_map_around_sgRNA_GGAATCCCTTCTGCAGCACC": "", "Nucleotide_percentage_quilt": "", "Nucleotide_conversion_map": ""}, "summary_plot_labels": {"Nucleotide_percentage_quilt_around_sgRNA_GGAATCCCTTCTGCAGCACC": "Composition of each base around the guide GGAATCCCTTCTGCAGCACC for the amplicon Reference", "Nucleotide_conversion_map_around_sgRNA_GGAATCCCTTCTGCAGCACC": "C->T conversion rates around the guide GGAATCCCTTCTGCAGCACC for the amplicon Reference", "Nucleotide_percentage_quilt": "Composition of each base for the amplicon Reference", "Nucleotide_conversion_map": "C->T conversion rates for the amplicon Reference"}, "summary_plot_datas": {"Nucleotide_percentage_quilt_around_sgRNA_GGAATCCCTTCTGCAGCACC": [["Nucleotide frequencies", "Nucleotide_frequency_summary.txt"], ["Modification frequencies", "MODIFICATION_FREQUENCY_SUMMARY.txt"]], "Nucleotide_conversion_map_around_sgRNA_GGAATCCCTTCTGCAGCACC": [["Nucleotide frequencies around sgRNA", "Nucleotide_frequency_summary_around_sgRNA_GGAATCCCTTCTGCAGCACC.txt"], ["Nucleotide percentages around sgRNA", "Nucleotide_percentage_summary_around_sgRNA_GGAATCCCTTCTGCAGCACC.txt"]], "Nucleotide_percentage_quilt": [["Nucleotide frequencies", "Nucleotide_frequency_summary.txt"], ["Modification frequencies", "MODIFICATION_FREQUENCY_SUMMARY.txt"]], "Nucleotide_conversion_map": [["Nucleotide frequencies", "Nucleotide_frequency_summary.txt"], ["Modification frequencies", "MODIFICATION_FREQUENCY_SUMMARY.txt"]]}, "window_nuc_pct_quilt_plot_names": ["Nucleotide_percentage_quilt_around_sgRNA_GGAATCCCTTCTGCAGCACC"], "nuc_pct_quilt_plot_names": ["Nucleotide_percentage_quilt"], "window_nuc_conv_plot_names": ["Nucleotide_conversion_map_around_sgRNA_GGAATCCCTTCTGCAGCACC"], "nuc_conv_plot_names": ["Nucleotide_conversion_map"]}, "batch_names_arr": ["Untreated", "Cas9"], "batch_input_names": {"Untreated": "Untreated", "Cas9": "Cas9"}, "completed_batch_arr": ["Untreated", "Cas9"], "nucleotide_frequency_summary_filename": "Nucleotide_frequency_summary.txt", "nucleotide_percentage_summary_filename": "Nucleotide_percentage_summary.txt", "modification_frequency_summary_filename": "MODIFICATION_FREQUENCY_SUMMARY.txt", "modification_percentage_summary_filename": "MODIFICATION_PERCENTAGE_SUMMARY.txt"}}

tests/expectedResults/CRISPRessoBatch_on_FANC/CRISPRessoBatch_RUNNING_LOG.txt

@@ -0,0 +1,7 @@
+[Command used]:
+/Users/cole/miniconda3/envs/crispresso/bin/CRISPRessoBatch -bs FANC.batch -a CGGATGTTCCAATCAGTACGCAGAGAGTCGCCGTCTCCAAGGTGAAAGCGGAAGTAGGGCCTTCGCGCACCTCATGGAATCCCTTCTGCAGCACCTGGATCGCTTTTCCGAGCTTCTGGCGGTCTCAAGCACTACCTACGTCAGCACCTGGGACCCCGCCACCGTGCGCCGGGCCTTGCAGTGGGCGCGCTACCTGCGCCACATCCATCGGCGCTTTGGTCGG -g GGAATCCCTTCTGCAGCACC --debug --base_editor
+
+[Execution log]:
+Reporting summary for amplicon: "Reference"
+All guides are equal. Performing comparison of batches for amplicon 'Reference'
+Analysis Complete!

tests/expectedResults/CRISPRessoBatch_on_FANC/CRISPRessoBatch_mapping_statistics.txt

@@ -0,0 +1,3 @@
+Batch	READS IN INPUTS	READS AFTER PREPROCESSING	READS ALIGNED	N_COMPUTED_ALN	N_CACHED_ALN	N_COMPUTED_NOTALN	N_CACHED_NOTALN
+Untreated	250	250	247	176	71	3	0
+Cas9	250	250	235	198	37	15	0

tests/expectedResults/CRISPRessoBatch_on_FANC/CRISPRessoBatch_quantification_of_editing_frequency.txt

@@ -0,0 +1,3 @@
+Batch	Amplicon	Unmodified%	Modified%	Reads_in_input	Reads_aligned_all_amplicons	Reads_aligned	Unmodified	Modified	Discarded	Insertions	Deletions	Substitutions	Only Insertions	Only Deletions	Only Substitutions	Insertions and Deletions	Insertions and Substitutions	Deletions and Substitutions	Insertions Deletions and Substitutions
+Untreated	Reference	100.0	0.0	250	247	247	247	0	0	0	0	0	0	0	0	0	0	0	0
+Cas9	Reference	73.61702128	26.38297872	250	235	235	173	62	0	8	49	7	6	49	5	0	2	0	0

tests/expectedResults/CRISPRessoBatch_on_FANC/CRISPRessoBatch_quantification_of_frameshift_splicing.txt

@@ -0,0 +1,3 @@
+Batch	Reference	total_reads	modified_frameshift	modified_non_frameshift	non_modified_non_frameshift	splicing_sites_modified	splice_sites_unmodified
+Untreated	Reference	247	0	0	0	0	247
+Cas9	Reference	235	0	0	0	0	235