Command Line Interface#

RNAdist#

usage: RNAdist <command> [<args>]

Sub-commands#

visualize#

Runs the Dash visualization tool

RNAdist visualize [-h] --input INPUT [INPUT ...] [--fasta FASTA] [--port PORT]
                  [--host HOST]

Named Arguments#

--input

Path to the prediction files generated using one of the prediction mechansims. It is possible to include multiple files using whitespace separated paths

--fasta

Fasta file containing sequences from the prediction. Leavong the default None will lead to missing nucleotide information (Default: None)

--port

Port to run the Dash server (Default: 8080)

Default: '8080'

--host

Host IP used by the dash server to serve the application (Default: 0.0.0.0)

Default: '0.0.0.0'

clote-ponty#

Calculates the clote-ponty matrix for every sequence in a fasta file

RNAdist clote-ponty [-h] --input INPUT --output OUTPUT
                    [--num_threads NUM_THREADS] [--temperature TEMPERATURE]
                    [--min_loop_size MIN_LOOP_SIZE] [--noGU {0,1}]

General Arguments#

--input

FASTA input file

--output

Pickled Output file that stores matrices. Can be visualized via RNAdist visualize

--num_threads

Number of parallel threads to use (Default: 1)

Default: 1

ViennaRNA Model Details#

--temperature

Temperature for RNA secondary structure prediction (Default: 37)

Default: 37.0

--min_loop_size

Minimum Loop size of RNA. (Default: 3)

Default: 3

--noGU

Possible choices: 0, 1

If set to 1 prevents GU pairs (Default: 0)

Default: 0

pmcomp#

Calculates the pmcomp matrix for every sequence in a fasta file

RNAdist pmcomp [-h] --input INPUT --output OUTPUT [--num_threads NUM_THREADS]
               [--temperature TEMPERATURE] [--min_loop_size MIN_LOOP_SIZE]
               [--noGU {0,1}]

General Arguments#

--input

FASTA input file

--output

Pickled Output file that stores matrices. Can be visualized via RNAdist visualize

--num_threads

Number of parallel threads to use (Default: 1)

Default: 1

ViennaRNA Model Details#

--temperature

Temperature for RNA secondary structure prediction (Default: 37)

Default: 37.0

--min_loop_size

Minimum Loop size of RNA. (Default: 3)

Default: 3

--noGU

Possible choices: 0, 1

If set to 1 prevents GU pairs (Default: 0)

Default: 0

sample#

Calculates the averaged distance matrix for every sequence in a fasta file using probabilistic backtracking

RNAdist sample [-h] --input INPUT --output OUTPUT [--num_threads NUM_THREADS]
               [--nr_samples NR_SAMPLES] [--non_redundant]
               [--temperature TEMPERATURE] [--min_loop_size MIN_LOOP_SIZE]
               [--noGU {0,1}]

General Arguments#

--input

FASTA input file

--output

Pickled Output file that stores matrices. Can be visualized via RNAdist visualize

--num_threads

Number of parallel threads to use (Default: 1)

Default: 1

--nr_samples

Number of samples used for expected distance calculation. (Default: 1000)

Default: 1000

--non_redundant

Triggers non-redundant sampling. Will adjust for unseen probability mass. If this is not intended you haveto use the Python API

Default: True

ViennaRNA Model Details#

--temperature

Temperature for RNA secondary structure prediction (Default: 37)

Default: 37.0

--min_loop_size

Minimum Loop size of RNA. (Default: 3)

Default: 3

--noGU

Possible choices: 0, 1

If set to 1 prevents GU pairs (Default: 0)

Default: 0

binding-site#

Calculates the expected distance of binding sites specified via the beds option

RNAdist binding-site [-h] --input INPUT --bed_files BED_FILES [BED_FILES ...]
                     [--names NAMES [NAMES ...]] --output OUTPUT
                     [--num_threads NUM_THREADS] [--temperature TEMPERATURE]
                     [--min_loop_size MIN_LOOP_SIZE] [--noGU {0,1}]

General Arguments#

--input

FASTA input file

--bed_files

whitespace seperated list of bed files containing binding sites (at least one)

--names

whitespace seperated list of names that will be shown in the output. Uses the bed filenames if not provided

--output

TSV Output file that stores expected distances of binding sites

--num_threads

Number of parallel threads to use (Default: 1)

Default: 1

ViennaRNA Model Details#

--temperature

Temperature for RNA secondary structure prediction (Default: 37)

Default: 37.0

--min_loop_size

Minimum Loop size of RNA. (Default: 3)

Default: 3

--noGU

Possible choices: 0, 1

If set to 1 prevents GU pairs (Default: 0)

Default: 0

extract#

Extracts TSV files from the prediction output that was generated via one of the prediction mechanisms

RNAdist extract [-h] --data_file DATA_FILE --outdir OUTDIR

Named Arguments#

--data_file: Path to the prediction files generated using one of the prediction mechansims.
--outdir: Path to the output directory, where TSV files will be saved