Rename FASTA entries

Rename entries in a FASTA file

Command identity

Canonical command:

rename_fasta_entries

Handler:

rename_fasta_entries

Aliases:

rename_fasta

Standalone executables:

pk_rename_fasta_entries, pk_rename_fasta

Categories:

Alignment & dataset utilities

Runtime interface

Synopsis

phykit rename_fasta_entries <fasta> [--idmap <idmap>] [--output <output>] [--json]

Arguments

This table is generated from the live command parser. It is the authoritative source for accepted spellings, required arguments, types, defaults, and choices.

Argument	Required	Type	Default	Choices
fasta	true	str	required	any
-i, --idmap	false	str	none	any
-o, --output	false	str	none	any
--json	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Output-file options: --output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Renames fasta entries.

Renaming fasta entries will follow the scheme of a tab-delimited file wherein the first column is the current fasta entry name and the second column is the new fasta entry name in the resulting output alignment. Note, the input fasta file does not need to be an alignment file.

phykit rename_fasta_entries <fasta> -i/--idmap <idmap> [-o/--output <output_file>] [--json]

Options:
<fasta>: first argument after function name should be a FASTA file
-i/--idmap: identifier map of current FASTA names (col1) and desired FASTA names (col2)
--json: optional argument to print results as JSON