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

Options

FASTA utilities

usage: fasta-utils [-h] [-v | --quiet] [--cite] [--manual] [--version]
                   {split,translate,uid} ...

Named Arguments

-v, --verbose	more verbose - includes debug messages Default: 20
--quiet	less verbose - only error and critical messages
--cite	Show citation for the framework
--manual	Show the script manual
--version	show program’s version number and exit

Sub-commands:

split

Splits a FASTA file in a number of fragments

fasta-utils split [-h] [-p PREFIX] [-n NUMBER] [-z] [-v | --quiet] [--cite]
                  [--manual] [--version]
                  [input_file]

Positional Arguments

input_file

Input FASTA file, defaults to stdin Default: -

Named Arguments

-p, --prefix	Prefix for the file name in output Default: “split”
-n, --number	Number of chunks into which split the FASTA file Default: 10
-z, --gzip	gzip output files Default: False
-v, --verbose	more verbose - includes debug messages Default: 20
--quiet	less verbose - only error and critical messages
--cite	Show citation for the framework
--manual	Show the script manual
--version	show program’s version number and exit

translate

Translate FASTA file in all 6 frames

fasta-utils translate [-h]
                      [-t {bac_plt,drs_mit,inv_mit,prt_mit,universal,vt_mit,yst_alt,yst_mit}]
                      [-v | --quiet] [--cite] [--manual] [--version]
                      [input_file] [output_file]

Positional Arguments

input_file	Input FASTA file, defaults to stdin Default: -
output_file	Input FASTA file, defaults to stdin Default: <open file ‘<stdout>’, mode ‘w’ at 0x7fa31cd94150>

Named Arguments

-t, --trans-table
	Possible choices: bac_plt, drs_mit, inv_mit, prt_mit, universal, vt_mit, yst_alt, yst_mit translation table Default: “universal”
-v, --verbose	more verbose - includes debug messages Default: 20
--quiet	less verbose - only error and critical messages
--cite	Show citation for the framework
--manual	Show the script manual
--version	show program’s version number and exit

uid

Changes the header to a uid (unique ID)

fasta-utils uid [-h] [-t TABLE] [-v | --quiet] [--cite] [--manual] [--version]
                [input_file] [output_file]

Positional Arguments

input_file	Input FASTA file, defaults to stdin Default: -
output_file	Input FASTA file, defaults to stdin Default: <open file ‘<stdout>’, mode ‘w’ at 0x7fa31cd94150>

Named Arguments

-t, --table	Filename of table of the changes (by default discards it)
-v, --verbose	more verbose - includes debug messages Default: 20
--quiet	less verbose - only error and critical messages
--cite	Show citation for the framework
--manual	Show the script manual
--version	show program’s version number and exit