fasta-utils - Fasta Utilities¶

Overview¶

New in version 0.3.0.

Scripts that includes some functionality to help use FASTA files with the framework

split command¶

Used to split a fasta file into smaller fragments

translate command¶

Used to translate nucleotide sequences into amino acids.

uid command¶

Used to change a FASTA file headers to a unique ID. A table (tab separated) with the changes made can be kept, using the –table option.

Changes¶

New in version 0.3.0.

Changed in version 0.3.1: added translate and uid command

Changed in version 0.3.4: ported to click

Options¶

fasta-utils¶

Main function

fasta-utils [OPTIONS] COMMAND [ARGS]...

Options

--version¶: Show the version and exit.

--cite¶

split¶

Splits a FASTA file [fasta-file] in a number of fragments

fasta-utils split [OPTIONS] [FASTA_FILE]

Options

-v, --verbose¶

-p, --prefix <prefix>¶

Prefix for the file name in output

Default:	split

-n, --number <number>¶

Number of chunks into which split the FASTA file

Default:	10

-z, --gzip¶: gzip output files

Arguments

FASTA_FILE¶: Optional argument

translate¶

Translate FASTA file [fasta-file] in all 6 frames to [output-file]

fasta-utils translate [OPTIONS] [FASTA_FILE] [OUTPUT_FILE]

Options

-v, --verbose¶

-t, --trans-table <trans_table>¶

translation table

Default:	universal
Options:	bac_plt\|drs_mit\|inv_mit\|prt_mit\|universal\|vt_mit\|yst_alt\|yst_mit

--progress¶: Shows Progress Bar

Arguments

FASTA_FILE¶: Optional argument

OUTPUT_FILE¶: Optional argument

uid¶

Changes each header of a FASTA file [file-file] to a uid (unique ID)

fasta-utils uid [OPTIONS] [FASTA_FILE] [OUTPUT_FILE]

Options

-v, --verbose¶

-t, --table <table>¶: Filename of a table to record the changes (by default discards it)

Arguments

FASTA_FILE¶: Optional argument

OUTPUT_FILE¶: Optional argument