NAME

fasxl -- translate sequences by a genetic code.

SYNOPSIS

fasxl [OPTION]... [MULTIFASTA-FILE]...

DESCRIPTION

fasxl takes multifasta format DNA or RNA codon sequences or alignments as input, and generates biological translations of those sequences as output. Gapped sequences on input are allowed with the -g, -k or -o options; the gap character "-" is required for correct interpretation.

Options specific to fasxl: -a, --annotate output translations as tagged values in descriptions -j, --join=<string> use <string> to join data -g, --gapped gapped translations in alignment with input -k, --keep keep input sequences in output (forces -g). -o, --codon2aa turn codon alignment into a protein alignment (best used for codon-based alignments, where gaps are mod 3 length and seqs are to be translated in frame 0) --CDS treat as CDS (for bacterial code, for example, treat init codons as M)(deprecated) -f, --frame=<int> frame for translation [0 (default),1, or 2]. -c, -t, --code=<int> NCBI genetic code tableID for translating sequences [1] -3 translate each sequence in all three forward frames -6 translate each sequence in all six frames -s, --stop=<char> character representing stop codons ["*"] -u, --unknown=<char> character representing unknown amino acids ["X"] --codes, --tables print NCBI table ids of genetic codes for -t option

Options general to FAST: -h, --help print a brief help message --man print full documentation --version print version -l, --log create/append to logfile -L, --logname=<string> use logfile name <string> -C, --comment=<string> save comment <string> to log --format=<format> use alternative format for input -m, --moltype=<[dna|rna|protein]> specify input sequence type -q, --fastq use fastq format as input and output

INPUT AND OUTPUT

fasxl is part of FAST, the FAST Analysis of Sequences Toolbox, based on Bioperl. Most core FAST utilities expect input and return output in multifasta format. Input can occur in one or more files or on STDIN. Output occurs to STDOUT. The FAST utility fasconvert can reformat other formats to and from multifasta.

OPTIONS

-a, --annotate

This option outputs translations as tagged values in descriptions. By default translations are outputted in the sequence.

-j, --join=<string>

Use a <string> to join data in the description. Default is a space character. Use "\t" to indicate a tab-character.

-g, --gapped

This option enables translation of gapped sequences.

-k, --keep

Keep inputted sequences in the output. This option also enables the translation of gapped sequences.

-o, --codon2aa

turn codon alignment into a protein alignment (best used for codon-based alignments, where gaps are mod 3 length and seqs are to be translated in frame 0)

-c, --cds

This option is deprecated. Treat as CDS (for bacterial code, for example, treat init codons as M).

-f, --frame=<int>

Specify the frame for translation [0,1,2]. By default frame 0 is used.

-c [int], --code=[int] -t [int], --table=[int]

Use NCBI genetic code tableID <int> for translating sequences.

--tables, --codes

Output a list of NCBI genetic code tableIDs and exit.

-3

Translate each sequence in all three forward frames.

-6

Translate each sequence in all six frames.

-s, --stop=<char>

Specify a string to representing stop codons. By default "*" is used.

-u, --unknown=<char>

Specify a string representing unknown amino acids. By default "X" is used.

-h, --help

Print a brief help message and exit.

--man

Print the manual page and exit.

--version

Print version information and exit.

-l, --log

Creates, or appends to, a generic FAST logfile in the current working directory. The logfile records date/time of execution, full command with options and arguments, and an optional comment.

-L [string], --logname=[string]

Use [string] as the name of the logfile. Default is "FAST.log.txt".

-C [string], --comment=[string]

Include comment [string] in logfile. No comment is saved by default.

--format=[format]

Use alternative format for input. See man page for "fasconvert" for allowed formats. This is for convenience; the FAST tools are designed to exchange data in Fasta format, and "fasta" is the default format for this tool.

-q --fastq

Use fastq format as input and output.

EXAMPLES

Translate each nucleotide seqeunces contained in file data.fas in all three forward reading frames.

fasxl -3 data.fas

Translate each nucleotide seqeunces contained in file data.fas in all six reading frames and only select sequences that start with Met and end with a stop codon.

fasxl -6 data.fas | fasgrep -s "^M.*\*$"

SEE ALSO

man perlre

perldoc perlre

Documentation on perl regular expressions.

man FAST

perldoc FAST

Introduction and cookbook for FAST

The FAST Home Page"

CITING

If you use FAST, please cite Lawrence et al. (2015). FAST: FAST Analysis of Sequences Toolbox. and Bioperl Stajich et al..