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