summarize-rpbp-predictions#

Summarizes the ORF prediction step and prepare data for the web application.

usage: summarize-rpbp-predictions [-h] [--min-samples MIN_SAMPLES] [-k]
                                  [--no-replicates] [--use-unfiltered]
                                  [--use-name-maps]
                                  [--match-standardized-orfs]
                                  [--circos-bin-width CIRCOS_BIN_WIDTH]
                                  [--circos-show-chroms CIRCOS_SHOW_CHROMS [CIRCOS_SHOW_CHROMS ...]]
                                  [--show-orf-periodicity]
                                  [--image-type IMAGE_TYPE] [--overwrite]
                                  [--log-file LOG_FILE] [--enable-ext-logging]
                                  [--log-stdout] [--no-log-stderr]
                                  [--logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                                  [--file-logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                                  [--stdout-logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                                  [--stderr-logging-level {NOTSET,DEBUG,INFO,WARNING,ERROR,CRITICAL}]
                                  config

Positional Arguments#

config: A YAML configuration file. The same used to run the pipeline.

Named Arguments#

--min-samples

An ORF is filtered out if not predicted in at least --min-samples number of samples. By default all ORFs are kept. This is ignored if merged replicates are included in the output.

Default: 1

-k, --keep-other

Include ORFs labeled as other, if present. They are discarded by default.

Default: False

--no-replicates

If Rp-Bp was run with --merge-replicates, predictions from merged replicates are included by default, unless this flag is present.

Default: False

--use-unfiltered

Use the unfiltered ORF predictions. Unless Rp-Bp was run with --write-unfiltered, these will not be available. By default, the filtered predictions are used.

Default: False

--use-name-maps

Use riboseq_sample_name_map and riboseq_condition_name_map from the config. Do not use this flag when preparing results for the dashboard, mapping is done in the app.

Default: False

--match-standardized-orfs

Add matching ORF names from https://doi.org/10.1038/s41587-022-01369-0 (Human data)

Default: False

--circos-bin-width

Bin width for counting ORF predictions along chromosomes. Same bin width for all chromosomes. Last bin adjusted ad hoc to chromosome size.

Default: 10000000

--circos-show-chroms

A list of chromosomes for which predictions are shown. By default, only numbered chromosomes (and X/x, Y/y) are shown, to avoid cluttering the figure. Use this option for organisms with a different nomenclature, or to show additional chromosomes or contigs.

Default: [’\d’, ‘X’, ‘x’, ‘Y’, ‘y’]

--show-orf-periodicity

Create bar charts showing the periodicity of each ORF type (not for the app).

Default: False

--image-type

Format for --show-orf-periodicity.

Default: “eps”

--overwrite

Overwrite existing output.

Default: False

logging options#

--log-file

Log file (logging is redirected to this file, in addition to stdout and stderr, if specified).

Default: “”

--enable-ext-logging

Enable logging for external programs that may be disabled by default, e.g. CmdStanPy.

Default: False

--log-stdout

Log to stdout (in addition to a file and stderr, if specified).

Default: False

--no-log-stderr

Do not send logging to stderr.

Default: False

--logging-level

Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL

Logging level for all logs.

Default: “WARNING”

--file-logging-level

Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL

Logging level for the log file. This option overrides --logging-level.

Default: “NOTSET”

--stdout-logging-level

Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL

Logging level for stdout. This option overrides --logging-level.

Default: “NOTSET”

--stderr-logging-level

Possible choices: NOTSET, DEBUG, INFO, WARNING, ERROR, CRITICAL

Logging level for stderr. This option overrides --logging-level.

Default: “NOTSET”