NAME

faswc - tally sequences and sequence characters

SYNOPSIS

faswc [OPTION]... [MULTIFASTA-FILE...]

DESCRIPTION

faswc takes sequence or alignment data on input and outputs tallies of sequences and/or sequence characters directly to STDOUT (in analogy to wc). If a list of files are given as arguments to faswc, tallies are calculated by file as well as in total. If input is over STDIN, only totals are output.

Options specific to faswc: -s, --sequences tally sequences only -c, --characters tally characters only

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 =head1 INPUT AND OUTPUT

faswc 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.

OPTIONS

-s, --sequences

Output tallies of sequences only by file and/or in total.

-c, --characters

Output tallies of sequence characters only by file and/or in total.

-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 "faslen" 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

Count the number of sequences in data1.fas and data2.fas and the total:

faswc -s data1.fas data2.fas

SEE ALSO

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. Bioinformatics and Bioperl Stajich et al..