NAME

fascomp -- analysis of monomer frequencies

SYNOPSIS

fascomp [OPTION]... [MULTIFASTA-FILE...]

DESCRIPTION

fascomp takes multifasta format sequence or alignment data as input, and counts the absolute or relative frequencies of monomers in each sequence individually and for all data on input. By default, absolute frequencies are computed and appended to the description. Optionally, fascomp --table will output a frequency table to STDOUT as tagged values, both for individual sequences and for all data on input. In table-mode if the character alphabet of the job is determined by either setting --moltype or from the type of the first sequence on input, and either --strict, --iupac or --alphabet is set, header labels will be output as well.

Options specific to fascomp: -n, --normalize compute relative frequencies -t, --table table-mode, output a table to STDOUT -j, --join=<string> use <string> to join tagged values in descriptions -s, --strict output moltype-dependent character header for table-mode -i, --iupac output character header including ambiguities for table-mode -a, --alphabet=<string> tally only characters if they are in the set <string>, as in "ACGT-" -p, --precision=<int> print relative frequencies with <int> digits after the decimal point -w, --width=<int> print frequencies in fields of width <int>

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

fascomp 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

-n --normalize

Compute relative frequencies.

-t --table

Output a table to STDOUT.

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

Use <string> to join tagged values in descriptions. Use "\t" to indicate a tab-character.

-s --strict

Output moltype-dependent character header for table-mode.

-i --iupac

Output character header including ambiguities for table-mode.

-a --alphabet=<string>

Tally only characters if they are in the set <string>, as in "ACGT-".

-p --precision=<int>

Print relative frequencies with <int> digits after the decimal point.

-w --width=<int>

Print frequencies in fields of width <int>

-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

Compute and annotate description with normalized base frequencies:

fascomp -n t/data/P450.fas

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..