Command-line reference¶

Every scanRBP invocation prints its version, config file path and data folder first. Run scanRBP -help for the built-in summary; this page is the fuller reference.

Usage forms¶

Form	Description
`scanRBP sequence output [options]`	Score a sequence given directly on the command line.
`scanRBP filename.fasta [options]`	Score every sequence in a FASTA file — one output set per sequence.
`scanRBP search search_term`	List database entries matching `search_term`. See Motif database & search.
`scanRBP config [folder]`	Show (no argument) or change (`folder`) the data storage folder in `~/.scanRBP`.

Scoring options¶

Option	Description
`-protein <term>`	Restrict scoring to database entries matching `term` (same matching as `search`). Default: score against every entry.
`-clip peaks.bed.gz`	Score against real CLIP peak data instead of a PWM. Requires a FASTA input with genomically-encoded sequence ids. See CLIP-based scoring.
`-cumulative`	Plot one protein's binding across every sequence in a FASTA file, instead of one heatmap per sequence. Requires `-protein`. See Cumulative plots.
`-nonzero`	Clip all negative scores to 0. Off by default.
`-force`	Overwrite existing output files instead of skipping already-processed sequences.
`-output_folder folder`	Write outputs here (default: current directory).

Heatmap options¶

Option	Description
`-heatmap title`	Generate a heatmap (PNG + PDF) with this title. Without it, only the `.tab.gz` score matrix is written.
`-annotate`	Print the numeric score inside each heatmap cell.
`-xlabels`	Show the sequence along the x-axis.
`-figsize "(w,h)"`	matplotlib/seaborn figure size in inches.
`-fontscale n`	Heatmap text scale (default `0.2`).
`-vlines "x1,x2"`	Dashed vertical guide lines at these x positions (negative values count from the sequence end).

Other¶

Option	Description
`-version`	Print the installed scanRBP version and exit.
`-help`	Print the built-in usage summary.