Command Line Reference

Note

All subcommands, arguments, and options listed in these documents can be printed, along with a short explanation of each, on the command line by running seismic [command(s)] --help. For example, seismic --help prints all options and subcommands for the command seismic, seismic graph --help prints all options and subcommands for the command seismic graph, and seismic graph profile --help prints all options and subcommands for the command seismic graph profile.

Run the entire workflow

seismic wf

Run the entire workflow.

Usage

seismic wf [OPTIONS] FASTA [INPUT_PATH]...

Options

--wf-branch <wf_branch>

Run a step under a new branch: give the step name then the branch name (may be used multiple times to branch different steps)

--demult, --no-demult

Enable demultiplexing

-x, --fastqx <fastqx>

FASTQ files of paired-end reads with mates 1 and 2 in separate files

-y, --fastqy <fastqy>

FASTQ file(s) of paired-end reads with mates 1 and 2 interleaved

-z, --fastqz <fastqz>

FASTQ file(s) of single-end reads

-X, --dmfastqx <dmfastqx>

Demultiplexed FASTQ files of mate 1 and mate 2 reads

-Y, --dmfastqy <dmfastqy>

Demultiplexed FASTQ files of paired-end reads interleaved in one file

-Z, --dmfastqz <dmfastqz>

Demultiplexed FASTQ files of single-end reads

--phred-enc <phred_enc>

Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files

-R, --refs-meta <refs_meta>

Add reference metadata from this CSV file to exported results

--barcode-start <barcode_start>

Index of start of barcode

--barcode-end <barcode_end>

Index of end of barcode

--read-pos <read_pos>

Expected position of the barcode in the read (1-indexed). Defaults to –barcode-start

--barcode <barcode>

A list of barcode name, barcode sequence, and barcode position (1-indexed relative to read start) to demultiplex

--mismatch-tolerance <mismatch_tolerance>

Consider patterns to match if they have up to this many mismatches. Will increase non-parallel computation at a factorial rate. Use caution Going above 2 mismatches. Does not apply to clipped sequences.

--index-tolerance <index_tolerance>

Allow patterns to be found in reads up to this distance from the reference index.

--allow-n, --no-allow-n

Allow N as a valid mismatch when –mismatch-tolerance ≥ 1. Increases memory consumption.

-o, --out-dir <out_dir>

Write all output files to this directory

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

--fastp, --no-fastp

Use fastp to QC, filter, and trim reads before alignment

--fastp-5, --no-fastp-5

Trim low-quality bases from the 5’ ends of reads

--fastp-3, --no-fastp-3

Trim low-quality bases from the 3’ ends of reads

--fastp-w <fastp_w>

Use this window size (nt) for –fastp-5 and –fastp-3

--fastp-m <fastp_m>

Use this mean quality threshold for –fastp-5 and –fastp-3

--fastp-poly-g <fastp_poly_g>

Trim poly(G) tails (two-color sequencing artifacts) from the 3’ end

Options:

yes | no | auto

--fastp-poly-g-min-len <fastp_poly_g_min_len>

Minimum number of Gs to consider a poly(G) tail for –fastp-poly-g

--fastp-poly-x, --no-fastp-poly-x

Trim poly(X) tails (i.e. of any nucleotide) from the 3’ end

--fastp-poly-x-min-len <fastp_poly_x_min_len>

Minimum number of bases to consider a poly(X) tail for –fastp-poly-x

--fastp-adapter-trimming, --no-fastp-adapter-trimming

Trim adapter sequences from the 3’ ends of reads

--fastp-adapter-1 <fastp_adapter_1>

Trim this adapter sequence from the 3’ ends of read 1s

--fastp-adapter-2 <fastp_adapter_2>

Trim this adapter sequence from the 3’ ends of read 2s

--fastp-adapter-fasta <fastp_adapter_fasta>

Trim adapter sequences in this FASTA file from the 3’ ends of reads

--fastp-detect-adapter-for-pe, --no-fastp-detect-adapter-for-pe

Automatically detect the adapter sequences for paired-end reads

--fastp-min-length <fastp_min_length>

Discard reads shorter than this length

--bt2-local, --bt2-end-to-end

Align reads in local mode rather than end-to-end mode

--bt2-discordant, --bt2-no-discordant

Output paired-end reads whose mates align discordantly

--bt2-mixed, --bt2-no-mixed

Attempt to align individual mates of pairs that fail to align

--bt2-dovetail, --bt2-no-dovetail

Consider dovetailed mate pairs to align concordantly

--bt2-contain, --bt2-no-contain

Consider nested mate pairs to align concordantly

--bt2-I <bt2_i>

Discard paired-end alignments shorter than this many bases

--bt2-X <bt2_x>

Discard paired-end alignments longer than this many bases

--bt2-score-min-e2e <bt2_score_min_e2e>

Discard alignments that score below this threshold in end-to-end mode

--bt2-score-min-loc <bt2_score_min_loc>

Discard alignments that score below this threshold in local mode

--bt2-i <bt2_s>

Seed Bowtie2 alignments at this interval

--bt2-L <bt2_l>

Use this seed length for Bowtie2

--bt2-gbar <bt2_gbar>

Do not place gaps within this many bases from the end of a read

--bt2-D <bt2_d>

Discard alignments if over this many consecutive seed extensions fail

--bt2-R <bt2_r>

Re-seed reads with repetitive seeds up to this many times

--bt2-dpad <bt2_dpad>

Pad the alignment matrix with this many bases (to allow gaps)

--bt2-orient <bt2_orient>

Require paired mates to have this orientation

Options:

fr | rf | ff

--bt2-un, --bt2-no-un

Output unaligned reads to a FASTQ file

--seed <seed>

Seed for the random number generator

--min-mapq <min_mapq>

Discard reads with mapping qualities below this threshold

-N, --min-reads <min_reads>

Discard alignment maps with fewer than this many reads

--sep-strands, --mix-strands

Separate each alignment map into forward- and reverse-strand reads

--f1r2-fwd, --f1r2-rev

With –sep-strands, consider forward mate 1s and reverse mate 2s to be forward-stranded

--rev-label <rev_label>

With –sep-strands, add this label to each reverse-strand reference

--min-phred <min_phred>

Mark base calls with Phred scores lower than this threshold as ambiguous

--batch-size <batch_size>

Limit batches to at most this many reads

--insert3, --insert5

Mark each insertion on the base to its 3’ (True) or 5’ (False) side

--ambindel, --no-ambindel

Mark all ambiguous insertions and deletions (indels)

--overhangs, --no-overhangs

Retain the overhangs of paired-end mates that dovetail

-5, --clip-end5 <clip_end5>

Clip this many bases from the 5’ end of each read

-3, --clip-end3 <clip_end3>

Clip this many bases from the 3’ end of each read

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--write-read-names, --no-write-read-names

Write the name of each read in a second set of batches (necessary for the options –drop-read or –drop-read-file)

--idmut-pos-table, --no-idmut-pos-table

Tabulate relationships per position for idmut data

--idmut-read-table, --no-idmut-read-table

Tabulate relationships per read for idmut data

--idmut-cx, --idmut-py

Use a fast (C extension module) version of the idmut algorithm; the slow (Python) version is still avilable as a fallback if the C extension cannot be loaded, and for debugging/benchmarking

-c, --region-coords <region_coords>

Select a region of a reference given its 5’ and 3’ end coordinates

-P, --region-primers <region_primers>

Select a region of a reference given its forward and reverse primers

--primer-gap <primer_gap>

Leave a gap of this many bases between the primer and the region

-i, --regions-file <regions_file>

Select regions of references from coordinates/primers in a CSV file

--count-del, --no-del

Count deletions as mutations

--count-ins, --no-ins

Count insertions as mutations

--no-mut <no_mut>

Do not count this type of mutation (overrides –count-del/ins)

--only-mut <only_mut>

Count only this type of mutation (overrides other mutation settings)

--probe <probe>

Use the default options for this chemical probe

Options:

DMS | SHAPE | ETC | none

--mask-a, --keep-a

Mask positions with base A

--mask-c, --keep-c

Mask positions with base C

--mask-g, --keep-g

Mask positions with base G

--mask-u, --keep-u

Mask positions with base U

--mask-polya <mask_polya>

Mask stretches of at least this many consecutive A bases (0 disables); defaults to 5 for chemical probes, 0 for none

--mask-pos <mask_pos>

Mask this position in this reference

--mask-pos-file <mask_pos_file>

Mask positions in references from a file

--min-ninfo-pos <min_ninfo_pos>

Mask positions with fewer than this many informative base calls

--max-fmut-pos <max_fmut_pos>

Mask positions with more than this fraction of mutated base calls

--drop-read <drop_read>

Drop the read with this name

--drop-read-file <drop_read_file>

Drop the reads with names in this file

--drop-discontig, --keep-discontig

Drop paired-end reads with discontiguous mates

--min-ncov-read <min_ncov_read>

Drop reads with fewer than this many bases covering the region

--min-fcov-read <min_fcov_read>

Drop reads covering less than this fraction of the region

--min-finfo-read <min_finfo_read>

Drop reads with less than this fraction of informative base calls

--max-fmut-read <max_fmut_read>

Drop reads with more than this fraction of mutated base calls

--min-mut-gap <min_mut_gap>

Filter out mutations separated by fewer than this many bases

--mut-collisions <mut_collisions>

If two mutations are closer than –min-mut-gap positions, MERGE the mutations, DROP the read, or AUTO-select based on the probe.

Options:

drop | merge | auto

--quick-unbias, --exact-unbias

Correct observer bias using a quick (typically linear time) heuristic

--quick-unbias-thresh <quick_unbias_thresh>

Treat mutated fractions under this threshold as 0 with –quick-unbias

--max-filter-iter <max_filter_iter>

Stop the filter step after this many iterations (0 for no limit)

--filter-pos-table, --no-filter-pos-table

Tabulate relationships per position for filter data

--filter-read-table, --no-filter-read-table

Tabulate relationships per read for filter data

--self-contained, --no-self-contained

Write self-contained batch files that do not require loading predecessor batches (Filter and Cluster steps), at the cost of larger files on disk

--scan, --no-scan

Scan the RNA for domains (filterscan) and cluster them (clusterscan)

-L, --tile-length <tile_length>

Make each tile this length (if 0, use 2x the median read length)

-O, --tile-min-overlap <tile_min_overlap>

Make adjacent tiles overlap by at least this fraction of length

--erase-tiles, --keep-tiles

Erase the filter reports/batches from the tiling step

--pair-fdr <pair_fdr>

Find correlated pairs at this false discovery rate (FDR)

--min-pairs <min_pairs>

Cluster only the regions with at least this many correlated pairs

--pair-distance-percentile <pair_distance_percentile>

Among pairs that survive the endpoint-peak filter, drop any pair whose L1 (Manhattan) distance to its nearest surviving neighbor exceeds this percentile of all such distances. Pairs more isolated than this threshold are treated as noise.

--endpoint-window <endpoint_window>

When testing whether a position is a significant hub of correlated pair endpoints, aggregate counts over a window of this many adjacent positions: forward (pos5, pos5+1, …, pos5+window) for 5’ ends, backward (pos3-window, …, pos3) for 3’ ends. Larger values boost statistical power for helices whose endpoints are not always at exactly the same position.

--min-nearby-pairs <min_nearby_pairs>

Minimum number of other surviving pairs that must lie within the pair-distance-percentile L1 threshold for a pair to be kept. Setting this above 1 filters out small coincidental clusters of noise pairs (‘buddy noise’) at the cost of potentially clipping domain edges.

--min-cluster-length <min_cluster_length>

Cluster only the regions with at least this many positions

--max-cluster-length <max_cluster_length>

Cluster only the regions with no more than this many positions

--gap-mode <gap_mode>

If there are gaps between regions to cluster, OMIT (do not cluster) the gaps, INSERT a new region into each gap, or EXPAND the existing regions to fill the gaps

Options:

omit | insert | expand

--min-clusters <min_clusters>

Start at this many clusters

-k, --max-clusters <max_clusters>

Stop at this many clusters (0 for no limit)

-e, --min-em-runs <min_em_runs>

Run EM (successfully) at least this number of times for each K

-E, --max-em-runs <max_em_runs>

Run EM (successfully or not) at most this number of times for each K

--em-thresh <em_thresh>

Stop EM when the log likelihood increases by less than this threshold

--min-em-iter <min_em_iter>

Run EM for at least this many iterations

--max-em-iter <max_em_iter>

Run EM for at most this many iterations

--max-pearson-run <max_pearson_run>

Remove runs with two clusters more similar than this correlation

--min-marcd-run <min_marcd_run>

Remove runs with two clusters that differ by less than this MARCD

--max-arcd-vs-ens-avg <max_arcd_vs_ens_avg>

Remove runs where a cluster differs by more than this ARCD from the ensemble average at any position

--max-gini-run <max_gini_run>

Remove runs where any cluster’s Gini coefficient exceeds this limit

--jackpot, --no-jackpot

Calculate the jackpotting quotient to find over-represented reads

--jackpot-conf-level <jackpot_conf_level>

Confidence level for the jackpotting quotient confidence interval

--max-jackpot-quotient <max_jackpot_quotient>

Remove runs whose jackpotting quotient exceeds this limit

--max-jackpot-sims <max_jackpot_sims>

Maximum number of simulations to compute the jackpotting quotient

--jackpot-max-data <jackpot_max_data>

Skip calculating the jackpotting quotient if the reads × positions exceeds this limit

--max-loglike-vs-best <max_loglike_vs_best>

Remove Ks with a log likelihood gap larger than this (0 for no limit)

--min-pearson-vs-best <min_pearson_vs_best>

Remove Ks where every run has less than this correlation vs. the best

--max-marcd-vs-best <max_marcd_vs_best>

Remove Ks where every run has more than this MARCD vs. the best

--try-all-ks, --stop-best-k

Try all numbers of clusters (Ks), even after finding the best number

--write-all-ks, --write-best-k

Write all numbers of clusters (Ks), rather than only the best number

--cluster-pos-table, --no-cluster-pos-table

Tabulate relationships per position for cluster data

--cluster-abundance-table, --no-cluster-abundance-table

Tabulate number of reads per cluster for cluster data

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--cluster, --no-cluster

Cluster reads to find alternative structures

--fold, --no-fold

Predict the secondary structure using the reactivities

-F, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--fold-table-region, --fold-full-region

If no regions are specified, whether to default to the table’s region or to the full region

--fold-dry-run, --fold-real-run

Only generate the fold command and input files; do not run folding

--fold-backend <fold_backend>

Model RNA structures using RNAstructure (Fold/ShapeKnots) or ViennaRNA (RNAfold/RNAsubopt); auto selects RNAstructure for DMS and ViennaRNA for other probes

Options:

auto | RNAstructure | ViennaRNA

--pseudoknots, --no-pseudoknots

Predict pseudoknotted structures (requires –fold-backend=RNAstructure; uses ShapeKnots when set, Fold otherwise)

--fold-energy-method <fold_energy_method>

Use this method to incorporate reactivities into folding energies. auto selects Cordero for DMS and Eddy for other probes; Eddy requires –fold-backend=ViennaRNA; Cordero requires –fold-backend=RNAstructure

Options:

auto | Deigan | Cordero | Eddy

--fold-temp <fold_temp>

Predict structures at this temperature (Celsius)

--deigan-slope <deigan_slope>

Slope (kcal/mol) for SHAPE reactivities using Deigan method; used only with –fold-energy-method=Deigan

--deigan-intercept <deigan_intercept>

Intercept (kcal/mol) for SHAPE reactivities using Deigan method; used only with –fold-energy-method=Deigan

--fold-quantile <fold_quantile>

Normalize and winsorize reactivities to this quantile for folding

--fold-constraint <fold_constraint>

Force bases to be paired/unpaired from a file of constraints

--fold-commands <fold_commands>

Command file for RNAFold

--eddy-prior-paired-file <eddy_prior_paired_file>

File of per-position prior probabilities of being paired for the Eddy method (passed as –sp-data with –sp-strategy Pp); only used with –fold-energy-method=Eddy and –fold-backend=ViennaRNA

--eddy-prior-unpaired-file <eddy_prior_unpaired_file>

File of per-position prior probabilities of being unpaired for the Eddy method (passed as –sp-data with –sp-strategy Pu); only used with –fold-energy-method=Eddy and –fold-backend=ViennaRNA

--fold-md <fold_md>

Limit base pair distances to this number of bases (0 for no limit)

--fold-mfe, --fold-sub

Predict only the minimum free energy (MFE) structure

--fold-max <fold_max>

Output at most this many structures (overriden by –fold-mfe)

--fold-percent <fold_percent>

Stop outputting structures when the % difference in energy exceeds this value (overriden by –fold-mfe)

--fold-edelta <fold_edelta>

Maximum absolute energy difference (kcal/mol) from the MFE for suboptimal structures output by RNAsubopt (overriden by –fold-mfe)

--fold-isolated, --fold-stacked

Allow isolated (non-stacked) base pairs when folding

--draw, --no-draw

Draw secondary structures with RNArtist.

--struct-num <struct_num>

Draw the specified structure (zero-indexed) or -1 for all structures. By default, draw the structure with the best AUROC.

--color, --no-color

Color bases by their reactivity

--draw-svg, --no-draw-svg

Output each drawing in a Scalable Vector Graphics file

--draw-png, --no-draw-png

Output each drawing in a Portable Network Graphics file

--update-rnartistcore, --no-update-rnartistcore

Check for and install updates to RNArtistCore.

--export, --no-export

Export each sample to SEISMICgraph (https://seismicrna.org)

-S, --samples-meta <samples_meta>

Add sample metadata from this CSV file to exported results

--all-pos, --unmasked-pos

Export all positions (not just unmasked positions)

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--hist-bins <hist_bins>

Number of bins in each histogram; must be ≥ 1

--hist-margin <hist_margin>

Autofill margins of at most this width in histograms of ratios

--struct-file <struct_file>

Compare mutational profiles to the structure(s) in this CT file

--terminal-pairs, --no-terminal-pairs

Include terminal base pairs (at the ends of stems) in ROC curves

--window <window>

Use a sliding window of this many bases

-n, --winmin <winmin>

Mask sliding windows with fewer than this number of data

--graph-quantile <graph_quantile>

Normalize and winsorize ratios to this quantile (0 disables)

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--graph-mprof, --no-graph-mprof

Graph mutational profiles

--graph-tmprof, --no-graph-tmprof

Graph typed mutational profiles

--graph-ncov, --no-graph-ncov

Graph coverages per position

--graph-mhist, --no-graph-mhist

Graph histograms of mutations per read

--graph-abundance, --no-graph-abundance

Graph abundance of each cluster

--graph-giniroll, --no-graph-giniroll

Graph rolling Gini coefficients

--graph-roc, --no-graph-roc

Graph receiver operating characteristic (ROC) curves

--graph-aucroll, --no-graph-aucroll

Graph rolling areas under ROC curves (AUC-ROC)

--graph-poscorr, --no-graph-poscorr

Graph phi correlations between positions

--graph-mutdist, --no-graph-mutdist

Graph distances between mutations

--mutdist-null, --no-mutdist-null

Include the null distribution of distances between mutations

--collate, --no-collate

Collate HTML graphs and SVG drawings into an HTML report file.

--name <name>

Prefix the HTML report with this name.

--verbose-name, --no-verbose-name

Add collated file information to report name.

--collate-out-dir <collate_out_dir>

Write collated report to this directory. By default, write to the lowest level directory common to all input graphs.

--include-svg, --no-include-svg

Include RNA structure drawings from the draw module.

--include-graph, --no-include-graph

Include graphs from the graph module.

--group <group>

Group collated graphs by one of ‘sample’, ‘graph’, ‘branches’, ‘region’, or ‘all’.

--portable, --no-portable

Embed collated graphs into the output HTML file for portability at the expense of live updates and file size.

Arguments

FASTA

Required argument

INPUT_PATH

Optional argument(s)

Run individual steps of the workflow

seismic demult

Demultiplex sequencing reads by their barcode.

Usage

seismic demult [OPTIONS] FASTA

Options

-x, --fastqx <fastqx>

FASTQ files of paired-end reads with mates 1 and 2 in separate files

-y, --fastqy <fastqy>

FASTQ file(s) of paired-end reads with mates 1 and 2 interleaved

-z, --fastqz <fastqz>

FASTQ file(s) of single-end reads

-X, --dmfastqx <dmfastqx>

Demultiplexed FASTQ files of mate 1 and mate 2 reads

-Y, --dmfastqy <dmfastqy>

Demultiplexed FASTQ files of paired-end reads interleaved in one file

-Z, --dmfastqz <dmfastqz>

Demultiplexed FASTQ files of single-end reads

--phred-enc <phred_enc>

Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files

-R, --refs-meta <refs_meta>

Add reference metadata from this CSV file to exported results

--barcode-start <barcode_start>

Index of start of barcode

--barcode-end <barcode_end>

Index of end of barcode

--read-pos <read_pos>

Expected position of the barcode in the read (1-indexed). Defaults to –barcode-start

--barcode <barcode>

A list of barcode name, barcode sequence, and barcode position (1-indexed relative to read start) to demultiplex

--mismatch-tolerance <mismatch_tolerance>

Consider patterns to match if they have up to this many mismatches. Will increase non-parallel computation at a factorial rate. Use caution Going above 2 mismatches. Does not apply to clipped sequences.

--index-tolerance <index_tolerance>

Allow patterns to be found in reads up to this distance from the reference index.

--allow-n, --no-allow-n

Allow N as a valid mismatch when –mismatch-tolerance ≥ 1. Increases memory consumption.

-o, --out-dir <out_dir>

Write all output files to this directory

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

-b, --branch <branch>

Create a new branch of the workflow with this name

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

FASTA

Required argument

seismic align

Trim FASTQ files and align them to reference sequences.

Usage

seismic align [OPTIONS] FASTA

Options

-x, --fastqx <fastqx>

FASTQ files of paired-end reads with mates 1 and 2 in separate files

-y, --fastqy <fastqy>

FASTQ file(s) of paired-end reads with mates 1 and 2 interleaved

-z, --fastqz <fastqz>

FASTQ file(s) of single-end reads

-X, --dmfastqx <dmfastqx>

Demultiplexed FASTQ files of mate 1 and mate 2 reads

-Y, --dmfastqy <dmfastqy>

Demultiplexed FASTQ files of paired-end reads interleaved in one file

-Z, --dmfastqz <dmfastqz>

Demultiplexed FASTQ files of single-end reads

--phred-enc <phred_enc>

Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files

-o, --out-dir <out_dir>

Write all output files to this directory

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

-b, --branch <branch>

Create a new branch of the workflow with this name

--fastp, --no-fastp

Use fastp to QC, filter, and trim reads before alignment

--fastp-5, --no-fastp-5

Trim low-quality bases from the 5’ ends of reads

--fastp-3, --no-fastp-3

Trim low-quality bases from the 3’ ends of reads

--fastp-w <fastp_w>

Use this window size (nt) for –fastp-5 and –fastp-3

--fastp-m <fastp_m>

Use this mean quality threshold for –fastp-5 and –fastp-3

--fastp-poly-g <fastp_poly_g>

Trim poly(G) tails (two-color sequencing artifacts) from the 3’ end

Options:

yes | no | auto

--fastp-poly-g-min-len <fastp_poly_g_min_len>

Minimum number of Gs to consider a poly(G) tail for –fastp-poly-g

--fastp-poly-x, --no-fastp-poly-x

Trim poly(X) tails (i.e. of any nucleotide) from the 3’ end

--fastp-poly-x-min-len <fastp_poly_x_min_len>

Minimum number of bases to consider a poly(X) tail for –fastp-poly-x

--fastp-adapter-trimming, --no-fastp-adapter-trimming

Trim adapter sequences from the 3’ ends of reads

--fastp-adapter-1 <fastp_adapter_1>

Trim this adapter sequence from the 3’ ends of read 1s

--fastp-adapter-2 <fastp_adapter_2>

Trim this adapter sequence from the 3’ ends of read 2s

--fastp-adapter-fasta <fastp_adapter_fasta>

Trim adapter sequences in this FASTA file from the 3’ ends of reads

--fastp-detect-adapter-for-pe, --no-fastp-detect-adapter-for-pe

Automatically detect the adapter sequences for paired-end reads

--fastp-min-length <fastp_min_length>

Discard reads shorter than this length

--bt2-local, --bt2-end-to-end

Align reads in local mode rather than end-to-end mode

--bt2-discordant, --bt2-no-discordant

Output paired-end reads whose mates align discordantly

--bt2-mixed, --bt2-no-mixed

Attempt to align individual mates of pairs that fail to align

--bt2-dovetail, --bt2-no-dovetail

Consider dovetailed mate pairs to align concordantly

--bt2-contain, --bt2-no-contain

Consider nested mate pairs to align concordantly

--bt2-I <bt2_i>

Discard paired-end alignments shorter than this many bases

--bt2-X <bt2_x>

Discard paired-end alignments longer than this many bases

--bt2-score-min-e2e <bt2_score_min_e2e>

Discard alignments that score below this threshold in end-to-end mode

--bt2-score-min-loc <bt2_score_min_loc>

Discard alignments that score below this threshold in local mode

--bt2-i <bt2_s>

Seed Bowtie2 alignments at this interval

--bt2-L <bt2_l>

Use this seed length for Bowtie2

--bt2-gbar <bt2_gbar>

Do not place gaps within this many bases from the end of a read

--bt2-D <bt2_d>

Discard alignments if over this many consecutive seed extensions fail

--bt2-R <bt2_r>

Re-seed reads with repetitive seeds up to this many times

--bt2-dpad <bt2_dpad>

Pad the alignment matrix with this many bases (to allow gaps)

--bt2-orient <bt2_orient>

Require paired mates to have this orientation

Options:

fr | rf | ff

--bt2-un, --bt2-no-un

Output unaligned reads to a FASTQ file

--seed <seed>

Seed for the random number generator

--min-mapq <min_mapq>

Discard reads with mapping qualities below this threshold

-N, --min-reads <min_reads>

Discard alignment maps with fewer than this many reads

--sep-strands, --mix-strands

Separate each alignment map into forward- and reverse-strand reads

--f1r2-fwd, --f1r2-rev

With –sep-strands, consider forward mate 1s and reverse mate 2s to be forward-stranded

--rev-label <rev_label>

With –sep-strands, add this label to each reverse-strand reference

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

FASTA

Required argument

seismic idmut

Identify mutations in aligned reads.

Usage

seismic idmut [OPTIONS] FASTA [INPUT_PATH]...

Options

--sep-strands, --mix-strands

Separate each alignment map into forward- and reverse-strand reads

--rev-label <rev_label>

With –sep-strands, add this label to each reverse-strand reference

-o, --out-dir <out_dir>

Write all output files to this directory

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

-b, --branch <branch>

Create a new branch of the workflow with this name

--min-mapq <min_mapq>

Discard reads with mapping qualities below this threshold

--phred-enc <phred_enc>

Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files

--min-phred <min_phred>

Mark base calls with Phred scores lower than this threshold as ambiguous

-N, --min-reads <min_reads>

Discard alignment maps with fewer than this many reads

--batch-size <batch_size>

Limit batches to at most this many reads

--insert3, --insert5

Mark each insertion on the base to its 3’ (True) or 5’ (False) side

--ambindel, --no-ambindel

Mark all ambiguous insertions and deletions (indels)

--overhangs, --no-overhangs

Retain the overhangs of paired-end mates that dovetail

-5, --clip-end5 <clip_end5>

Clip this many bases from the 5’ end of each read

-3, --clip-end3 <clip_end3>

Clip this many bases from the 3’ end of each read

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--write-read-names, --no-write-read-names

Write the name of each read in a second set of batches (necessary for the options –drop-read or –drop-read-file)

--idmut-pos-table, --no-idmut-pos-table

Tabulate relationships per position for idmut data

--idmut-read-table, --no-idmut-read-table

Tabulate relationships per read for idmut data

--idmut-cx, --idmut-py

Use a fast (C extension module) version of the idmut algorithm; the slow (Python) version is still avilable as a fallback if the C extension cannot be loaded, and for debugging/benchmarking

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

--keep-tmp, --erase-tmp

Keep temporary files after finishing

Arguments

FASTA

Required argument

INPUT_PATH

Optional argument(s)

seismic pool

Merge samples (vertically) from the IDmut step.

Usage

seismic pool [OPTIONS] POOLED_SAMPLE [INPUT_PATH]...

Options

--idmut-pos-table, --no-idmut-pos-table

Tabulate relationships per position for idmut data

--idmut-read-table, --no-idmut-read-table

Tabulate relationships per read for idmut data

--min-pearson <min_pearson>

Pool samples only if their Pearson correlation is at least this large

--max-marcd <max_marcd>

Pool samples only if their mean arsince distance is at most this

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

POOLED_SAMPLE

Required argument

INPUT_PATH

Optional argument(s)

seismic filter

Define mutations and regions to filter reads and positions.

Usage

seismic filter [OPTIONS] [INPUT_PATH]...

Options

-b, --branch <branch>

Create a new branch of the workflow with this name

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

-c, --region-coords <region_coords>

Select a region of a reference given its 5’ and 3’ end coordinates

-P, --region-primers <region_primers>

Select a region of a reference given its forward and reverse primers

--primer-gap <primer_gap>

Leave a gap of this many bases between the primer and the region

-i, --regions-file <regions_file>

Select regions of references from coordinates/primers in a CSV file

--count-del, --no-del

Count deletions as mutations

--count-ins, --no-ins

Count insertions as mutations

--no-mut <no_mut>

Do not count this type of mutation (overrides –count-del/ins)

--only-mut <only_mut>

Count only this type of mutation (overrides other mutation settings)

--probe <probe>

Use the default options for this chemical probe

Options:

DMS | SHAPE | ETC | none

--mask-a, --keep-a

Mask positions with base A

--mask-c, --keep-c

Mask positions with base C

--mask-g, --keep-g

Mask positions with base G

--mask-u, --keep-u

Mask positions with base U

--mask-polya <mask_polya>

Mask stretches of at least this many consecutive A bases (0 disables); defaults to 5 for chemical probes, 0 for none

--mask-pos <mask_pos>

Mask this position in this reference

--mask-pos-file <mask_pos_file>

Mask positions in references from a file

--min-ninfo-pos <min_ninfo_pos>

Mask positions with fewer than this many informative base calls

--max-fmut-pos <max_fmut_pos>

Mask positions with more than this fraction of mutated base calls

--drop-read <drop_read>

Drop the read with this name

--drop-read-file <drop_read_file>

Drop the reads with names in this file

--drop-discontig, --keep-discontig

Drop paired-end reads with discontiguous mates

--min-ncov-read <min_ncov_read>

Drop reads with fewer than this many bases covering the region

--min-fcov-read <min_fcov_read>

Drop reads covering less than this fraction of the region

--min-finfo-read <min_finfo_read>

Drop reads with less than this fraction of informative base calls

--max-fmut-read <max_fmut_read>

Drop reads with more than this fraction of mutated base calls

--min-mut-gap <min_mut_gap>

Filter out mutations separated by fewer than this many bases

--mut-collisions <mut_collisions>

If two mutations are closer than –min-mut-gap positions, MERGE the mutations, DROP the read, or AUTO-select based on the probe.

Options:

drop | merge | auto

--quick-unbias, --exact-unbias

Correct observer bias using a quick (typically linear time) heuristic

--quick-unbias-thresh <quick_unbias_thresh>

Treat mutated fractions under this threshold as 0 with –quick-unbias

--max-filter-iter <max_filter_iter>

Stop the filter step after this many iterations (0 for no limit)

--filter-pos-table, --no-filter-pos-table

Tabulate relationships per position for filter data

--filter-read-table, --no-filter-read-table

Tabulate relationships per read for filter data

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--self-contained, --no-self-contained

Write self-contained batch files that do not require loading predecessor batches (Filter and Cluster steps), at the cost of larger files on disk

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

INPUT_PATH

Optional argument(s)

seismic cluster

Infer structure ensembles by clustering reads’ mutations.

Usage

seismic cluster [OPTIONS] [INPUT_PATH]...

Options

-b, --branch <branch>

Create a new branch of the workflow with this name

--min-clusters <min_clusters>

Start at this many clusters

-k, --max-clusters <max_clusters>

Stop at this many clusters (0 for no limit)

-e, --min-em-runs <min_em_runs>

Run EM (successfully) at least this number of times for each K

-E, --max-em-runs <max_em_runs>

Run EM (successfully or not) at most this number of times for each K

--em-thresh <em_thresh>

Stop EM when the log likelihood increases by less than this threshold

--min-em-iter <min_em_iter>

Run EM for at least this many iterations

--max-em-iter <max_em_iter>

Run EM for at most this many iterations

--max-pearson-run <max_pearson_run>

Remove runs with two clusters more similar than this correlation

--min-marcd-run <min_marcd_run>

Remove runs with two clusters that differ by less than this MARCD

--max-arcd-vs-ens-avg <max_arcd_vs_ens_avg>

Remove runs where a cluster differs by more than this ARCD from the ensemble average at any position

--max-gini-run <max_gini_run>

Remove runs where any cluster’s Gini coefficient exceeds this limit

--jackpot, --no-jackpot

Calculate the jackpotting quotient to find over-represented reads

--jackpot-conf-level <jackpot_conf_level>

Confidence level for the jackpotting quotient confidence interval

--max-jackpot-quotient <max_jackpot_quotient>

Remove runs whose jackpotting quotient exceeds this limit

--max-jackpot-sims <max_jackpot_sims>

Maximum number of simulations to compute the jackpotting quotient

--jackpot-max-data <jackpot_max_data>

Skip calculating the jackpotting quotient if the reads × positions exceeds this limit

--max-loglike-vs-best <max_loglike_vs_best>

Remove Ks with a log likelihood gap larger than this (0 for no limit)

--min-pearson-vs-best <min_pearson_vs_best>

Remove Ks where every run has less than this correlation vs. the best

--max-marcd-vs-best <max_marcd_vs_best>

Remove Ks where every run has more than this MARCD vs. the best

--try-all-ks, --stop-best-k

Try all numbers of clusters (Ks), even after finding the best number

--write-all-ks, --write-best-k

Write all numbers of clusters (Ks), rather than only the best number

--cluster-pos-table, --no-cluster-pos-table

Tabulate relationships per position for cluster data

--cluster-abundance-table, --no-cluster-abundance-table

Tabulate number of reads per cluster for cluster data

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--self-contained, --no-self-contained

Write self-contained batch files that do not require loading predecessor batches (Filter and Cluster steps), at the cost of larger files on disk

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--seed <seed>

Seed for the random number generator

Arguments

INPUT_PATH

Optional argument(s)

seismic join

Merge regions (horizontally) from the Filter or Cluster step.

Usage

seismic join [OPTIONS] JOINED_REGION [INPUT_PATH]...

Options

-j, --join-clusts <join_clusts>

Specify which clusters to join clusters using this CSV file

--filter-pos-table, --no-filter-pos-table

Tabulate relationships per position for filter data

--filter-read-table, --no-filter-read-table

Tabulate relationships per read for filter data

--cluster-pos-table, --no-cluster-pos-table

Tabulate relationships per position for cluster data

--cluster-abundance-table, --no-cluster-abundance-table

Tabulate number of reads per cluster for cluster data

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

JOINED_REGION

Required argument

INPUT_PATH

Optional argument(s)

seismic filterscan

Scan an RNA for domains of correlated base pairs.

Usage

seismic filterscan [OPTIONS] [INPUT_PATH]...

Options

-b, --branch <branch>

Create a new branch of the workflow with this name

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

-c, --region-coords <region_coords>

Select a region of a reference given its 5’ and 3’ end coordinates

-P, --region-primers <region_primers>

Select a region of a reference given its forward and reverse primers

--primer-gap <primer_gap>

Leave a gap of this many bases between the primer and the region

-i, --regions-file <regions_file>

Select regions of references from coordinates/primers in a CSV file

--count-del, --no-del

Count deletions as mutations

--count-ins, --no-ins

Count insertions as mutations

--no-mut <no_mut>

Do not count this type of mutation (overrides –count-del/ins)

--only-mut <only_mut>

Count only this type of mutation (overrides other mutation settings)

--probe <probe>

Use the default options for this chemical probe

Options:

DMS | SHAPE | ETC | none

--mask-a, --keep-a

Mask positions with base A

--mask-c, --keep-c

Mask positions with base C

--mask-g, --keep-g

Mask positions with base G

--mask-u, --keep-u

Mask positions with base U

--mask-polya <mask_polya>

Mask stretches of at least this many consecutive A bases (0 disables); defaults to 5 for chemical probes, 0 for none

--mask-pos <mask_pos>

Mask this position in this reference

--mask-pos-file <mask_pos_file>

Mask positions in references from a file

--min-ninfo-pos <min_ninfo_pos>

Mask positions with fewer than this many informative base calls

--max-fmut-pos <max_fmut_pos>

Mask positions with more than this fraction of mutated base calls

--drop-read <drop_read>

Drop the read with this name

--drop-read-file <drop_read_file>

Drop the reads with names in this file

--drop-discontig, --keep-discontig

Drop paired-end reads with discontiguous mates

--min-ncov-read <min_ncov_read>

Drop reads with fewer than this many bases covering the region

--min-fcov-read <min_fcov_read>

Drop reads covering less than this fraction of the region

--min-finfo-read <min_finfo_read>

Drop reads with less than this fraction of informative base calls

--max-fmut-read <max_fmut_read>

Drop reads with more than this fraction of mutated base calls

--min-mut-gap <min_mut_gap>

Filter out mutations separated by fewer than this many bases

--mut-collisions <mut_collisions>

If two mutations are closer than –min-mut-gap positions, MERGE the mutations, DROP the read, or AUTO-select based on the probe.

Options:

drop | merge | auto

--quick-unbias, --exact-unbias

Correct observer bias using a quick (typically linear time) heuristic

--quick-unbias-thresh <quick_unbias_thresh>

Treat mutated fractions under this threshold as 0 with –quick-unbias

--max-filter-iter <max_filter_iter>

Stop the filter step after this many iterations (0 for no limit)

--filter-pos-table, --no-filter-pos-table

Tabulate relationships per position for filter data

--filter-read-table, --no-filter-read-table

Tabulate relationships per read for filter data

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--self-contained, --no-self-contained

Write self-contained batch files that do not require loading predecessor batches (Filter and Cluster steps), at the cost of larger files on disk

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

-L, --tile-length <tile_length>

Make each tile this length (if 0, use 2x the median read length)

-O, --tile-min-overlap <tile_min_overlap>

Make adjacent tiles overlap by at least this fraction of length

--erase-tiles, --keep-tiles

Erase the filter reports/batches from the tiling step

--pair-fdr <pair_fdr>

Find correlated pairs at this false discovery rate (FDR)

--min-pairs <min_pairs>

Cluster only the regions with at least this many correlated pairs

--pair-distance-percentile <pair_distance_percentile>

Among pairs that survive the endpoint-peak filter, drop any pair whose L1 (Manhattan) distance to its nearest surviving neighbor exceeds this percentile of all such distances. Pairs more isolated than this threshold are treated as noise.

--endpoint-window <endpoint_window>

When testing whether a position is a significant hub of correlated pair endpoints, aggregate counts over a window of this many adjacent positions: forward (pos5, pos5+1, …, pos5+window) for 5’ ends, backward (pos3-window, …, pos3) for 3’ ends. Larger values boost statistical power for helices whose endpoints are not always at exactly the same position.

--min-nearby-pairs <min_nearby_pairs>

Minimum number of other surviving pairs that must lie within the pair-distance-percentile L1 threshold for a pair to be kept. Setting this above 1 filters out small coincidental clusters of noise pairs (‘buddy noise’) at the cost of potentially clipping domain edges.

--min-cluster-length <min_cluster_length>

Cluster only the regions with at least this many positions

--max-cluster-length <max_cluster_length>

Cluster only the regions with no more than this many positions

--gap-mode <gap_mode>

If there are gaps between regions to cluster, OMIT (do not cluster) the gaps, INSERT a new region into each gap, or EXPAND the existing regions to fill the gaps

Options:

omit | insert | expand

Arguments

INPUT_PATH

Optional argument(s)

seismic clusterscan

Cluster the domains detected by filterscan.

Usage

seismic clusterscan [OPTIONS] [INPUT_PATH]...

Options

-b, --branch <branch>

Create a new branch of the workflow with this name

--min-clusters <min_clusters>

Start at this many clusters

-k, --max-clusters <max_clusters>

Stop at this many clusters (0 for no limit)

-e, --min-em-runs <min_em_runs>

Run EM (successfully) at least this number of times for each K

-E, --max-em-runs <max_em_runs>

Run EM (successfully or not) at most this number of times for each K

--em-thresh <em_thresh>

Stop EM when the log likelihood increases by less than this threshold

--min-em-iter <min_em_iter>

Run EM for at least this many iterations

--max-em-iter <max_em_iter>

Run EM for at most this many iterations

--max-pearson-run <max_pearson_run>

Remove runs with two clusters more similar than this correlation

--min-marcd-run <min_marcd_run>

Remove runs with two clusters that differ by less than this MARCD

--max-arcd-vs-ens-avg <max_arcd_vs_ens_avg>

Remove runs where a cluster differs by more than this ARCD from the ensemble average at any position

--max-gini-run <max_gini_run>

Remove runs where any cluster’s Gini coefficient exceeds this limit

--jackpot, --no-jackpot

Calculate the jackpotting quotient to find over-represented reads

--jackpot-conf-level <jackpot_conf_level>

Confidence level for the jackpotting quotient confidence interval

--max-jackpot-quotient <max_jackpot_quotient>

Remove runs whose jackpotting quotient exceeds this limit

--max-jackpot-sims <max_jackpot_sims>

Maximum number of simulations to compute the jackpotting quotient

--jackpot-max-data <jackpot_max_data>

Skip calculating the jackpotting quotient if the reads × positions exceeds this limit

--max-loglike-vs-best <max_loglike_vs_best>

Remove Ks with a log likelihood gap larger than this (0 for no limit)

--min-pearson-vs-best <min_pearson_vs_best>

Remove Ks where every run has less than this correlation vs. the best

--max-marcd-vs-best <max_marcd_vs_best>

Remove Ks where every run has more than this MARCD vs. the best

--try-all-ks, --stop-best-k

Try all numbers of clusters (Ks), even after finding the best number

--write-all-ks, --write-best-k

Write all numbers of clusters (Ks), rather than only the best number

--cluster-pos-table, --no-cluster-pos-table

Tabulate relationships per position for cluster data

--cluster-abundance-table, --no-cluster-abundance-table

Tabulate number of reads per cluster for cluster data

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--self-contained, --no-self-contained

Write self-contained batch files that do not require loading predecessor batches (Filter and Cluster steps), at the cost of larger files on disk

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--seed <seed>

Seed for the random number generator

Arguments

INPUT_PATH

Optional argument(s)

seismic table

Tabulate counts of relationships per read and position.

Usage

seismic table [OPTIONS] [INPUT_PATH]...

Options

--idmut-pos-table, --no-idmut-pos-table

Tabulate relationships per position for idmut data

--idmut-read-table, --no-idmut-read-table

Tabulate relationships per read for idmut data

--filter-pos-table, --no-filter-pos-table

Tabulate relationships per position for filter data

--filter-read-table, --no-filter-read-table

Tabulate relationships per read for filter data

--cluster-pos-table, --no-cluster-pos-table

Tabulate relationships per position for cluster data

--cluster-abundance-table, --no-cluster-abundance-table

Tabulate number of reads per cluster for cluster data

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

INPUT_PATH

Optional argument(s)

seismic fold

Predict RNA secondary structures using mutation rates.

Usage

seismic fold [OPTIONS] [INPUT_PATH]...

Options

-b, --branch <branch>

Create a new branch of the workflow with this name

-F, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--fold-table-region, --fold-full-region

If no regions are specified, whether to default to the table’s region or to the full region

--fold-dry-run, --fold-real-run

Only generate the fold command and input files; do not run folding

--fold-backend <fold_backend>

Model RNA structures using RNAstructure (Fold/ShapeKnots) or ViennaRNA (RNAfold/RNAsubopt); auto selects RNAstructure for DMS and ViennaRNA for other probes

Options:

auto | RNAstructure | ViennaRNA

--pseudoknots, --no-pseudoknots

Predict pseudoknotted structures (requires –fold-backend=RNAstructure; uses ShapeKnots when set, Fold otherwise)

--fold-energy-method <fold_energy_method>

Use this method to incorporate reactivities into folding energies. auto selects Cordero for DMS and Eddy for other probes; Eddy requires –fold-backend=ViennaRNA; Cordero requires –fold-backend=RNAstructure

Options:

auto | Deigan | Cordero | Eddy

--fold-temp <fold_temp>

Predict structures at this temperature (Celsius)

--deigan-slope <deigan_slope>

Slope (kcal/mol) for SHAPE reactivities using Deigan method; used only with –fold-energy-method=Deigan

--deigan-intercept <deigan_intercept>

Intercept (kcal/mol) for SHAPE reactivities using Deigan method; used only with –fold-energy-method=Deigan

--fold-quantile <fold_quantile>

Normalize and winsorize reactivities to this quantile for folding

--fold-constraint <fold_constraint>

Force bases to be paired/unpaired from a file of constraints

--fold-commands <fold_commands>

Command file for RNAFold

--eddy-prior-paired-file <eddy_prior_paired_file>

File of per-position prior probabilities of being paired for the Eddy method (passed as –sp-data with –sp-strategy Pp); only used with –fold-energy-method=Eddy and –fold-backend=ViennaRNA

--eddy-prior-unpaired-file <eddy_prior_unpaired_file>

File of per-position prior probabilities of being unpaired for the Eddy method (passed as –sp-data with –sp-strategy Pu); only used with –fold-energy-method=Eddy and –fold-backend=ViennaRNA

--fold-md <fold_md>

Limit base pair distances to this number of bases (0 for no limit)

--fold-mfe, --fold-sub

Predict only the minimum free energy (MFE) structure

--fold-max <fold_max>

Output at most this many structures (overriden by –fold-mfe)

--fold-percent <fold_percent>

Stop outputting structures when the % difference in energy exceeds this value (overriden by –fold-mfe)

--fold-edelta <fold_edelta>

Maximum absolute energy difference (kcal/mol) from the MFE for suboptimal structures output by RNAsubopt (overriden by –fold-mfe)

--fold-isolated, --fold-stacked

Allow isolated (non-stacked) base pairs when folding

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

INPUT_PATH

Optional argument(s)

seismic graph

seismic graph profile

Bar graph of relationships(s) per position.

Usage

seismic graph profile [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

--graph-quantile <graph_quantile>

Normalize and winsorize ratios to this quantile (0 disables)

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph delprof

Bar graph of differences between two profiles per position.

Usage

seismic graph delprof [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

--graph-quantile <graph_quantile>

Normalize and winsorize ratios to this quantile (0 disables)

--comppair, --no-comppair

Compare every pair of table files

--compself, --no-compself

Compare every table file with itself

-o, --out-dir <out_dir>

Write all output files to this directory

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph scatter

Scatter plot comparing two profiles.

Usage

seismic graph scatter [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

--graph-quantile <graph_quantile>

Normalize and winsorize ratios to this quantile (0 disables)

--comppair, --no-comppair

Compare every pair of table files

--compself, --no-compself

Compare every table file with itself

-o, --out-dir <out_dir>

Write all output files to this directory

-m, --metric <metric>

Metric to compare mutation rates: ‘pcc’ = Pearson correlation coefficient (r), ‘scc’ = Spearman correlation coefficient (ρ), ‘r2’ = coefficient of determination (R²), ‘marcd’ = mean arcsine distance (MARCD)

Options:

marcd | pcc | scc | r2

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph corroll

Rolling correlation/comparison of two profiles.

Usage

seismic graph corroll [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

--graph-quantile <graph_quantile>

Normalize and winsorize ratios to this quantile (0 disables)

--window <window>

Use a sliding window of this many bases

-n, --winmin <winmin>

Mask sliding windows with fewer than this number of data

--comppair, --no-comppair

Compare every pair of table files

--compself, --no-compself

Compare every table file with itself

-o, --out-dir <out_dir>

Write all output files to this directory

-m, --metric <metric>

Metric to compare mutation rates: ‘pcc’ = Pearson correlation coefficient (r), ‘scc’ = Spearman correlation coefficient (ρ), ‘r2’ = coefficient of determination (R²), ‘marcd’ = mean arcsine distance (MARCD)

Options:

marcd | pcc | scc | r2

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph giniroll

Rolling Gini coefficient.

Usage

seismic graph giniroll [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

--graph-quantile <graph_quantile>

Normalize and winsorize ratios to this quantile (0 disables)

--window <window>

Use a sliding window of this many bases

-n, --winmin <winmin>

Mask sliding windows with fewer than this number of data

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph snrroll

Rolling signal-to-noise ratio.

Usage

seismic graph snrroll [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

--graph-quantile <graph_quantile>

Normalize and winsorize ratios to this quantile (0 disables)

--window <window>

Use a sliding window of this many bases

-n, --winmin <winmin>

Mask sliding windows with fewer than this number of data

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph histpos

Histogram of relationship(s) per position.

Usage

seismic graph histpos [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

--graph-quantile <graph_quantile>

Normalize and winsorize ratios to this quantile (0 disables)

--hist-bins <hist_bins>

Number of bins in each histogram; must be ≥ 1

--hist-margin <hist_margin>

Autofill margins of at most this width in histograms of ratios

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph histread

Histogram of relationship(s) per read.

Usage

seismic graph histread [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

--graph-quantile <graph_quantile>

Normalize and winsorize ratios to this quantile (0 disables)

--hist-bins <hist_bins>

Number of bins in each histogram; must be ≥ 1

--hist-margin <hist_margin>

Autofill margins of at most this width in histograms of ratios

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph mutdist

Distance between the closest two mutations in each read.

Usage

seismic graph mutdist [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

-r, --rels <rels>

Graph these relationship(s)

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--mutdist-null, --no-mutdist-null

Include the null distribution of distances between mutations

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph poscorr

Phi correlations between pairs of positions.

Usage

seismic graph poscorr [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

-r, --rels <rels>

Graph these relationship(s)

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph roc

ROC curve comparing a profile to a structure.

Usage

seismic graph roc [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

--graph-quantile <graph_quantile>

Normalize and winsorize ratios to this quantile (0 disables)

--struct-file <struct_file>

Compare mutational profiles to the structure(s) in this CT file

-b, --branch <branch>

Create a new branch of the workflow with this name

-F, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--fold-table-region, --fold-full-region

If no regions are specified, whether to default to the table’s region or to the full region

--terminal-pairs, --no-terminal-pairs

Include terminal base pairs (at the ends of stems) in ROC curves

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph aucroll

Rolling AUC-ROC comparing a profile to a structure.

Usage

seismic graph aucroll [OPTIONS] [INPUT_PATH]...

Options

--cgroup <cgroup>

Put each Cluster in its own file, each K in its own file, or All clusters in one file

Options:

c | k | a

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--use-ratio, --use-count

Graph ratios or counts

-r, --rels <rels>

Graph these relationship(s)

--graph-quantile <graph_quantile>

Normalize and winsorize ratios to this quantile (0 disables)

--struct-file <struct_file>

Compare mutational profiles to the structure(s) in this CT file

-b, --branch <branch>

Create a new branch of the workflow with this name

-F, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--fold-table-region, --fold-full-region

If no regions are specified, whether to default to the table’s region or to the full region

--terminal-pairs, --no-terminal-pairs

Include terminal base pairs (at the ends of stems) in ROC curves

--window <window>

Use a sliding window of this many bases

-n, --winmin <winmin>

Mask sliding windows with fewer than this number of data

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic graph abundance

Abundance of each cluster.

Usage

seismic graph abundance [OPTIONS] [INPUT_PATH]...

Options

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--use-ratio, --use-count

Graph ratios or counts

--csv, --no-csv

Output the data for each graph in a Comma-Separated Values file

--html, --no-html

Output each graph in an interactive HyperText Markup Language file

--svg, --no-svg

Output each graph in a Scalable Vector Graphics file

--pdf, --no-pdf

Output each graph in a Portable Document Format file

--png, --no-png

Output each graph in a Portable Network Graphics file

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic draw

Draw RNA structures with reactivities using RNArtistCore.

Usage

seismic draw [OPTIONS] [INPUT_PATH]...

Options

--fold-table-region, --fold-full-region

If no regions are specified, whether to default to the table’s region or to the full region

--struct-num <struct_num>

Draw the specified structure (zero-indexed) or -1 for all structures. By default, draw the structure with the best AUROC.

--color, --no-color

Color bases by their reactivity

--draw-svg, --no-draw-svg

Output each drawing in a Scalable Vector Graphics file

--draw-png, --no-draw-png

Output each drawing in a Portable Network Graphics file

--update-rnartistcore, --no-update-rnartistcore

Check for and install updates to RNArtistCore.

--force, --no-force

Force all tasks to run, overwriting any existing output files

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic collate

Collate HTML graphs and SVG drawings into an HTML report file.

Usage

seismic collate [OPTIONS] [INPUT_PATH]...

Options

--name <name>

Prefix the HTML report with this name.

--verbose-name, --no-verbose-name

Add collated file information to report name.

--collate-out-dir <collate_out_dir>

Write collated report to this directory. By default, write to the lowest level directory common to all input graphs.

--include-svg, --no-include-svg

Include RNA structure drawings from the draw module.

--include-graph, --no-include-graph

Include graphs from the graph module.

--group <group>

Group collated graphs by one of ‘sample’, ‘graph’, ‘branches’, ‘region’, or ‘all’.

--portable, --no-portable

Embed collated graphs into the output HTML file for portability at the expense of live updates and file size.

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

INPUT_PATH

Optional argument(s)

seismic export

Export each sample to SEISMICgraph (https://seismicrna.org).

Usage

seismic export [OPTIONS] [INPUT_PATH]...

Options

-S, --samples-meta <samples_meta>

Add sample metadata from this CSV file to exported results

-R, --refs-meta <refs_meta>

Add reference metadata from this CSV file to exported results

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--all-pos, --unmasked-pos

Export all positions (not just unmasked positions)

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

Utility commands

seismic splitbam

Split a BAM file into one file for each reference.

Usage

seismic splitbam [OPTIONS] FASTA [INPUT_PATH]...

Options

--phred-enc <phred_enc>

Specify the Phred score encoding of FASTQ and SAM/BAM/CRAM files

-o, --out-dir <out_dir>

Write all output files to this directory

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--force, --no-force

Force all tasks to run, overwriting any existing output files

--keep-tmp, --erase-tmp

Keep temporary files after finishing

-b, --branch <branch>

Create a new branch of the workflow with this name

--bt2-local, --bt2-end-to-end

Align reads in local mode rather than end-to-end mode

--bt2-discordant, --bt2-no-discordant

Output paired-end reads whose mates align discordantly

--bt2-mixed, --bt2-no-mixed

Attempt to align individual mates of pairs that fail to align

--bt2-dovetail, --bt2-no-dovetail

Consider dovetailed mate pairs to align concordantly

--bt2-contain, --bt2-no-contain

Consider nested mate pairs to align concordantly

--bt2-I <bt2_i>

Discard paired-end alignments shorter than this many bases

--bt2-X <bt2_x>

Discard paired-end alignments longer than this many bases

--bt2-score-min-loc <bt2_score_min_loc>

Discard alignments that score below this threshold in local mode

--bt2-score-min-e2e <bt2_score_min_e2e>

Discard alignments that score below this threshold in end-to-end mode

--bt2-i <bt2_s>

Seed Bowtie2 alignments at this interval

--bt2-L <bt2_l>

Use this seed length for Bowtie2

--bt2-D <bt2_d>

Discard alignments if over this many consecutive seed extensions fail

--bt2-R <bt2_r>

Re-seed reads with repetitive seeds up to this many times

--bt2-gbar <bt2_gbar>

Do not place gaps within this many bases from the end of a read

--bt2-dpad <bt2_dpad>

Pad the alignment matrix with this many bases (to allow gaps)

--bt2-orient <bt2_orient>

Require paired mates to have this orientation

Options:

fr | rf | ff

--seed <seed>

Seed for the random number generator

--min-mapq <min_mapq>

Discard reads with mapping qualities below this threshold

-N, --min-reads <min_reads>

Discard alignment maps with fewer than this many reads

--sep-strands, --mix-strands

Separate each alignment map into forward- and reverse-strand reads

--f1r2-fwd, --f1r2-rev

With –sep-strands, consider forward mate 1s and reverse mate 2s to be forward-stranded

--rev-label <rev_label>

With –sep-strands, add this label to each reverse-strand reference

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

FASTA

Required argument

INPUT_PATH

Optional argument(s)

seismic cleanfa

Clean the names and sequences in FASTA files.

Usage

seismic cleanfa [OPTIONS] [INPUT_PATH]...

Options

--inplace, --no-inplace

Modify files in-place instead of writing new files (CAUTION: you cannot recover the original files afterwards)

-o, --out-dir <out_dir>

Write all output files to this directory

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic list

List positions to mask.

Usage

seismic list [OPTIONS] [INPUT_PATH]...

Options

-b, --branch <branch>

Create a new branch of the workflow with this name

--min-ninfo-pos <min_ninfo_pos>

Mask positions with fewer than this many informative base calls

--max-fmut-pos <max_fmut_pos>

Mask positions with more than this fraction of mutated base calls

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic renumct

Renumber connectivity table (CT) files given a 5’ position.

Usage

seismic renumct [OPTIONS]

Options

--ct-pos-5 <ct_pos_5>

Connectivity table (CT) file or directory of CT files and the 5’ position to assign to each file

--inplace, --no-inplace

Modify files in-place instead of writing new files (CAUTION: you cannot recover the original files afterwards)

-o, --out-dir <out_dir>

Write all output files to this directory

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

seismic ct2db

Convert connectivity table (CT) to dot-bracket (DB) files.

Usage

seismic ct2db [OPTIONS] [INPUT_PATH]...

Options

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic db2ct

Convert dot-bracket (DB) to connectivity table (CT) files.

Usage

seismic db2ct [OPTIONS] [INPUT_PATH]...

Options

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic importmm

Import RNA Framework Mutation Map (MM) files as IDmut outputs.

Usage

seismic importmm [OPTIONS] [INPUT_PATH]...

Options

-o, --out-dir <out_dir>

Write all output files to this directory

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

-b, --branch <branch>

Create a new branch of the workflow with this name

-s, --sample <sample>

Required Give this name to the imported sample

-N, --min-reads <min_reads>

Discard alignment maps with fewer than this many reads

--batch-size <batch_size>

Limit batches to at most this many reads

--insert3, --insert5

Mark each insertion on the base to its 3’ (True) or 5’ (False) side

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--write-read-names, --no-write-read-names

Write the name of each read in a second set of batches (necessary for the options –drop-read or –drop-read-file)

--idmut-pos-table, --no-idmut-pos-table

Tabulate relationships per position for idmut data

--idmut-read-table, --no-idmut-read-table

Tabulate relationships per read for idmut data

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

INPUT_PATH

Optional argument(s)

seismic migrate

Migrate output directories from v0.24 to v0.25

Usage

seismic migrate [OPTIONS] [INPUT_PATH]...

Options

-o, --out-dir <out_dir>

Write all output files to this directory

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)

seismic fold datapath

Guess the DATAPATH for RNAstructure.

Usage

seismic fold datapath [OPTIONS]

seismic test

Run all unit tests.

Usage

seismic test [OPTIONS]

Options

-v, --verbose

Log more messages (-v for debug, -vv for trace) on stderr

seismic sim

seismic sim total

Simulate FASTQ files from scratch.

Usage

seismic sim total [OPTIONS]

Options

--max-tries <max_tries>

Simulate the parameters with up to this many attempts

--mask-a, --keep-a

Mask positions with base A

--mask-c, --keep-c

Mask positions with base C

--mask-g, --keep-g

Mask positions with base G

--mask-u, --keep-u

Mask positions with base U

--mask-polya <mask_polya>

Mask stretches of at least this many consecutive A bases (0 disables); defaults to 5 for chemical probes, 0 for none

--max-fraction-ident <max_fraction_ident>

Retry if any two clusters have more than this fraction of identical mutation rates

--max-pearson-sim <max_pearson_sim>

Retry if any two clusters have a Pearson correlation larger than this

--min-marcd-sim <min_marcd_sim>

Retry if any two clusters have a MARCD less than this (0 disables)

--profile-name <profile_name>

Give the simulated structure and parameters this profile name

-s, --sample <sample>

Give this name to the simulated sample

--paired-end, --single-end

Simulate paired-end or single-end reads

--read-length <read_length>

Simulate reads with this many base calls

--reverse-fraction <reverse_fraction>

Simulate this fraction of reverse-oriented reads

--probe <probe>

Use the default options for this chemical probe

Options:

DMS | SHAPE | ETC | none

--min-mut-gap-weights <min_mut_gap_weights>

Comma-separated gap:weight pairs defining a mixture of min_mut_gap biases, e.g. ‘0:0.2,1:0.3,2:0.5’. Defaults are probe-specific. Pass an empty string to disable.

--mut-collisions <mut_collisions>

If two mutations are closer than –min-mut-gap positions, MERGE the mutations, DROP the read, or AUTO-select based on the probe.

Options:

drop | merge | auto

--injected-mut-probs <injected_mut_probs>

Comma-separated offset:prob pairs (offset ≥ 1) defining the probability of injecting a mutation that many positions 5’ of an existing mutation, e.g. ‘1:0.1,2:0.01’ (used with –mut-collisions merge). Defaults are probe-specific; pass an empty string to disable.

--fq-gzip, --fq-text

Simulate FASTQ files with gzip compression or as plain text

--num-reads <num_reads>

Simulate this many reads

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

--seed <seed>

Seed for the random number generator

--sim-dir <sim_dir>

Write all simulated files to this directory

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--fold-backend <fold_backend>

Model RNA structures using RNAstructure (Fold/ShapeKnots) or ViennaRNA (RNAfold/RNAsubopt); auto selects RNAstructure for DMS and ViennaRNA for other probes

Options:

auto | RNAstructure | ViennaRNA

--pseudoknots, --no-pseudoknots

Predict pseudoknotted structures (requires –fold-backend=RNAstructure; uses ShapeKnots when set, Fold otherwise)

-F, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--fold-constraint <fold_constraint>

Force bases to be paired/unpaired from a file of constraints

--fold-temp <fold_temp>

Predict structures at this temperature (Celsius)

--fold-md <fold_md>

Limit base pair distances to this number of bases (0 for no limit)

--fold-mfe, --fold-sub

Predict only the minimum free energy (MFE) structure

--fold-max <fold_max>

Output at most this many structures (overriden by –fold-mfe)

--fold-min <fold_min>

Require at least this many structures (overriden by –fold-mfe)

--fold-percent <fold_percent>

Stop outputting structures when the % difference in energy exceeds this value (overriden by –fold-mfe)

--fold-edelta <fold_edelta>

Maximum absolute energy difference (kcal/mol) from the MFE for suboptimal structures output by RNAsubopt (overriden by –fold-mfe)

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--clust-conc <clust_conc>

Set the concentration parameter for simulating cluster proportions

--center-fmean <center_fmean>

Set the mean read center as a fraction of the region length

--center-fvar <center_fvar>

Set the variance of the read center as a fraction of its maximum

--length-fmean <length_fmean>

Set the mean read length as a fraction of the region length

--length-fvar <length_fvar>

Set the variance of the read length as a fraction of its maximum

-p, --pmut-paired <pmut_paired>

Set the mean rate of each kind of mutation for paired bases

-u, --pmut-unpaired <pmut_unpaired>

Set the mean rate of each kind of mutation for unpaired bases

-v, --vmut-paired <vmut_paired>

Set the relative variance of mutation rates of each kind of paired base

-w, --vmut-unpaired <vmut_unpaired>

Set the relative variance of mutation rates of each kind of unpaired base

-c, --region-coords <region_coords>

Select a region of a reference given its 5’ and 3’ end coordinates

-P, --region-primers <region_primers>

Select a region of a reference given its forward and reverse primers

--refs <refs>

Give this name to the file of simulated references

--ref <ref>

Give this name to the simulated reference

--reflen <reflen>

Simulate a reference sequence with this many bases

seismic sim ref

Simulate a FASTA file of a reference sequence.

Usage

seismic sim ref [OPTIONS]

Options

--sim-dir <sim_dir>

Write all simulated files to this directory

--refs <refs>

Give this name to the file of simulated references

--ref <ref>

Give this name to the simulated reference

--reflen <reflen>

Simulate a reference sequence with this many bases

--force, --no-force

Force all tasks to run, overwriting any existing output files

--seed <seed>

Seed for the random number generator

seismic sim fold

Simulate secondary structure(s) a reference sequence.

Usage

seismic sim fold [OPTIONS] FASTA

Options

--sim-dir <sim_dir>

Write all simulated files to this directory

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--profile-name <profile_name>

Give the simulated structure and parameters this profile name

--probe <probe>

Use the default options for this chemical probe

Options:

DMS | SHAPE | ETC | none

--fold-backend <fold_backend>

Model RNA structures using RNAstructure (Fold/ShapeKnots) or ViennaRNA (RNAfold/RNAsubopt); auto selects RNAstructure for DMS and ViennaRNA for other probes

Options:

auto | RNAstructure | ViennaRNA

--pseudoknots, --no-pseudoknots

Predict pseudoknotted structures (requires –fold-backend=RNAstructure; uses ShapeKnots when set, Fold otherwise)

-F, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--fold-constraint <fold_constraint>

Force bases to be paired/unpaired from a file of constraints

--fold-temp <fold_temp>

Predict structures at this temperature (Celsius)

--fold-md <fold_md>

Limit base pair distances to this number of bases (0 for no limit)

--fold-mfe, --fold-sub

Predict only the minimum free energy (MFE) structure

--fold-max <fold_max>

Output at most this many structures (overriden by –fold-mfe)

--fold-min <fold_min>

Require at least this many structures (overriden by –fold-mfe)

--fold-percent <fold_percent>

Stop outputting structures when the % difference in energy exceeds this value (overriden by –fold-mfe)

--fold-edelta <fold_edelta>

Maximum absolute energy difference (kcal/mol) from the MFE for suboptimal structures output by RNAsubopt (overriden by –fold-mfe)

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

FASTA

Required argument

seismic sim params

Simulate parameter files.

Usage

seismic sim params [OPTIONS]

Options

--ct-file <ct_file>

Simulate parameters using the structure(s) in this CT file

--clust-conc <clust_conc>

Set the concentration parameter for simulating cluster proportions

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--seed <seed>

Seed for the random number generator

--center-fmean <center_fmean>

Set the mean read center as a fraction of the region length

--center-fvar <center_fvar>

Set the variance of the read center as a fraction of its maximum

--length-fmean <length_fmean>

Set the mean read length as a fraction of the region length

--length-fvar <length_fvar>

Set the variance of the read length as a fraction of its maximum

-p, --pmut-paired <pmut_paired>

Set the mean rate of each kind of mutation for paired bases

-u, --pmut-unpaired <pmut_unpaired>

Set the mean rate of each kind of mutation for unpaired bases

-v, --vmut-paired <vmut_paired>

Set the relative variance of mutation rates of each kind of paired base

-w, --vmut-unpaired <vmut_unpaired>

Set the relative variance of mutation rates of each kind of unpaired base

--probe <probe>

Use the default options for this chemical probe

Options:

DMS | SHAPE | ETC | none

-c, --region-coords <region_coords>

Select a region of a reference given its 5’ and 3’ end coordinates

-P, --region-primers <region_primers>

Select a region of a reference given its forward and reverse primers

seismic sim muts

Simulate the rate of each kind of mutation at each position.

Usage

seismic sim muts [OPTIONS]

Options

--ct-file <ct_file>

Simulate parameters using the structure(s) in this CT file

-p, --pmut-paired <pmut_paired>

Set the mean rate of each kind of mutation for paired bases

-u, --pmut-unpaired <pmut_unpaired>

Set the mean rate of each kind of mutation for unpaired bases

-v, --vmut-paired <vmut_paired>

Set the relative variance of mutation rates of each kind of paired base

-w, --vmut-unpaired <vmut_unpaired>

Set the relative variance of mutation rates of each kind of unpaired base

--probe <probe>

Use the default options for this chemical probe

Options:

DMS | SHAPE | ETC | none

-c, --region-coords <region_coords>

Select a region of a reference given its 5’ and 3’ end coordinates

-P, --region-primers <region_primers>

Select a region of a reference given its forward and reverse primers

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--seed <seed>

Seed for the random number generator

seismic sim ends

Simulate the proportions of 5’ and 3’ end coordinates.

Usage

seismic sim ends [OPTIONS]

Options

--ct-file <ct_file>

Simulate parameters using the structure(s) in this CT file

--center-fmean <center_fmean>

Set the mean read center as a fraction of the region length

--center-fvar <center_fvar>

Set the variance of the read center as a fraction of its maximum

--length-fmean <length_fmean>

Set the mean read length as a fraction of the region length

--length-fvar <length_fvar>

Set the variance of the read length as a fraction of its maximum

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

seismic sim clusts

Simulate the proportions of 5’ and 3’ end coordinates.

Usage

seismic sim clusts [OPTIONS]

Options

--ct-file <ct_file>

Simulate parameters using the structure(s) in this CT file

--clust-conc <clust_conc>

Set the concentration parameter for simulating cluster proportions

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--seed <seed>

Seed for the random number generator

seismic sim idmut

Simulate an IDmut dataset.

Usage

seismic sim idmut [OPTIONS]

Options

-d, --param-dir <param_dir>

Simulate data using parameter files in this directory

--profile-name <profile_name>

Give the simulated structure and parameters this profile name

-s, --sample <sample>

Give this name to the simulated sample

-b, --branch <branch>

Create a new branch of the workflow with this name

--paired-end, --single-end

Simulate paired-end or single-end reads

--read-length <read_length>

Simulate reads with this many base calls

--reverse-fraction <reverse_fraction>

Simulate this fraction of reverse-oriented reads

--probe <probe>

Use the default options for this chemical probe

Options:

DMS | SHAPE | ETC | none

--min-mut-gap-weights <min_mut_gap_weights>

Comma-separated gap:weight pairs defining a mixture of min_mut_gap biases, e.g. ‘0:0.2,1:0.3,2:0.5’. Defaults are probe-specific. Pass an empty string to disable.

--mut-collisions <mut_collisions>

If two mutations are closer than –min-mut-gap positions, MERGE the mutations, DROP the read, or AUTO-select based on the probe.

Options:

drop | merge | auto

--injected-mut-probs <injected_mut_probs>

Comma-separated offset:prob pairs (offset ≥ 1) defining the probability of injecting a mutation that many positions 5’ of an existing mutation, e.g. ‘1:0.1,2:0.01’ (used with –mut-collisions merge). Defaults are probe-specific; pass an empty string to disable.

--num-reads <num_reads>

Simulate this many reads

--batch-size <batch_size>

Limit batches to at most this many reads

--write-read-names, --no-write-read-names

Write the name of each read in a second set of batches (necessary for the options –drop-read or –drop-read-file)

--brotli-level <brotli_level>

Compress pickle files with this level of Brotli (0 - 11)

--force, --no-force

Force all tasks to run, overwriting any existing output files

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--seed <seed>

Seed for the random number generator

seismic sim fastq

Simulate a FASTQ file.

Usage

seismic sim fastq [OPTIONS] [INPUT_PATH]...

Options

-d, --param-dir <param_dir>

Simulate data using parameter files in this directory

--profile-name <profile_name>

Give the simulated structure and parameters this profile name

-s, --sample <sample>

Give this name to the simulated sample

--paired-end, --single-end

Simulate paired-end or single-end reads

--read-length <read_length>

Simulate reads with this many base calls

--reverse-fraction <reverse_fraction>

Simulate this fraction of reverse-oriented reads

--probe <probe>

Use the default options for this chemical probe

Options:

DMS | SHAPE | ETC | none

--min-mut-gap-weights <min_mut_gap_weights>

Comma-separated gap:weight pairs defining a mixture of min_mut_gap biases, e.g. ‘0:0.2,1:0.3,2:0.5’. Defaults are probe-specific. Pass an empty string to disable.

--mut-collisions <mut_collisions>

If two mutations are closer than –min-mut-gap positions, MERGE the mutations, DROP the read, or AUTO-select based on the probe.

Options:

drop | merge | auto

--injected-mut-probs <injected_mut_probs>

Comma-separated offset:prob pairs (offset ≥ 1) defining the probability of injecting a mutation that many positions 5’ of an existing mutation, e.g. ‘1:0.1,2:0.01’ (used with –mut-collisions merge). Defaults are probe-specific; pass an empty string to disable.

--fq-gzip, --fq-text

Simulate FASTQ files with gzip compression or as plain text

--num-reads <num_reads>

Simulate this many reads

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

--force, --no-force

Force all tasks to run, overwriting any existing output files

--seed <seed>

Seed for the random number generator

Arguments

INPUT_PATH

Optional argument(s)

seismic sim abstract

Abstract simulation parameters from tables and structures.

Usage

seismic sim abstract [OPTIONS] [INPUT_PATH]...

Options

--fold-table-region, --fold-full-region

If no regions are specified, whether to default to the table’s region or to the full region

-F, --fold-regions-file <fold_regions_file>

Fold regions of references from coordinates/primers in a CSV file

--fold-coords <fold_coords>

Fold a region of a reference given its 5’ and 3’ end coordinates

--fold-primers <fold_primers>

Fold a region of a reference given its forward and reverse primers

--struct-file <struct_file>

Compare mutational profiles to the structure(s) in this CT file

-b, --branch <branch>

Create a new branch of the workflow with this name

--min-aucroc <min_aucroc>

Skip tables/profiles where the AUC-ROC is less than this value

--verify-times, --no-verify-times

Verify that report files from later steps have later timestamps

--num-cpus <num_cpus>

Use up to this many CPUs simultaneously

Arguments

INPUT_PATH

Optional argument(s)