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]
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