API Reference

The arguments for the CLI and Python API are the same. The CLI is just a wrapper around the Python API.

CLI

dreem aggregate

dreem aggregate [OPTIONS]

Options

--fasta <fasta>

FASTA file of all reference sequences in the project

-bv, --bv-files <bv_files>

Tuple of paths. Give the path to the sample folder to process every section. Give the path to a report to process a single section.

--library <library>

Library CSV file

--samples <samples>

Samples file

-cf, --clustering-file <clustering_file>

Path to the json clustering file from dreem clustering.

-rs, --rnastructure-path <rnastructure_path>

Path to the RNAstructure executable folder (e.g. /home/user/RNAstructure/exe/). Use this option if RNAstructure is not in your PATH.

-rst, --rnastructure-use-temp <rnastructure_use_temp>

Use the temperature signal to make predictions with RNAstructure

-rsa, --rnastructure-fold-args <rnastructure_fold_args>

Additional arguments to pass to RNAstructure’s Fold command

-rsd, --rnastructure-use-dms <rnastructure_use_dms>

Use the DMS signal to make predictions with RNAstructure

-rsdmin, --rnastructure-dms-min-unpaired-value <rnastructure_dms_min_unpaired_value>

Minimum unpaired value for using the dms signal as an input for RNAstructure

-rsdmax, --rnastructure-dms-max-paired-value <rnastructure_dms_max_paired_value>

Maximum paired value for using the dms signal as an input for RNAstructure

-rspa, --rnastructure-deltag-ensemble <rnastructure_deltag_ensemble>

Use RNAstructure partition function to predict free energy

-rspr, --rnastructure_probability <rnastructure_probability>

Use RNAstructure partition function to predict per-base pairing probability

-v, --verbose

Print info or info+debug messages to stdout

--out-dir <out_dir>

Where to output all finished files

--temp-dir <temp_dir>

Where to write all temporary files

--save-temp, --erase-temp

Whether to save or erase temporary files after the program exits

Python

dreem.aggregate.run(fasta: str, bv_files: list = (), *, out_dir: str = './output', temp_dir: str = './temp', save_temp: bool = False, library: str = '', samples: str = '', clustering_file: str = '', rnastructure_path: str = '', rnastructure_use_temp: bool = False, rnastructure_fold_args: str = '', rnastructure_use_dms: str = False, rnastructure_dms_min_unpaired_value: float = 0.07, rnastructure_dms_max_paired_value: float = 0.01, rnastructure_deltag_ensemble: bool = False, rnastructure_probability: bool = False, verbose: bool = 0)

Run the aggregate module.

Parameters

  • fasta (str) – FASTA file of all reference sequences in the project [positional or keyword]

  • bv_files (list) – Tuple of paths. Give the path to the sample folder to process every section. Give the path to a report to process a single section. [positional or keyword, default: ()]

  • out_dir (str) – Where to output all finished files [keyword-only, default: ‘./output’]

  • temp_dir (str) – Where to write all temporary files [keyword-only, default: ‘./temp’]

  • save_temp (bool) – Whether to save or erase temporary files after the program exits [keyword-only, default: False]

  • library (str) – Library CSV file [keyword-only, default: ‘’]

  • samples (str) – Samples file [keyword-only, default: ‘’]

  • clustering_file (str) – Path to the json clustering file from dreem clustering. [keyword-only, default: ‘’]

  • rnastructure_path (str) – Path to the RNAstructure executable folder (e.g. /home/user/RNAstructure/exe/). Use this option if RNAstructure is not in your PATH. [keyword-only, default: ‘’]

  • rnastructure_use_temp (bool) – Use the temperature signal to make predictions with RNAstructure [keyword-only, default: False]

  • rnastructure_fold_args (str) – Additional arguments to pass to RNAstructure’s Fold command [keyword-only, default: ‘’]

  • rnastructure_use_dms (str) – Use the DMS signal to make predictions with RNAstructure [keyword-only, default: False]

  • rnastructure_dms_min_unpaired_value (float) – Minimum unpaired value for using the dms signal as an input for RNAstructure [keyword-only, default: 0.07]

  • rnastructure_dms_max_paired_value (float) – Maximum paired value for using the dms signal as an input for RNAstructure [keyword-only, default: 0.01]

  • rnastructure_deltag_ensemble (bool) – Use RNAstructure partition function to predict free energy [keyword-only, default: False]

  • rnastructure_probability (bool) – Use RNAstructure partition function to predict per-base pairing probability [keyword-only, default: False]

  • verbose (bool) – Print info or info+debug messages to stdout [keyword-only, default: 0]