Faidx

Extract entries from FASTA files

Command identity

Canonical command:

faidx

Handler:

faidx

Aliases:

ge, get_entry

Standalone executables:

pk_faidx, pk_ge, pk_get_entry

Categories:

Alignment & dataset utilities

Runtime interface

Synopsis

phykit faidx <fasta> [--entry <entry>] [--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
-e, --entry	false	str	none	any
--json	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Unless the guidance below states otherwise, results are emitted as command output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Extracts a sequence entry from a fasta file.

This function works similarly to the faidx function in samtools, but does not require an indexing step.

To obtain multiple entries, input multiple entries separated by a comma (,). For example, if you want entries named "seq_0" and "seq_1", the string "seq_0,seq_1" should be associated with the -e argument.

phykit faidx <fasta> -e/--entry <fasta entry> [--json]

Options:
<fasta>: first argument after function name should be a fasta file
-e/--entry: entry name to be extracted from the inputted fasta file
--json: optional argument to print results as JSON