NAME

fascodon - counts codon usage

SYNOPSIS

fascodon [options] [MULTIFASTA-FILE...]

DESCRIPTION

fascodon takes multifasta format sequence or alignment data as input, and analyzes codon usage and other coding characteristics of the data. By default, fascodon analyzes each sequence record individually, outputting raw codon frequencies appended to the description of each record, which allows sorting or filtering of data with other FAST tools. Optionally, fascodon -t in "table-mode" outputs data in tabular format, followed by an aggregate summary of all the data on input. By default, start codons are analyzed separately, assuming that all sequences are at least two codons long.

Options specific to fascodon: -r, --rscu annotate with RSCU values rather than raw frequency counts -j, --join=<string> use <string> to join tagged values in descriptions --no-starts do not analyze start codons separately -p, --precision=<int> print RSCU with <int> digits after the decimal point -w, --width=<int> print frequencies in fields of width <int> -t, --table table-mode, outputs codon frequency table to STDOUT -s, --summary in table-mode, only output summaries for all data -b, --base-order=<string> use base-order <string> to enumerate codons default order is "TCAG" -o, --amino-order:<string> enumerate codons by amino acids they encode optionally, only for amino acids in <string>, or if no argument, use default "ARNDCQEGHILKMFPSTWYV*"; -c, --code=<int> use NCBI genetic code tableID <int> to translate --codes print NCBI tableIDs of genetic codes for -c option --verbose issue warnings about coding properties to STDERR

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 --moltype=<[dna|rna|protein]> specify input sequence type -q, --fastq use fastq format as input and output

INPUT AND OUTPUT

fascodon 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

-r --rscu

Output Relative Synonymous Codon Usage (RSCU) values rather than raw frequencies (default).

-c [int] --code=[int]

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

--codes

Output a list of NCBI genetic code tableIDs and exit.

-b [string] --base-order=[string]

Use bases in [string] order to enumerate codons. Default is "TCAG."

--verbose,

Issue warnings to STDERR about sequences with premature stop codons, that do not end in stop codons, sequences that are not divisible by 3, etc.

-o --amino-order -o [string] --amino-order=[string]

Enumerate codons by the amino acids they encode. If no option argument is given, codons are enumerated in the default order "ARNDCQEGHILKMFPSTWYV*". If option argument is given, it determines which amino acids (codon families) will be analyzed and in what order.

-j [string] --join=[string]

Use <string> to join tagged value output in sequence record descriptions. Use with argument "\t" to indicate a tab-character.

-t --table

Print output in a table to STDOUT.

-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.

-m [dna|rna|protein], --moltype=[dna|rna|protein]

Specify the type of sequence on input (should not be needed in most cases, but sometimes Bioperl cannot guess and complains when processing data).

-q, --fastq

use fastq format as input and output.

EXAMPLES

Print codon usage of sequences:

cat data.fas | fascodon

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..