natDir='test_data/native_reads/' ampDir='test_data/amplified_reads/' rcsvDir='test_data/recursive_test/' natFsq="test_data/fastqs.native.fasta" natFqDir='test_data/native_reads.for_fastq_ann/' nrModFn='../tombo/tombo/tombo_models/tombo.DNA.model' altModFn='../tombo/tombo/tombo_models/tombo.DNA.5mC.model' poreModel="r9_250bps.nucleotide.5mer.template.model" genomeFn="e_coli.K12.NEB5alpha.fasta" mmiFn="e_coli.K12.NEB5alpha.mmi" genomeLocs='"CP017100.1:1505285" "CP017100.1:2873680"' strandGenomeLocs='"CP017100.1:1505285:+" "CP017100.1:2873680:-"' modLocsFn='modified_positions.bed' unmodLocsFn='unmodified_positions.bed' runHelps=false runResquiggle=true printf "********* Testing help commands **********\n" tombo -h || { echo 'Main tombo help failed. Likely a syntax error.' ; exit 1; } if [ $runHelps == true ] then tombo resquiggle -h tombo preprocess annotate_raw_with_fastqs -h tombo filter clear_filters -h tombo filter stuck -h tombo filter level_coverage -h tombo filter q_score -h tombo filter raw_signal_matching -h tombo filter genome_locations -h tombo detect_modifications de_novo -h tombo detect_modifications alternative_model -h tombo detect_modifications model_sample_compare -h tombo detect_modifications level_sample_compare -h tombo detect_modifications aggregate_per_read_stats -h tombo text_output browser_files -h tombo text_output signif_sequence_context -h tombo plot max_coverage -h tombo plot genome_locations -h tombo plot motif_centered -h tombo plot max_difference -h tombo plot most_significant -h tombo plot motif_with_stats -h tombo plot per_read -h tombo plot roc -h tombo plot per_read_roc -h tombo plot kmer -h tombo plot cluster_most_significant -h tombo build_model estimate_scale -h tombo build_model event_resquiggle -h tombo build_model estimate_reference -h tombo build_model estimate_alt_reference -h fi if [ $runResquiggle == true ] then printf "\n\n********* Testing re-squiggle command **********\n" tombo resquiggle \ $natDir $genomeFn \ --failed-reads-filename testing.native.failed_read.txt \ --processes 8 --overwrite --num-most-common-errors 5 tombo resquiggle \ $ampDir $genomeFn \ --failed-reads-filename testing.amplified.failed_read.txt \ --processes 8 --overwrite --num-most-common-errors 5 printf "\n\n********* Testing FASTQ annotation and re-squiggle **********\n" tombo preprocess annotate_raw_with_fastqs --fast5-basedir $natFqDir \ --fastq-filenames $natFsq --overwrite tombo resquiggle \ $natFqDir $genomeFn \ --corrected-group FastqAnnotation \ --processes 8 --overwrite printf "\n\n********* Testing minimap2 index **********\n" tombo resquiggle \ $natDir $mmiFn \ --corrected-group RawMinimapIndexCorrected \ --processes 8 --overwrite printf "\n\n********* Testing re-squiggle command with filename **********\n" tombo resquiggle \ $natDir $genomeFn --tombo-model-filename $nrModFn \ --corrected-group RawWFilenameCorrected \ --processes 8 --overwrite tombo resquiggle \ $ampDir $genomeFn --tombo-model-filename $nrModFn \ --corrected-group RawWFilenameCorrected \ --processes 8 --overwrite printf "\n\n********* Testing event-based resquiggle **********\n" tombo build_model event_resquiggle \ $natDir $genomeFn --minimap2-executable ./minimap2 \ --corrected-group RawEventCorrected --processes 8 --overwrite printf "\n\n********* Testing pA normalization **********\n" tombo build_model event_resquiggle \ $natDir $genomeFn \ --minimap2-executable ./minimap2 \ --normalization-type pA_raw --processes 8 \ --corrected-group RawGenomeCorrected_pA_raw_000 --overwrite tombo build_model event_resquiggle \ $natDir $genomeFn --minimap2-executable ./minimap2 \ --normalization-type pA --pore-model-filename $poreModel \ --corrected-group RawGenomeCorrected_pA_000 --overwrite \ --processes 8 printf "\n\n********* Testing recursive resquiggle **********\n" tombo resquiggle \ $rcsvDir $genomeFn \ --processes 8 --overwrite printf "\n\n********* Testing re-squiggle length filters **********\n" tombo resquiggle \ $natDir $genomeFn \ --corrected-group RawWLengthFilter \ --signal-length-range 0 500000 \ --sequence-length-range 0 35000 \ --processes 8 --overwrite fi printf "\n\n********* Testing filter functions **********\n" tombo filter clear_filters --fast5-basedirs $natDir tombo filter stuck --fast5-basedirs $natDir \ --obs-per-base-filter 99:200 100:1000 tombo filter level_coverage --fast5-basedirs $natDir \ --percent-to-filter 10 tombo filter q_score --fast5-basedirs $natDir --q-score 10 tombo filter raw_signal_matching --fast5-basedirs $natDir \ --signal-matching-score 0.75 tombo filter clear_filters --fast5-basedirs $natDir tombo filter genome_locations --fast5-basedirs $natDir \ --include-regions CP017100.1:1,485,920-1,558,736 --include-partial-overlap tombo filter genome_locations --fast5-basedirs $natDir \ --include-regions CP017100.1:1,485,920-1,558,736 tombo filter clear_filters --fast5-basedirs $natDir printf "\n\n********* Testing estimate global scale function **********\n" tombo build_model estimate_scale $natDir printf "\n\n********* Testing single sample genome-anchored plotting functions **********\n" tombo plot max_coverage --fast5-basedirs $natDir \ --num-bases 21 --overplot-threshold 1000 \ --pdf-filename testing.max_cov.1_samp.pdf tombo plot genome_locations --fast5-basedirs $ampDir \ --genome-locations $genomeLocs \ --num-bases 21 --overplot-threshold 1000 \ --pdf-filename testing.genome_loc.1_samp.pdf tombo plot motif_centered --fast5-basedirs $natDir --motif ATC \ --genome-fasta $genomeFn \ --num-bases 21 --overplot-threshold 1000 \ --pdf-filename testing.motif_centered.1_samp.pdf tombo plot motif_centered --fast5-basedirs $natDir --motif TWA \ --genome-fasta $genomeFn \ --num-bases 21 --overplot-threshold 1000 \ --pdf-filename testing.motif_centered.palindrome.1_samp.pdf tombo plot motif_centered --fast5-basedirs $natDir --motif ATC \ --genome-fasta $genomeFn \ --num-bases 21 --overplot-threshold 1000 --deepest-coverage \ --pdf-filename testing.motif_centered.deepest.1_samp.pdf tombo plot motif_centered --fast5-basedirs $natDir --motif NNCCWGG \ --plot-alternate-model 5mC --genome-fasta $genomeFn \ --num-bases 21 --overplot-threshold 1000 \ --pdf-filename testing.motif_centered.w_model.pdf tombo plot max_coverage --fast5-basedirs $rcsvDir \ --num-bases 21 --overplot-threshold 1000 \ --pdf-filename testing.max_cov.1_samp.recursive.pdf printf "\n\n********* Testing multiple sample genome-anchored plotting functions **********\n" tombo plot max_coverage --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1000 \ --pdf-filename testing.max_cov.2_samp.pdf tombo plot genome_locations --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --genome-locations $genomeLocs \ --num-bases 21 --overplot-threshold 1000 \ --pdf-filename testing.genome_loc.2_samp.pdf tombo plot motif_centered --fast5-basedirs $natDir --motif ATC \ --genome-fasta $genomeFn \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1000 \ --pdf-filename testing.motif_centered.2_samp.pdf tombo plot motif_centered --fast5-basedirs $natDir --motif TWA \ --genome-fasta $genomeFn \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1000 \ --pdf-filename testing.motif_centered.palindrome.2_samp.pdf tombo plot motif_centered --fast5-basedirs $natDir --motif ATC \ --genome-fasta $genomeFn \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1000 --deepest-coverage \ --pdf-filename testing.motif_centered.deepest.2_samp.pdf printf "\n\n********* Testing statistical testing. **********\n" rm test_stats.de_novo.tombo.stats test_stats.2samp.tombo.stats \ test_stats.alt_model.5mC.tombo.stats \ test_stats.alt_default_model.5mC.tombo.stats \ test_stats.alt_default_model.6mA.tombo.stats \ test_stats.de_novo.tombo.per_read_stats test_stats.2samp.tombo.per_read_stats \ test_stats.alt_model.5mC.tombo.per_read_stats \ test_stats.alt_default_model.5mC.tombo.per_read_stats \ test_stats.alt_default_model.6mA.tombo.per_read_stats \ test_standard.model test_stats.de_novo.new_thresh.tombo.stats \ test_alt.model test_alt.use_densities.model \ test_stats.alt_native.motif.dcm.tombo.stats \ test_stats.alt_native.motif.dam.tombo.stats \ test_stats.alt_amp_samp.motif.dcm.tombo.stats \ test_stats.alt_amp_samp.motif.dam.tombo.stats tombo detect_modifications de_novo --fast5-basedirs $natDir \ --minimum-test-reads 5 \ --statistics-file-basename test_stats.de_novo \ --per-read-statistics-basename test_stats.de_novo tombo detect_modifications de_novo --fast5-basedirs $natDir \ --minimum-test-reads 5 --single-read-threshold 0.1 0.75 \ --statistics-file-basename test_stats.de_novo.two_way_thresh \ --per-read-statistics-basename test_stats.de_novo.two_way_thresh tombo detect_modifications model_sample_compare --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --minimum-test-reads 1 --sample-only-estimates \ --statistics-file-basename test_stats.2samp \ --per-read-statistics-basename test_stats.2samp tombo detect_modifications model_sample_compare --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --minimum-test-reads 5 \ --statistics-file-basename test_stats.2samp_w_post \ --per-read-statistics-basename test_stats.2samp_w_post tombo detect_modifications level_sample_compare --fast5-basedirs $natDir \ --alternate-fast5-basedirs $ampDir \ --minimum-test-reads 5 \ --statistics-file-basename test_stats.2samp_levels tombo detect_modifications alternative_model --fast5-basedirs $natDir \ --alternate-bases 5mC 6mA \ --statistics-file-basename test_stats.alt_default_model \ --per-read-statistics-basename test_stats.alt_default_model tombo detect_modifications alternative_model --fast5-basedirs $natDir \ --tombo-model-filename $nrModFn \ --alternate-model-filenames $altModFn \ --statistics-file-basename test_stats.alt_model \ --per-read-statistics-basename test_stats.alt_model printf "\n\n********* Testing model estimation. **********\n" tombo build_model estimate_reference --fast5-basedirs $natDir \ --tombo-model-filename test_standard.model \ --upstream-bases 1 --downstream-bases 1 --minimum-kmer-observations 1 tombo build_model estimate_alt_reference --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --tombo-model-filename test_standard.model \ --alternate-model-filename test_alt.model \ --alternate-model-name 5mC --alternate-model-base C \ --minimum-kmer-observations 1 --save-density-basename test_save_dens tombo build_model estimate_alt_reference \ --alternate-density-filename test_save_dens.alternate_density.txt \ --control-density-filename test_save_dens.control_density.txt \ --tombo-model-filename test_standard.model \ --alternate-model-filename test_alt.use_densities.model \ --alternate-model-name 5mC --alternate-model-base C \ --minimum-kmer-observations 1 tombo build_model estimate_motif_alt_reference --fast5-basedirs $natDir \ --alternate-model-filename test_alt.motif_model \ --alternate-model-name dcm --motif-description CCWGG:2 \ --minimum-kmer-observations 1 printf "\n\n********* Testing aggregate per-read stats **********\n" tombo detect_modifications aggregate_per_read_stats --minimum-test-reads 5 \ --single-read-threshold 0.4 \ --statistics-filename test_stats.de_novo.new_thresh.tombo.stats \ --per-read-statistics-filename test_stats.de_novo.tombo.per_read_stats printf "\n\n********* Testing ROC and Precision-Recall plotting **********\n" tombo plot roc --genome-fasta e_coli.K12.NEB5alpha.fasta \ --statistics-filenames test_stats.2samp.tombo.stats \ test_stats.2samp_w_post.tombo.stats \ test_stats.2samp_levels.tombo.stats \ test_stats.alt_default_model.5mC.tombo.stats \ test_stats.alt_default_model.6mA.tombo.stats \ test_stats.de_novo.tombo.stats test_stats.de_novo.new_thresh.tombo.stats \ --motif-descriptions \ CCWGG:2:"dcm 5mC Samp Comp Model"::GATC:2:"dam 6mA Samp Comp Model" \ CCWGG:2:"dcm 5mC Samp Comp w/ post"::GATC:2:"dam 6mA Samp Comp w/ post" \ CCWGG:2:"dcm 5mC Samp Comp Levels"::GATC:2:"dam 6mA Samp Comp Levels" \ CCWGG:2:"dcm 5mC Alt Test" GATC:2:"dam 6mA Alt Test" \ CCWGG:2:"dcm 5mC De Novo"::GATC:2:"dam 6mA De Novo" \ CCWGG:2:"dcm 5mC De Novo New Thresh"::GATC:2:"dam 6mA De Novo New Thresh" tombo plot per_read_roc --genome-fasta e_coli.K12.NEB5alpha.fasta \ --per-read-statistics-filenames test_stats.2samp.tombo.per_read_stats \ test_stats.2samp_w_post.tombo.per_read_stats \ test_stats.alt_default_model.5mC.tombo.per_read_stats \ test_stats.alt_default_model.6mA.tombo.per_read_stats \ test_stats.de_novo.tombo.per_read_stats --motif-descriptions \ CCWGG:2:"dcm 5mC Samp Comp Model"::GATC:2:"dam 6mA Samp Comp Model" \ CCWGG:2:"dcm 5mC Samp Comp w/ post"::GATC:2:"dam 6mA Samp Comp w/ post" \ CCWGG:2:"dcm 5mC Alt Test" GATC:2:"dam 6mA Alt Test" \ CCWGG:2:"dcm 5mC De Novo"::GATC:2:"dam 6mA De Novo" printf "\n\n********* Testing Sample Compare ROC and Precision-Recall plotting **********\n" tombo detect_modifications alternative_model --fast5-basedirs $natDir \ --alternate-bases dam dcm \ --statistics-file-basename test_stats.alt_native.motif \ --per-read-statistics-basename test_stats.alt_native.motif tombo detect_modifications alternative_model --fast5-basedirs $ampDir \ --alternate-bases dam dcm \ --statistics-file-basename test_stats.alt_amp_samp.motif \ --per-read-statistics-basename test_stats.alt_amp_samp.motif tombo detect_modifications de_novo --fast5-basedirs $ampDir \ --minimum-test-reads 5 \ --statistics-file-basename test_stats.de_novo.amp \ --per-read-statistics-basename test_stats.de_novo.amp tombo detect_modifications alternative_model --fast5-basedirs $ampDir \ --alternate-bases 5mC 6mA \ --statistics-file-basename test_stats.alt_default_model.amp \ --per-read-statistics-basename test_stats.alt_default_model.amp tombo plot sample_compare_roc --genome-fasta e_coli.K12.NEB5alpha.fasta \ --statistics-filenames \ test_stats.alt_native.motif.dcm.tombo.stats \ test_stats.alt_native.motif.dam.tombo.stats \ test_stats.de_novo.tombo.stats \ test_stats.alt_default_model.5mC.tombo.stats \ test_stats.alt_default_model.6mA.tombo.stats \ --control-statistics-filenames \ test_stats.alt_amp_samp.motif.dcm.tombo.stats \ test_stats.alt_amp_samp.motif.dam.tombo.stats \ test_stats.de_novo.amp.tombo.stats \ test_stats.alt_default_model.amp.5mC.tombo.stats \ test_stats.alt_default_model.amp.6mA.tombo.stats \ --motif-descriptions CCWGG:2:"dcm 5mC Alt Test" \ GATC:2:"dam 6mA Alt Test" \ CCWGG:2:"dcm 5mC De novo"::GATC:2:"dam 6mA De novo" \ CCWGG:2:"5mC all-context Alt Test" GATC:2:"6mA all-context Alt Test" \ --pdf-filename test_stats.samp_comp_roc.pdf tombo plot sample_compare_per_read_roc \ --genome-fasta e_coli.K12.NEB5alpha.fasta \ --per-read-statistics-filenames \ test_stats.alt_native.motif.dcm.tombo.per_read_stats \ test_stats.alt_native.motif.dam.tombo.per_read_stats \ test_stats.de_novo.tombo.per_read_stats \ test_stats.alt_default_model.5mC.tombo.per_read_stats \ test_stats.alt_default_model.6mA.tombo.per_read_stats \ --per-read-control-statistics-filenames \ test_stats.alt_amp_samp.motif.dcm.tombo.per_read_stats \ test_stats.alt_amp_samp.motif.dam.tombo.per_read_stats \ test_stats.de_novo.amp.tombo.per_read_stats \ test_stats.alt_default_model.amp.5mC.tombo.per_read_stats \ test_stats.alt_default_model.amp.6mA.tombo.per_read_stats \ --motif-descriptions CCWGG:2:"dcm 5mC Alt Test" \ GATC:2:"dam 6mA Alt Test" \ CCWGG:2:"dcm 5mC De novo"::GATC:2:"dam 6mA De novo" \ CCWGG:2:"5mC all-context Alt Test" GATC:2:"6mA all-context Alt Test" \ --pdf-filename test_stats.samp_comp_per_read_roc.pdf printf "\n\n********* Testing Known Site ROC and Precision-Recall plotting **********\n" tombo plot roc \ --statistics-filenames test_stats.alt_native.motif.dcm.tombo.stats \ --modified-locations "dcm 5mC":$modLocsFn \ --unmodified-locations $unmodLocsFn tombo plot per_read_roc \ --per-read-statistics-filenames \ test_stats.alt_native.motif.dcm.tombo.per_read_stats \ --modified-locations "dcm 5mC":$modLocsFn \ --unmodified-locations $unmodLocsFn printf "\n\n********* Testing mutliple sample statistical testing genome-anchored plotting functions **********\n" tombo plot max_difference --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1000 \ --pdf-filename testing.max_diff.pdf tombo plot most_significant --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1000 \ --statistics-filename test_stats.2samp.tombo.stats \ --pdf-filename testing.most_signif.2samp.pdf tombo plot most_significant --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1000 \ --statistics-filename test_stats.2samp_levels.tombo.stats \ --pdf-filename testing.most_signif.2samp_levels.pdf tombo plot most_significant --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1000 \ --statistics-filename test_stats.de_novo.tombo.stats \ --pdf-filename testing.most_signif.model.pdf tombo plot most_significant --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1000 \ --plot-standard-model \ --statistics-filename test_stats.alt_model.5mC.tombo.stats \ --pdf-filename testing.most_signif.alt_model_5mC.pdf tombo plot motif_with_stats --fast5-basedirs $natDir \ --motif CAW --genome-fasta $genomeFn --overplot-threshold 1000 \ --plot-standard-model --statistics-filename test_stats.de_novo.tombo.stats \ --pdf-filename testing.motif_w_stats.pdf tombo plot motif_with_stats --fast5-basedirs $natDir \ --tombo-model-filename $nrModFn --motif CCWGG \ --genome-fasta $genomeFn --overplot-threshold 1000 \ --statistics-filename test_stats.de_novo.tombo.stats \ --pdf-filename testing.motif_w_stats.model.pdf tombo plot motif_with_stats --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir --motif CCWGG \ --genome-fasta $genomeFn --overplot-threshold 1000 \ --statistics-filename test_stats.2samp.tombo.stats \ --pdf-filename testing.motif_w_stats.2samp.pdf tombo plot motif_with_stats --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir --motif CCWGG \ --genome-fasta $genomeFn --overplot-threshold 1000 \ --statistics-filename test_stats.2samp_levels.tombo.stats \ --pdf-filename testing.motif_w_stats.2samp_levels.pdf tombo plot motif_with_stats --fast5-basedirs $natDir \ --plot-alternate-model 5mC --motif NNCCWGG --genome-fasta $genomeFn \ --statistics-filename test_stats.alt_model.5mC.tombo.stats \ --pdf-filename testing.motif_w_stats.alt_model_5mC.pdf tombo plot motif_with_stats --fast5-basedirs $natDir \ --plot-alternate-model 6mA --motif NGATC --genome-fasta $genomeFn \ --statistics-filename test_stats.alt_default_model.6mA.tombo.stats \ --pdf-filename testing.motif_w_stats.alt_model_6mA.alt_dist.pdf printf "\n\n********* Testing overplotting options **********\n" tombo plot max_coverage --fast5-basedirs $natDir \ --num-bases 21 --overplot-threshold 1 --overplot-type Downsample \ --pdf-filename testing.max_coverage.Downsample.pdf tombo plot max_coverage --fast5-basedirs $natDir \ --num-bases 21 --overplot-threshold 1 --overplot-type Boxplot \ --pdf-filename testing.max_coverage.Boxplot.pdf tombo plot max_coverage --fast5-basedirs $natDir \ --num-bases 21 --overplot-threshold 1 --overplot-type Quantile \ --pdf-filename testing.max_coverage.Quantile.pdf tombo plot max_coverage --fast5-basedirs $natDir \ --num-bases 21 --overplot-threshold 1 --overplot-type Density \ --pdf-filename testing.max_coverage.Density.pdf tombo plot max_coverage --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1 --overplot-type Downsample \ --pdf-filename testing.max_coverage.2samp.Downsample.pdf tombo plot max_coverage --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1 --overplot-type Boxplot \ --pdf-filename testing.max_coverage.2samp.Boxplot.pdf tombo plot max_coverage --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1 --overplot-type Quantile \ --pdf-filename testing.max_coverage.2samp.Quantile.pdf tombo plot max_coverage --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --num-bases 21 --overplot-threshold 1 --overplot-type Density \ --pdf-filename testing.max_coverage.2samp.Density.pdf printf "\n\n********* Testing model-based plotting **********\n" tombo plot max_coverage --fast5-basedirs $natDir \ --tombo-model-filename $nrModFn \ --pdf-filename testing.max_cov.1_samp.model.pdf tombo plot most_significant --fast5-basedirs $natDir \ --tombo-model-filename $nrModFn \ --statistics-filename test_stats.de_novo.tombo.stats \ --pdf-filename testing.model_plotting.pdf tombo plot most_significant --fast5-basedirs $natDir \ --tombo-model-filename $nrModFn \ --statistics-filename test_stats.de_novo.tombo.stats \ --overplot-threshold 1 --overplot-type Downsample \ --pdf-filename testing.model_plotting.downsample.pdf tombo plot most_significant --fast5-basedirs $natDir \ --tombo-model-filename $nrModFn \ --statistics-filename test_stats.de_novo.tombo.stats \ --overplot-threshold 1 --overplot-type Boxplot \ --pdf-filename testing.model_plotting.boxplot.pdf tombo plot most_significant --fast5-basedirs $natDir \ --tombo-model-filename $nrModFn \ --statistics-filename test_stats.de_novo.tombo.stats \ --overplot-threshold 1 --overplot-type Quantile \ --pdf-filename testing.model_plotting.quant.pdf tombo plot most_significant --fast5-basedirs $natDir \ --tombo-model-filename $nrModFn \ --statistics-filename test_stats.de_novo.tombo.stats \ --overplot-threshold 1 --overplot-type Density \ --pdf-filename testing.model_plotting.density.pdf tombo plot genome_locations --fast5-basedirs $natDir \ --tombo-model-filename $nrModFn \ --alternate-model-filename $altModFn \ --genome-locations $genomeLocs \ --num-bases 21 --overplot-threshold 1000 \ --pdf-filename testing.genome_loc.two_model_comp.pdf printf "\n\n********* Testing event-resquiggled plotting **********\n" tombo plot max_coverage --fast5-basedirs $natDir \ --tombo-model-filename $nrModFn \ --pdf-filename testing.max_cov.1_samp.model.model_resq.pdf \ --corrected-group RawEventCorrected tombo plot most_significant --fast5-basedirs $natDir \ --tombo-model-filename $nrModFn \ --corrected-group RawEventCorrected \ --statistics-filename test_stats.de_novo.tombo.stats \ --pdf-filename testing.model_plotting.resq_most_signif.pdf tombo plot max_coverage --fast5-basedirs $natDir \ --tombo-model-filename $nrModFn \ --pdf-filename testing.max_cov.1_samp.model.model_resq.pdf \ --corrected-group RawEventCorrected printf "\n\n********* Testing per-read testing plot **********\n" tombo plot per_read --genome-locations $genomeLocs --num-bases 101 \ --per-read-statistics-filename test_stats.2samp.tombo.per_read_stats \ --genome-fasta $genomeFn --pdf-filename testing.per_read.samp_comp.pdf tombo plot per_read --genome-locations $genomeLocs --num-bases 101 \ --per-read-statistics-filename test_stats.de_novo.tombo.per_read_stats \ --genome-fasta $genomeFn --pdf-filename testing.de_novo.per_read.pdf tombo plot per_read --fast5-basedirs $natDir \ --genome-locations $genomeLocs --num-bases 101 \ --per-read-statistics-filename test_stats.alt_model.5mC.tombo.per_read_stats \ --pdf-filename testing.per_read.w_alt.pdf tombo plot per_read --genome-locations $genomeLocs --num-bases 101 \ --per-read-statistics-filename test_stats.alt_model.5mC.tombo.per_read_stats \ --pdf-filename testing.per_read.wo_seq.pdf # plot locs that should cluster tombo detect_modifications alternative_model --fast5-basedirs $ampDir $natDir \ --alternate-bases dam dcm \ --statistics-file-basename test_stats.alt_both_samp.motif \ --per-read-statistics-basename test_stats.alt_both_samp.motif tombo plot per_read --genome-locations $genomeLocs --num-bases 10001 \ --per-read-statistics-filename \ test_stats.alt_both_samp.motif.dcm.tombo.per_read_stats \ --genome-fasta $genomeFn \ --pdf-filename testing.per_read.w_alt_motif.pdf printf "\n\n********* Testing text output commands **********\n" tombo text_output signif_sequence_context --fast5-basedirs $natDir $ampDir \ --statistics-filename test_stats.de_novo.tombo.stats \ --sequences-filename testing_signif_regions.from_fast5s.fasta tombo text_output signif_sequence_context \ --statistics-filename test_stats.de_novo.tombo.stats \ --sequences-filename testing_signif_regions.from_fasta.fasta \ --genome-fasta $genomeFn tombo text_output browser_files --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --file-types coverage signal signal_sd dwell difference tombo text_output browser_files --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --file-types coverage fraction signal signal_sd dwell difference \ --statistics-filename test_stats.2samp.tombo.stats tombo text_output browser_files --file-types statistic \ --statistics-filename test_stats.2samp_levels.tombo.stats tombo text_output browser_files --file-types fraction dampened_fraction \ valid_coverage --statistics-filename \ test_stats.de_novo.two_way_thresh.tombo.stats tombo text_output browser_files --file-types fraction dampened_fraction \ valid_coverage --statistics-filename \ test_stats.alt_default_model.5mC.tombo.stats \ --browser-file-basename test_stats.alt_5mC printf "\n\n********* Testing other plotting commands **********\n" tombo plot cluster_most_significant --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --genome-fasta $genomeFn --num-regions 100 \ --statistics-filename test_stats.2samp.tombo.stats tombo plot cluster_most_significant --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --genome-fasta $genomeFn --num-regions 100 \ --r-data-filename testing.cluster_data.RData \ --statistics-filename test_stats.2samp.tombo.stats tombo plot cluster_most_significant --fast5-basedirs $natDir \ --control-fast5-basedirs $ampDir \ --genome-fasta $genomeFn --num-regions 100 \ --statistics-filename test_stats.2samp_levels.tombo.stats \ --pdf-filename testing.cluster_most_signif.2samp_levels.pdf tombo plot kmer --fast5-basedirs $natDir \ --num-kmer-threshold 0 \ --pdf-filename testing.kmer_dist.median.all_events.pdf tombo plot kmer --fast5-basedirs $natDir --read-mean \ --num-kmer-threshold 1 \ --pdf-filename testing.kmer_dist.median.pdf tombo plot kmer --fast5-basedirs $natDir --read-mean \ --corrected-group RawGenomeCorrected_pA_raw_000 \ --num-kmer-threshold 1 \ --pdf-filename testing.kmer_dist.pA_raw.pdf tombo plot kmer --fast5-basedirs $natDir --read-mean \ --corrected-group RawGenomeCorrected_pA_000 \ --num-kmer-threshold 1 \ --pdf-filename testing.kmer_dist.pA.pdf