# Command reference Full `--help` for every `crisprware` subcommand. The [module pages](modules/index.md) cover the options you reach for most; this page is the complete listing. ## preprocess_annotation ```text usage: crisprware preprocess_annotation [-h] -g GTF [-t [TPM_FILES ...]] [-f {salmon,kallisto,flair,mandalorian,infer}] [--mean MEAN] [--median MEDIAN] [--min MIN] [--max MAX] [-n TOP_N] [-c {median,mean,min,max}] [-m [{metagene,consensus,longest,shortest} ...]] [-w TSS_WINDOW TSS_WINDOW] [-e TES_WINDOW TES_WINDOW] [-x TX_TO_GENE] [--strip_tx_id] [-o OUTPUT_DIRECTORY] Preprocess GTF/GFF annotations with optional RNA-seq filtering. options: -h, --help show this help message and exit -g GTF, --gtf GTF GTF/GFF file to use for isoform filtering. -t [TPM_FILES ...], --tpm_files [TPM_FILES ...] A list of one or more isoform quantification files produced by Salmon, Kallisto or FLAIR (FLAIR outputs counts, not TPMs). The first column should contain only the transcript_id and should exactly match the transcript_ids in --gtf. All transcript_ids in each TPM file must be common across all files and must be found in the GTF file. -f {salmon,kallisto,flair,mandalorian,infer}, --type {salmon,kallisto,flair,mandalorian,infer} Specify TPM input type. 'infer' guesses the input type based on the header line. [default: "infer"]. --mean MEAN For a given isoform, the mean tpm/count across samples must be at least this to be considered, else discard isoform. [default: 0.0] --median MEDIAN For a given isoform, the median tpm/count across samples must be at least this to be considered, else discard isoform. [default: 0.0] --min MIN For a given isoform, each sample must have at least this tpm/count to be considered, else discard isoform. [default: 0.0] --max MAX For a given isoform, at least one sample must have at least this tpm/count to be considered, else discard isoform. [default: 0.0] -n TOP_N, --top_n TOP_N For a given gene, rank all isoforms by median_tpm, keep the top_n ranked isoforms and discard the rest. '-1' to keep all isoforms. [default: -1] -c {median,mean,min,max}, --top_n_column {median,mean,min,max} The metric by which to rank and filter top isoforms. Used with '-n' to select expressed transcripts. [default: median] -m [{metagene,consensus,longest,shortest} ...], --model [{metagene,consensus,longest,shortest} ...] Whether to output 'metagene', 'consensus', 'longest', 'shortest' model. 'longest' and 'shortest' select, for a given gene, the transcript with the longest or shortest CDS, for now noncoding genes are ignored. Output is always after tpm filtering has been applied. Multiple entries are allowed e.g. --model metagene consensus longest [default: None] -w TSS_WINDOW TSS_WINDOW, --tss_window TSS_WINDOW TSS_WINDOW Pass two, space-separated, integers to specifiy the bp window around the TSS as '' ''. Strand-orientation is inferred, i.e. '' will be in the 5' direction of the TSS and in the 3' direction. e.g. --tss_window 250 150. [default: None] -e TES_WINDOW TES_WINDOW, --tes_window TES_WINDOW TES_WINDOW Pass two, space-separated, integers to specifiy the bp window around the transcription end site, TES, as '' ''. Strand-orientation is inferred, i.e. '' will be in the 5' direction of the TES and in the 3' direction. e.g. --tss_window 0 150. [default: None] -x TX_TO_GENE, --tx_to_gene TX_TO_GENE A TSV with transcript IDs in the first column and Gene IDs in the second. The transcript IDs must match the first column entries of the --quant_files. If this is not provided it will be deduced from the GTF/GFF3 and saved as './tmp/tx2gene.tsv'. --strip_tx_id Set this flag if there are transcript IDs in the quantification files but not in the GTF/GFF3. [default: False] -o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY Path to output. [default: current directory] ``` ## index_genome ```text usage: crisprware index_genome [-h] -f FASTA [-k [LOCATIONS_TO_KEEP ...]] [--feature FEATURE] [-w CONTEXT_WINDOW CONTEXT_WINDOW] -p PAM -l PROTOSPACER_LENGTH [--pam_5_prime] [--bin_width BIN_WIDTH] [-o OUTPUT_DIRECTORY] Build a crispr-ots off-target index (PAM, protospacer length, and PAM orientation define the enzyme). options: -h, --help show this help message and exit -f FASTA, --fasta FASTA FASTA file to use as a reference for index creation. -k [LOCATIONS_TO_KEEP ...], --locations_to_keep [LOCATIONS_TO_KEEP ...] List of BED/GTF files with coordinates to use for index creation. These locations will be used for off- target scoring. If multiple files are passed, coordinates will be merged with a union operation. Leave empty to use entire fasta. --feature FEATURE For any GTF/GFF in '--locations_to_keep', only this feature will be used for determining appropriate sgRNA. The feature should match an entry in the third column of the GTF/GFF. [default: 'transcript'] -w CONTEXT_WINDOW CONTEXT_WINDOW, --context_window CONTEXT_WINDOW CONTEXT_WINDOW Pass two, space-separated, integers to specifiy the nucleotide window around the --locations_to_keep '' ''. This can be used to expand the window around the final intervals e.g. '-w 1000 1500' expands chr1 2000 3500 -> chr1 1000 5000 Good for CRISPRi/a [default: 20 20] -p PAM, --pam PAM PAM motif as an IUPAC string, e.g. NGG (SpCas9), NAG, TTTV or TTTN (Cas12a). With --protospacer_length and --pam_5_prime this fully defines the indexed off- target sites. -l PROTOSPACER_LENGTH, --protospacer_length PROTOSPACER_LENGTH Protospacer (spacer) length in bases, e.g. 20 for SpCas9 or 23 for Cas12a. --pam_5_prime Set if the PAM is 5' of the protospacer (Cas12a-style). Omit for a 3' PAM (SpCas9-style). [default: False] --bin_width BIN_WIDTH crispr-ots bin-prefix width (1-15); higher = faster GPU scan but a larger index. Sweet spots: ~9-10 SpCas9 full-human, 14 for Cas12a full-human on a 24 GB GPU. [default: engine default] -o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY Path to output. [default: current directory] ``` ## generate_guides ```text usage: crisprware generate_guides [-h] -f FASTA [-p PAM] [-l SGRNA_LENGTH] [-w CONTEXT_WINDOW CONTEXT_WINDOW] [-5 ACTIVE_SITE_OFFSET_5] [-3 ACTIVE_SITE_OFFSET_3] [-k [LOCATIONS_TO_KEEP ...]] [--feature FEATURE] [--join_operation {merge,intersect}] [--locations_to_discard [LOCATIONS_TO_DISCARD ...]] [--prefix PREFIX] [--gc_range GC_RANGE GC_RANGE] [--discard_poly_T] [--discard_poly_G] [--restriction_patterns [RESTRICTION_PATTERNS ...]] [--flank_5 FLANK_5] [--flank_3 FLANK_3] [--min_chr_length MIN_CHR_LENGTH] [--pam_5_prime] [--coords_as_active_site] [-t THREADS] [--chunk_size CHUNK_SIZE] [-o OUTPUT_DIRECTORY] Generate sgRNA sequences matching specified PAM. options: -h, --help show this help message and exit -f FASTA, --fasta FASTA FASTA file to use as a reference for sgRNA generation. -p PAM, --pam PAM Protospacer adjacent motif to match. All IUPAC ambiguity codes are accepted as well as standard ATCG. [default: NGG] -l SGRNA_LENGTH, --sgRNA_length SGRNA_LENGTH Length of sgRNA to generate. [default: 20] -w CONTEXT_WINDOW CONTEXT_WINDOW, --context_window CONTEXT_WINDOW CONTEXT_WINDOW Pass two, space-separated, integers to specifiy the nucleotide window around the sgRNA as '' ''. This can be used for downstream scoring, For Ruleset3 use -w 4 6 to obtain an appropriate score context. [default: 4 6] -5 ACTIVE_SITE_OFFSET_5, --active_site_offset_5 ACTIVE_SITE_OFFSET_5 Where cut occurs relative to PAM 5' end. To avoid error, use '=' sign when passing a negative number, e.g. --active_site_offset_5=-1 [default: -4] -3 ACTIVE_SITE_OFFSET_3, --active_site_offset_3 ACTIVE_SITE_OFFSET_3 Where cut occurs relative to PAM 5' end. [default: -2] To avoid error, use '=' sign when passing a negative number, e.g. --active_site_offset_3=-3 [default: -4] -k [LOCATIONS_TO_KEEP ...], --locations_to_keep [LOCATIONS_TO_KEEP ...] List of BED/GTF files with coordinates in which the sgRNA desired. If the sgRNA cutsite does not intersect coordinates in these files they are discarded. Leave blank to keep all sgRNA. e.g. atac_peak.bed genes.gtf --feature FEATURE For any GTF/GFF in '--locations_to_keep', only this feature will be used for determining appropriate sgRNA. The feature should match an entry in the third column of the GTF/GFF. [default: 'exon'] --join_operation {merge,intersect} How to treat '--locations_to_keep' if multiple files are passed. Either 'merge' or 'intersect' can be used and work as described in Bedtools. If 'merge', sgRNA will be kept if its cutsite intersects an entry in ANY of the files, if 'intersect' the cutsite must intersect an entry in EACH file. [default: 'intersect'] --locations_to_discard [LOCATIONS_TO_DISCARD ...] List of BED/GTF files with coordinates where sgRNA should not target. If the sgRNA cutsite intersects coordinates in these files the sgRNA is discarded. Leave blank to keep all sgRNA. e.g. TSS.bed coding_genes.gtf --prefix PREFIX Prefix to use for sgRNA identifiers. [default: None] --gc_range GC_RANGE GC_RANGE Pass two, space-separated, integers to specifiy the percentile range of GC content e.g. '--gc_range 25 75'. [default: 0 100] --discard_poly_T Whether to discard polyT (>TTT) sgRNA. Recommend True for PolIII promoters [default: False] --discard_poly_G Whether to discard polyT (>GGGG) sgRNA. [default: False] --restriction_patterns [RESTRICTION_PATTERNS ...] Reject sgRNA with these restriction patterns. Also checks 5'flank+sgRNA+3'flank, and reverse complement, if provided. For multiple values, separate by space. e.g. GCGGCCGC TCTAGA CACCTGC --flank_5 FLANK_5 include the 5' context of the lentivirus vector. Used in conjunction with --restriction_patterns to remove incompatible sgRNA --flank_3 FLANK_3 include the 3' context of the lentivirus vector. Used in conjunction with --restriction_patterns to remove incompatible sgRNA --min_chr_length MIN_CHR_LENGTH Minimum chromosome length to consider for sgRNA generation. [default: 20] --pam_5_prime If the PAM is positioned 5' to the protospacer set this flag, e.g. for Cas12a sgRNAs [default: False] --coords_as_active_site Whether to output bed coordinates at the active site rather than the coordinates of the entire protospacer. For purposes of keeping or discarding sgRNAs, overlap with the active site coordinates will be used regardless [default: True] -t THREADS, --threads THREADS Number of worker processes. Parallelism scales with the number of genome windows (see --chunk_size), not the PAM count, so this can usefully exceed it. [default: 4] --chunk_size CHUNK_SIZE Genome window size in bp for parallel scanning; smaller = more/finer tasks (better load balance, slightly more overhead). [default: 5,000,000] -o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY Path to output. [default: current directory] ``` ## score_guides ```text usage: crisprware score_guides [-h] -b GRNA_BED [-i [GUIDESCAN2_INDICES ...]] [--tracr {Hsu2013,Chen2013,both}] [-t THREADS] [--threshold THRESHOLD] [--mismatches MISMATCHES] [--rna_bulges RNA_BULGES] [--dna_bulges DNA_BULGES] [--mode {succinct,complete}] [--alt_pams [ALT_PAMS ...]] [-d] [--skip_rs3] [--skip_gs2] [--min_rs3 MIN_RS3] [--cas12a_scorer {none,enpam_gb,deepcpf1,enseq_deepcpf1,seq_deepcpf1variants,both} [{none,enpam_gb,deepcpf1,enseq_deepcpf1,seq_deepcpf1variants,both} ...]] [--cas12a_variant CAS12A_VARIANT] [--min_deepcpf1 MIN_DEEPCPF1] [--min_enpam_gb MIN_ENPAM_GB] [--min_enseq_deepcpf1 MIN_ENSEQ_DEEPCPF1] [--cas9_scorer {none,deepspcas9,deephf_wt_u6,deephf_esp,deephf_hf} [{none,deepspcas9,deephf_wt_u6,deephf_esp,deephf_hf} ...]] [--min_deepspcas9 MIN_DEEPSPCAS9] [--min_deephf MIN_DEEPHF] [--chunk_size CHUNK_SIZE] [-k] [-o OUTPUT_DIRECTORY] [--ucscgb UCSCGB] [--chrom_sizes CHROM_SIZES] [--crispr_ots_bin CRISPR_OTS_BIN] [--ucscgb_scanner {gpu,cpu}] [--ucscgb_cfd_threshold UCSCGB_CFD_THRESHOLD] [--ucscgb_list_cap UCSCGB_LIST_CAP] [--ucscgb_blank_threshold UCSCGB_BLANK_THRESHOLD] [--ucscgb_reuse_offtargets] [--ucscgb_2xnls | --no-ucscgb_2xnls] [--ucscgb_chunk_max UCSCGB_CHUNK_MAX] [--ucscgb_gpus UCSCGB_GPUS] [--ucscgb_keep_chunks] Score guides with RS3 cleavage and crispr-ots/Guidescan2 off-target specificity. options: -h, --help show this help message and exit -b GRNA_BED, --grna_bed GRNA_BED grnas.bed ouput of generate_guides. -i [GUIDESCAN2_INDICES ...], --guidescan2_indices [GUIDESCAN2_INDICES ...] One or more, space-separate Guidescan2 indices. A specificity score will be calculated against each index separately. --tracr {Hsu2013,Chen2013,both} TracrRNA version for cleavage scoring. Either 'Hsu2013' or 'Chen2013' or 'both', see https://github.com/gpp-rnd/rs3 for details. -t THREADS, --threads THREADS Number of threads [default: 8] --threshold THRESHOLD Threshold for Guidescan2 off-target hits. If off- targets are found this distance away the gRNA will be discarded, i.e. set to 2 to discard any guides with a 0, 1 or 2 mismatches from another PAM adjacent sequence. --threshold=-1 to retain all guides [default: 2] --mismatches MISMATCHES Number of mismatches for Guidescan2 off-target scoring [default: 3] --rna_bulges RNA_BULGES RNA bulges for Guidescan2 off-target scoring [default: 0] --dna_bulges DNA_BULGES DNA bulges for Guidescan2 off-target scoring [default: 0] --mode {succinct,complete} Whether Guidescan2 temporary output should be succinct or complete mode [default: 0] --alt_pams [ALT_PAMS ...] One or more, space-separate alternative pams for off- target consideration. e.g. NAG -d, --drop_duplicates Drop exact duplicate gRNAs before scoring to save time. Set flag to retain duplicates. [default: True] --skip_rs3 Set flag to skip RS3 scoring [default: False] --skip_gs2 Set flag to skip Guidescan2 scoring [default: False] --min_rs3 MIN_RS3 Minimum cleavage RS3 score. RS3 cleavage scores are formatted as z-scores, so this is interpreted as a standard deviation cutoff. Functionality also available in rank_guides.py. Applying at this stage can increase speed by filtering before off-target scoring. [default: None] --cas12a_scorer {none,enpam_gb,deepcpf1,enseq_deepcpf1,seq_deepcpf1variants,both} [{none,enpam_gb,deepcpf1,enseq_deepcpf1,seq_deepcpf1variants,both} ...] One or more Cas12a on-target scorers (space- separated). enpam_gb for en(As)Cas12a; deepcpf1 for wildtype AsCas12a/LbCas12a (Kim 2018); enseq_deepcpf1 for wildtype AsCas12a (Chen 2025, modern); seq_deepcpf1variants for variant-specific scoring (requires --cas12a_variant). 'both' is the legacy alias for 'enpam_gb deepcpf1'. Multiple values may be combined (e.g. --cas12a_scorer enpam_gb deepcpf1 enseq_deepcpf1). Mutually exclusive with --tracr (RS3 is SpCas9-only); implies --skip_rs3. [default: none] --cas12a_variant CAS12A_VARIANT Cas12a variant name (e.g. AsCas12a_Ultra, enAsCas12a-HF1, LbCas12a, HyperFi-AsCas12a). Required when --cas12a_scorer is seq_deepcpf1variants. See crisprware.scorers.seq_deepcpf1variants for the full 23-variant list. --min_deepcpf1 MIN_DEEPCPF1 Minimum DeepCpf1 score (raw regression, ~[0, 100]). Applied after scoring; analogous to --min_rs3. [default: None] --min_enpam_gb MIN_ENPAM_GB Minimum enPAM+GB score (probability-like, [0, 1]). Applied after scoring; analogous to --min_rs3. [default: None] --min_enseq_deepcpf1 MIN_ENSEQ_DEEPCPF1 Minimum enseq-DeepCpf1 / seq-DeepCpf1variants score (probability, [0, 1]). Applied after scoring. [default: None] --cas9_scorer {none,deepspcas9,deephf_wt_u6,deephf_esp,deephf_hf} [{none,deepspcas9,deephf_wt_u6,deephf_esp,deephf_hf} ...] One or more additional SpCas9 on-target scorers (space-separated) to run alongside RS3. deepspcas9: Kim 2019 inception-CNN (Sci Adv); 30-nt context (4 + 20 protospacer + 3 PAM + 3 downstream); unbounded regression. deephf_*: Wang 2019 BiLSTM (Nat Commun) for three Cas9 variants -- wildtype SpCas9 (wt_u6), eSpCas9 (esp), SpCas9-HF1 (hf); 23-nt protospacer+PAM input; output in [0, 1]. Multiple values may be combined (e.g. --cas9_scorer deepspcas9 deephf_wt_u6 deephf_esp deephf_hf). Runs in parallel with --tracr (no mutex). [default: none] --min_deepspcas9 MIN_DEEPSPCAS9 Minimum DeepSpCas9 score (unbounded regression, ~[0, 100]). Applied after scoring; analogous to --min_rs3. [default: None] --min_deephf MIN_DEEPHF Minimum DeepHF score (probability, [0, 1]). Applied to whichever deephf_* variant is selected. [default: None] --chunk_size CHUNK_SIZE Number of gRNAs to hold in memory for cleavage scoring and off-target filtering. Reduce if memory constrained. Increasing may improve runtime [default: 100000] -k, --keep_tmp Set flag to keep temporary Guidescan2 output [default: False] -o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY Path to output. [default: current directory] UCSC browser track (Cas12a): --ucscgb UCSCGB Alternative output path: write a UCSC Genome Browser Cas12a track (cas12a.bb, crisprDetails.tab.gz + .gzi, cas12aTargets.as) to this directory. Runs the selected --cas12a_scorer on-target models plus a streaming crispr-ots off-target pass (--output-mode both, skipping off-targets for perfect-match guides) against the first -i index. Implies Cas12a mode and retains duplicate guides. [default: None] --chrom_sizes CHROM_SIZES chrom.sizes file (chromsize) for bedToBigBed when --ucscgb is set. --crispr_ots_bin CRISPR_OTS_BIN Path to the crispr-ots binary used for the --ucscgb streaming pass (must support --output-mode/--scanner; default: 'crispr-ots' on PATH). --ucscgb_scanner {gpu,cpu} Scanner for the --ucscgb off-target pass [default: gpu]. --ucscgb_cfd_threshold UCSCGB_CFD_THRESHOLD CFD floor for the off-target list written to crisprDetails (counts are unaffected — they come from the unfloored Mode-1 totals). [default: 0.023] --ucscgb_list_cap UCSCGB_LIST_CAP Max off-targets listed per guide in crisprDetails (top by score) [default: 100]. --ucscgb_blank_threshold UCSCGB_BLANK_THRESHOLD Guides with more than this many off-targets get an empty list (counts kept) — the viewer shows 'Too many off-targets'. [default: 2000] --ucscgb_reuse_offtargets Reuse an existing off-target enumerate output (offtargets.csv + .ot.tsv) in the --ucscgb dir instead of re-running crispr-ots. Use when re-assembling a track after an adapter-only change (the engine output is unchanged), skipping the GPU pass. [default: off] --ucscgb_2xnls, --no-ucscgb_2xnls Also score off-targets with the 2xNLS-Cas12a matrix and emit its TTTV/TTTN specificity columns (a second, aggregated off-target pass — the off-target list still comes from the enCas12a pass). [default: on; use --no- ucscgb_2xnls to skip] --ucscgb_chunk_max UCSCGB_CHUNK_MAX If >0, build the track in chunks of at most this many guides and merge the per-chunk tracks into one (recomputing crisprDetails.tab byte offsets). Bounds peak memory and disk, and enables multi-GPU fan-out via --ucscgb_gpus. 0 = single pass over all guides. [default: 0] --ucscgb_gpus UCSCGB_GPUS Comma-separated CUDA device ids to fan --ucscgb_chunk_max chunks across (e.g. '0,1,2,3,4,5,6,7'); each concurrent chunk's off-target pass is pinned to one device, so chunks never share a GPU. Only used when --ucscgb_chunk_max>0. [default: single device 0]. --ucscgb_keep_chunks Keep the per-chunk working dir (/chunks/) after merging, for inspection or resume. [default: delete after a successful merge]. ``` ## rank_guides ```text usage: crisprware rank_guides [-h] -k SCORED_GUIDES -t TARGETS [--target_mode {gene,tx}] [-f FEATURE] [-p PERCENTILE_RANGE PERCENTILE_RANGE] [-n NUMBER_OF_GUIDES] [--min_spacing MIN_SPACING] [--output_all] [--plot_histogram] [-c [FILTERING_COLUMNS ...]] [-m [MINIMUM_VALUES ...]] [-r [RANKING_COLUMNS ...]] [-w [COLUMN_WEIGHTS ...]] [--normalize_columns] [-o OUTPUT_DIRECTORY] Rank and select best guides based on scoring criteria. options: -h, --help show this help message and exit -k SCORED_GUIDES, --scored_guides SCORED_GUIDES .bed output from score_guides. -t TARGETS, --targets TARGETS BED/GTF/GFF used to select final guides per target. For GTF/GFF, set --target_mode to either 'gene' or 'tx'. For BED, targets are each entry. Use '-- number_of_targets' to set the number of guides chosen for each target. --target_mode {gene,tx} If a GTF/GFF is used to select targets, gRNAs can be grouped at either the 'tx' or 'gene' level e.g. '-- target_mode gene -n 10' chooses 10 guides per gene, ' --target_mode tx -n 10' chooses 10 per transcript [default: gene]. -f FEATURE, --feature FEATURE If GTF/GFF passed, use this feature for processing e.g. 'exon', 'CDS', '5UTR', etc. The feature appears in the third column of the GTF/GFF [default: CDS]. -p PERCENTILE_RANGE PERCENTILE_RANGE, --percentile_range PERCENTILE_RANGE PERCENTILE_RANGE Allowable range of guide for each transcript and feature set, e.g. '-p 60 80 -f exon' returns gRNAs in the 60th to 80th percentile of exons for a given transcript. Default setting returns guides anywhere in the CDS for each transcript [default: 0 100] -n NUMBER_OF_GUIDES, --number_of_guides NUMBER_OF_GUIDES Number of guides returned per target.'-1' to keep all guides [default: -1] --min_spacing MIN_SPACING The minimum nucleotide space between guides for a given target. e.g. --min_spacing 10, requires guides 10 nts appart. 0 to allow overlapping guides.[default: 0] --output_all Set flag to save gRNA-target TSVs at each stage of filtering rather than just the end.[default: False] --plot_histogram Set flag to plot a histogram of the distribution of gRNAs per target after each filtering step. Sets '-- output_all' to True.[default: False] -c [FILTERING_COLUMNS ...], --filtering_columns [FILTERING_COLUMNS ...] One or more space-separated column names used for filtering. Uses raw values. e.g. '-c rs3_z_score specificity_Hg38_index'. -m [MINIMUM_VALUES ...], --minimum_values [MINIMUM_VALUES ...] A space-separated list of minimum values for each column in passed by --ranking_columns. e.g. '-c rs3_z_score specificity_Hg38_index -m "-1" 0.2' Default is no minimum [default: None] -r [RANKING_COLUMNS ...], --ranking_columns [RANKING_COLUMNS ...] One or more space-separated column names used for guide ranking. e.g. '-r rs3_score_Hsu2013 rs3_score_Chen2013'. -w [COLUMN_WEIGHTS ...], --column_weights [COLUMN_WEIGHTS ...] A space-separated list of weight values for each column in passed by --ranking_columns. e.g. '-c rs3_score specificity_Hg38_index -w 1 0' Default is equal weighting for all ranking columns. --normalize_columns Scale ranking column values to 0 to 1 [default: True] -o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY Path to output. [default: current directory] ```