Commands, Arguments, Options

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.

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

Options

--demult-on, --demult-off

Enable demultiplexing

-x, --fastqx <fastqx>

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

--phred-enc <phred_enc>

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

--barcode-start <barcode_start>

Index of start of barcode

--barcode-end <barcode_end>

Length of barcode

-o, --out-dir <out_dir>

Write all output files to this directory

--parallel-demultiplexing <parallel_demultiplexing>

Whether to run demultiplexing at maximum speed by submitting multithreaded grep functions

--clipped <clipped>

Designates the amount of clipped patterns to search for in the sample, will raise compution time

--mismatch-tolerence <mismatch_tolerence>

Designates the allowable amount of mismatches allowed in a string and still be considered a valid pattern find. 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>

Designates the allowable amount of distance you allow the pattern to be found in a read from the reference index

--demulti-overwrite <demulti_overwrite>

Desiginates whether to overwrite the grepped fastq. should only be used if changing setting on the same sample

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

-R, --refs-meta <refs_meta>

Add reference metadata from this CSV file to exported results

-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

--force, --no-force

Force all tasks to run, overwriting any existing output files

--parallel, --serial

Run tasks in parallel or in series

--max-procs <max_procs>

Run up to this many processes simultaneously

--fastqc, --no-fastqc

Run FastQC on the initial and trimmed FASTQ files

--qc-extract, --qc-no-extract

Unzip FastQC report files

--cut, --no-cut

Use Cutadapt to trim reads before alignment

--cut-a1 <cut_a1>

Trim this 3’ adapter from read 1

--cut-g1 <cut_g1>

Trim this 5’ adapter from read 1

--cut-a2 <cut_a2>

Trim this 3’ adapter from read 2

--cut-g2 <cut_g2>

Trim this 5’ adapter from read 2

--cut-O <cut_o>

Require at least this many bases of an adapter to trim it

--cut-e <cut_e>

Tolerate at most this fraction of errors in adapter sequences

--cut-q1 <cut_q1>

Trim base calls below this Phred score from read 1

--cut-q2 <cut_q2>

Trim base calls below this Phred score from read 2

--cut-m <cut_m>

Discard reads shorter than this length after trimming

--cut-indels, --cut-no-indels

Allow errors in adapter sequences to be insertions and deletions

--cut-discard-trimmed, --cut-keep-trimmed

Discard reads in which an adapters were found

--cut-discard-untrimmed, --cut-keep-untrimmed

Discard reads in which no adapters were found

--cut-nextseq, --cut-no-nextseq

Trim high-quality Gs from the 3’ end (for Illumina NextSeq and iSeq)

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

Run Bowtie2 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

--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 plus- and minus-strand reads

--f1r2-plus, --f1r2-minus

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

--minus-label <minus_label>

With –sep-strands, append this label to each minus-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

--ambindel, --no-ambindel

Mark all ambiguous insertions and deletions

--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)

-P, --pool <pool>

Pooled sample name

-c, --mask-coords <mask_coords>

Mask a section of a reference given its 5’ and 3’ end coordinates

-p, --mask-primers <mask_primers>

Mask a section 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 section

-s, --mask-sections-file <mask_sections_file>

Mask sections of references from coordinates/primers in a CSV file

--mask-del, --keep-del

Mask deletions

--mask-ins, --keep-ins

Mask insertions

--mask-mut <mask_mut>

Mask this type of mutation

--mask-polya <mask_polya>

Mask stretches of at least this many consecutive A bases (0 disables)

--mask-gu, --keep-gu

Mask G and U bases

--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 unambiguous base calls

--max-fmut-pos <max_fmut_pos>

Mask positions with more than this fraction of mutated base calls

--mask-discontig, --keep-discontig

Mask paired-end reads with discontiguous mates

--min-ncov-read <min_ncov_read>

Mask reads with fewer than this many bases covering the section

--min-finfo-read <min_finfo_read>

Mask reads with less than this fraction of unambiguous base calls

--max-fmut-read <max_fmut_read>

Mask reads with more than this fraction of mutated base calls

--min-mut-gap <min_mut_gap>

Mask reads with two mutations separated by fewer than this many bases

--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

-k, --max-clusters <max_clusters>

Attempt to find at most this many clusters

-e, --em-runs <em_runs>

Repeat EM this many times for each number of clusters

--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 (times number of clusters)

--max-em-iter <max_em_iter>

Run EM for at most this many iterations (times number of clusters)

-J, --joined <joined>

Joined section name

-j, --join-clusts <join_clusts>

Join clusters from this CSV file

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

Make a table counting relationships per position

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

Make a table counting relationships per read

--table-clust, --no-table-clust

Make a table counting reads per cluster (only for clustered data)

--fold, --no-fold

Predict the secondary structure using the RNAstructure Fold program

-f, --fold-sections-file <fold_sections_file>

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

--fold-coords <fold_coords>

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

--fold-primers <fold_primers>

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

--fold-full, --fold-table

If no sections are specified, whether to default to the full section or to the table’s section

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--fold-temp <fold_temp>

Predict structures at this temperature (Kelvin)

--fold-constraint <fold_constraint>

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

--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)

--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>

Graph each INDIVidual cluster in its own file, each ORDER in its own file, or UNITE all clusters in one file containing all orders

Options:

indiv | order | unite

--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

-w, --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

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

Graph rolling Gini coefficients

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

Graph receiver operating characteristic curves

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

Graph rolling areas under receiver operating characteristic curves

Arguments

FASTA

Required argument

INPUT_PATH

Optional argument(s)

Run individual steps of the workflow

seismic demult

Split multiplexed FASTQ files by their barcodes.

seismic demult [OPTIONS] FASTA

Options

-x, --fastqx <fastqx>

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

--phred-enc <phred_enc>

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

--barcode-start <barcode_start>

Index of start of barcode

--barcode-end <barcode_end>

Length of barcode

-o, --out-dir <out_dir>

Write all output files to this directory

--parallel-demultiplexing <parallel_demultiplexing>

Whether to run demultiplexing at maximum speed by submitting multithreaded grep functions

--clipped <clipped>

Designates the amount of clipped patterns to search for in the sample, will raise compution time

--mismatch-tolerence <mismatch_tolerence>

Designates the allowable amount of mismatches allowed in a string and still be considered a valid pattern find. 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>

Designates the allowable amount of distance you allow the pattern to be found in a read from the reference index

--demulti-overwrite <demulti_overwrite>

Desiginates whether to overwrite the grepped fastq. should only be used if changing setting on the same sample

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

-R, --refs-meta <refs_meta>

Add reference metadata from this CSV file to exported results

Arguments

FASTA

Required argument

seismic align

Trim FASTQ files and align them to reference sequences.

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

--force, --no-force

Force all tasks to run, overwriting any existing output files

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--parallel, --serial

Run tasks in parallel or in series

--max-procs <max_procs>

Run up to this many processes simultaneously

--fastqc, --no-fastqc

Run FastQC on the initial and trimmed FASTQ files

--qc-extract, --qc-no-extract

Unzip FastQC report files

--cut, --no-cut

Use Cutadapt to trim reads before alignment

--cut-a1 <cut_a1>

Trim this 3’ adapter from read 1

--cut-g1 <cut_g1>

Trim this 5’ adapter from read 1

--cut-a2 <cut_a2>

Trim this 3’ adapter from read 2

--cut-g2 <cut_g2>

Trim this 5’ adapter from read 2

--cut-O <cut_o>

Require at least this many bases of an adapter to trim it

--cut-e <cut_e>

Tolerate at most this fraction of errors in adapter sequences

--cut-q1 <cut_q1>

Trim base calls below this Phred score from read 1

--cut-q2 <cut_q2>

Trim base calls below this Phred score from read 2

--cut-m <cut_m>

Discard reads shorter than this length after trimming

--cut-indels, --cut-no-indels

Allow errors in adapter sequences to be insertions and deletions

--cut-discard-trimmed, --cut-keep-trimmed

Discard reads in which an adapters were found

--cut-discard-untrimmed, --cut-keep-untrimmed

Discard reads in which no adapters were found

--cut-nextseq, --cut-no-nextseq

Trim high-quality Gs from the 3’ end (for Illumina NextSeq and iSeq)

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

Run Bowtie2 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

--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 plus- and minus-strand reads

--f1r2-plus, --f1r2-minus

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

--minus-label <minus_label>

With –sep-strands, append this label to each minus-strand reference

Arguments

FASTA

Required argument

seismic relate

Compute relationships between references and aligned reads.

seismic relate [OPTIONS] FASTA [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

--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

--ambindel, --no-ambindel

Mark all ambiguous insertions and deletions

--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)

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

--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 mask

Define mutations and sections to filter reads and positions.

seismic mask [OPTIONS] [INPUT_PATH]...

Options

-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, --mask-coords <mask_coords>

Mask a section of a reference given its 5’ and 3’ end coordinates

-p, --mask-primers <mask_primers>

Mask a section 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 section

-s, --mask-sections-file <mask_sections_file>

Mask sections of references from coordinates/primers in a CSV file

--mask-del, --keep-del

Mask deletions

--mask-ins, --keep-ins

Mask insertions

--mask-mut <mask_mut>

Mask this type of mutation

--mask-polya <mask_polya>

Mask stretches of at least this many consecutive A bases (0 disables)

--mask-gu, --keep-gu

Mask G and U bases

--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 unambiguous base calls

--max-fmut-pos <max_fmut_pos>

Mask positions with more than this fraction of mutated base calls

--mask-discontig, --keep-discontig

Mask paired-end reads with discontiguous mates

--min-ncov-read <min_ncov_read>

Mask reads with fewer than this many bases covering the section

--min-finfo-read <min_finfo_read>

Mask reads with less than this fraction of unambiguous base calls

--max-fmut-read <max_fmut_read>

Mask reads with more than this fraction of mutated base calls

--min-mut-gap <min_mut_gap>

Mask reads with two mutations separated by fewer than this many bases

--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

--brotli-level <brotli_level>

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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

INPUT_PATH

Optional argument(s)

seismic cluster

Infer alternative structures by clustering reads’ mutations.

seismic cluster [OPTIONS] [INPUT_PATH]...

Options

-k, --max-clusters <max_clusters>

Attempt to find at most this many clusters

-e, --em-runs <em_runs>

Repeat EM this many times for each number of clusters

--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 (times number of clusters)

--max-em-iter <max_em_iter>

Run EM for at most this many iterations (times number of clusters)

--brotli-level <brotli_level>

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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

--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

Arguments

INPUT_PATH

Optional argument(s)

seismic table

Count mutations for each read and position; output tables.

seismic table [OPTIONS] [INPUT_PATH]...

Options

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

Make a table counting relationships per position

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

Make a table counting relationships per read

--table-clust, --no-table-clust

Make a table counting reads per cluster (only for clustered data)

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

seismic fold

Predict RNA secondary structures using mutation rates.

seismic fold [OPTIONS] [INPUT_PATH]...

Options

-f, --fold-sections-file <fold_sections_file>

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

--fold-coords <fold_coords>

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

--fold-primers <fold_primers>

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

--fold-full, --fold-table

If no sections are specified, whether to default to the full section or to the table’s section

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--fold-temp <fold_temp>

Predict structures at this temperature (Kelvin)

--fold-constraint <fold_constraint>

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

--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)

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

--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.

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

Options

-r, --rels <rels>

Graph these relationship(s)

--use-ratio, --use-count

Graph ratios or counts

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--cgroup <cgroup>

Graph each INDIVidual cluster in its own file, each ORDER in its own file, or UNITE all clusters in one file containing all orders

Options:

indiv | order | unite

--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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

seismic graph delprof

Bar graph of differences between two profiles per position.

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

Options

-r, --rels <rels>

Graph these relationship(s)

--use-ratio, --use-count

Graph ratios or counts

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 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

--cgroup <cgroup>

Graph each INDIVidual cluster in its own file, each ORDER in its own file, or UNITE all clusters in one file containing all orders

Options:

indiv | order | unite

--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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

seismic graph scatter

Scatter plot comparing two profiles.

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

Options

-r, --rels <rels>

Graph these relationship(s)

--use-ratio, --use-count

Graph ratios or counts

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 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

--cgroup <cgroup>

Graph each INDIVidual cluster in its own file, each ORDER in its own file, or UNITE all clusters in one file containing all orders

Options:

indiv | order | unite

--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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

seismic graph corroll

Rolling correlation/comparison of two profiles.

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

Options

-r, --rels <rels>

Graph these relationship(s)

--use-ratio, --use-count

Graph ratios or counts

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 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

-w, --window <window>

Use a sliding window of this many bases

-n, --winmin <winmin>

Mask sliding windows with fewer than this number of data

-m, --metric <metric>

Metric to compare mutation rates: ‘nrmsd’ = normalized root-mean-square deviation (NRMSD), ‘pcc’ = Pearson correlation coefficient (r), ‘scc’ = Spearman correlation coefficient (ρ), ‘r2’ = coefficient of determination (R²)

Options:

nrmsd | pcc | scc | r2

--cgroup <cgroup>

Graph each INDIVidual cluster in its own file, each ORDER in its own file, or UNITE all clusters in one file containing all orders

Options:

indiv | order | unite

--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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

seismic graph histpos

Histogram of relationship(s) per position.

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

Options

-r, --rels <rels>

Graph these relationship(s)

--use-ratio, --use-count

Graph ratios or counts

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 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

--cgroup <cgroup>

Graph each INDIVidual cluster in its own file, each ORDER in its own file, or UNITE all clusters in one file containing all orders

Options:

indiv | order | unite

--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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

seismic graph histread

Histogram of relationship(s) per read.

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

Options

-r, --rels <rels>

Graph these relationship(s)

--use-ratio, --use-count

Graph ratios or counts

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 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

--cgroup <cgroup>

Graph each INDIVidual cluster in its own file, each ORDER in its own file, or UNITE all clusters in one file containing all orders

Options:

indiv | order | unite

--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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

seismic graph roc

ROC curve comparing a profile to a structure.

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

Options

-r, --rels <rels>

Graph these relationship(s)

--use-ratio, --use-count

Graph ratios or counts

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--struct-file <struct_file>

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

-f, --fold-sections-file <fold_sections_file>

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

--fold-coords <fold_coords>

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

--fold-primers <fold_primers>

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

--fold-full, --fold-table

If no sections are specified, whether to default to the full section or to the table’s section

--cgroup <cgroup>

Graph each INDIVidual cluster in its own file, each ORDER in its own file, or UNITE all clusters in one file containing all orders

Options:

indiv | order | unite

--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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

seismic graph aucroll

Rolling AUC-ROC comparing a profile to a structure.

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

Options

-r, --rels <rels>

Graph these relationship(s)

--use-ratio, --use-count

Graph ratios or counts

-q, --quantile <quantile>

Normalize and winsorize ratios to this quantile (0.0 disables)

--struct-file <struct_file>

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

-f, --fold-sections-file <fold_sections_file>

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

--fold-coords <fold_coords>

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

--fold-primers <fold_primers>

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

--fold-full, --fold-table

If no sections are specified, whether to default to the full section or to the table’s section

-w, --window <window>

Use a sliding window of this many bases

-n, --winmin <winmin>

Mask sliding windows with fewer than this number of data

--cgroup <cgroup>

Graph each INDIVidual cluster in its own file, each ORDER in its own file, or UNITE all clusters in one file containing all orders

Options:

indiv | order | unite

--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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

Extra Utilities

Note

For every extra utility (that is not part of the main workflow), the name begins with +.

seismic +listpos

List positions meeting specific criteria.

seismic +listpos [OPTIONS] [INPUT_PATH]...

Options

--max-fmut-pos <max_fmut_pos>

Mask positions with more than this fraction of mutated base calls

--complement, --no-complement

List the complement

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

seismic +addclust

Add more clusters to a dataset that was already clustered.

seismic +addclust [OPTIONS] [INPUT_PATH]...

Options

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

-k, --max-clusters <max_clusters>

Attempt to find at most this many clusters

--brotli-level <brotli_level>

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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

seismic +delclust

Delete clusters from a dataset that was already clustered.

seismic +delclust [OPTIONS] [INPUT_PATH]...

Options

-t, --tmp-pfx <tmp_pfx>

Write all temporary files to a directory with this prefix

-k, --max-clusters <max_clusters>

Attempt to find at most this many clusters

--brotli-level <brotli_level>

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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

seismic +cleanfa

Clean the names and sequences in FASTA files.

seismic +cleanfa [OPTIONS] [INPUT_PATH]...

Options

--inplace, --newfile

Modify files in-place instead of writing new files (WARNING: 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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

INPUT_PATH

Optional argument(s)

seismic +renumct

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

seismic +renumct [OPTIONS]

Options

-c, --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, --newfile

Modify files in-place instead of writing new files (WARNING: 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

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

seismic +test

Test if SEISMIC-RNA is working properly.

seismic +test [OPTIONS]

Options

-v, --verbose

Print info (-v) or info and debug (-vv) messages on stdout

seismic +sim

seismic +sim total

Simulate FASTQ files from scratch.

seismic +sim total [OPTIONS]

Options

-P, --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

--min-mut-gap <min_mut_gap>

Mask reads with two mutations separated by fewer than this many bases

--fq-gzip, --fq-text

Simulate FASTQ files with gzip compression or as plain text

-n, --num-reads <num_reads>

Simulate this many reads

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

--force, --no-force

Force all tasks to run, overwriting any existing output files

-o, --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

-f, --fold-sections-file <fold_sections_file>

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

--fold-coords <fold_coords>

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

--fold-primers <fold_primers>

Fold a section 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 (Kelvin)

--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)

--keep-tmp, --erase-tmp

Keep temporary files after finishing

-c, --clust-conc <clust_conc>

Set the concentration parameter for simulating cluster proportions

-3, --end3-fmean <end3_fmean>

Set the mean 3’ end as a fraction of the section length

-l, --insert-fmean <insert_fmean>

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

-e, --ends-var <ends_var>

Set the variance of end coordinates as a fraction of its supremum

-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 paired bases

-w, --vmut-unpaired <vmut_unpaired>

Set the relative variance of mutation rates of unpaired bases

-R, --refs <refs>

Give this name to the file of simulated references

-r, --ref <ref>

Give this name to the simulated reference

-N, --reflen <reflen>

Simulate a reference sequence with this many bases

seismic +sim ref

Simulate a FASTA file of a reference sequence.

seismic +sim ref [OPTIONS]

Options

-o, --sim-dir <sim_dir>

Write all simulated files to this directory

-R, --refs <refs>

Give this name to the file of simulated references

-r, --ref <ref>

Give this name to the simulated reference

-N, --reflen <reflen>

Simulate a reference sequence with this many bases

--force, --no-force

Force all tasks to run, overwriting any existing output files

seismic +sim fold

Simulate secondary structure(s) a reference sequence.

seismic +sim fold [OPTIONS] FASTA

Options

-o, --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

-P, --profile-name <profile_name>

Give the simulated structure and parameters this profile name

-f, --fold-sections-file <fold_sections_file>

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

--fold-coords <fold_coords>

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

--fold-primers <fold_primers>

Fold a section 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 (Kelvin)

--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)

--keep-tmp, --erase-tmp

Keep temporary files after finishing

--force, --no-force

Force all tasks to run, overwriting any existing output files

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

Arguments

FASTA

Required argument

seismic +sim params

Simulate parameter files.

seismic +sim params [OPTIONS]

Options

-i, --ct-file <ct_file>

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

-c, --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

--parallel, --serial

Run tasks in parallel or in series

--max-procs <max_procs>

Run up to this many processes simultaneously

-3, --end3-fmean <end3_fmean>

Set the mean 3’ end as a fraction of the section length

-l, --insert-fmean <insert_fmean>

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

-e, --ends-var <ends_var>

Set the variance of end coordinates as a fraction of its supremum

-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 paired bases

-w, --vmut-unpaired <vmut_unpaired>

Set the relative variance of mutation rates of unpaired bases

seismic +sim muts

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

seismic +sim muts [OPTIONS]

Options

-i, --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 paired bases

-w, --vmut-unpaired <vmut_unpaired>

Set the relative variance of mutation rates of unpaired bases

--force, --no-force

Force all tasks to run, overwriting any existing output files

--parallel, --serial

Run tasks in parallel or in series

--max-procs <max_procs>

Run up to this many processes simultaneously

seismic +sim ends

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

seismic +sim ends [OPTIONS]

Options

-i, --ct-file <ct_file>

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

-3, --end3-fmean <end3_fmean>

Set the mean 3’ end as a fraction of the section length

-l, --insert-fmean <insert_fmean>

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

-e, --ends-var <ends_var>

Set the variance of end coordinates as a fraction of its supremum

--force, --no-force

Force all tasks to run, overwriting any existing output files

--parallel, --serial

Run tasks in parallel or in series

--max-procs <max_procs>

Run up to this many processes simultaneously

seismic +sim clusts

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

seismic +sim clusts [OPTIONS]

Options

-i, --ct-file <ct_file>

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

-c, --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

--parallel, --serial

Run tasks in parallel or in series

--max-procs <max_procs>

Run up to this many processes simultaneously

seismic +sim relate

Simulate a Relate dataset.

seismic +sim relate [OPTIONS]

Options

-d, --param-dir <param_dir>

Simulate data using parameter files in this directory

-P, --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

--min-mut-gap <min_mut_gap>

Mask reads with two mutations separated by fewer than this many bases

-n, --num-reads <num_reads>

Simulate this many reads

--batch-size <batch_size>

Limit batches to at most this many reads

--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

--parallel, --serial

Run tasks in parallel or in series

--max-procs <max_procs>

Run up to this many processes simultaneously

seismic +sim fastq

Simulate a FASTQ file.

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

Options

-d, --param-dir <param_dir>

Simulate data using parameter files in this directory

-P, --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

--min-mut-gap <min_mut_gap>

Mask reads with two mutations separated by fewer than this many bases

--fq-gzip, --fq-text

Simulate FASTQ files with gzip compression or as plain text

-n, --num-reads <num_reads>

Simulate this many reads

--max-procs <max_procs>

Run up to this many processes simultaneously

--parallel, --serial

Run tasks in parallel or in series

--force, --no-force

Force all tasks to run, overwriting any existing output files

Arguments

INPUT_PATH

Optional argument(s)