NAME

fashead - print first sequence records on input

SYNOPSIS

fashead [OPTION]... [MULTIFASTA-FILE]...

DESCRIPTION

fashead takes sequence or alignment data as input, and outputs the first n sequence records of each input file or, if no files are specified, of the standard input. fashead by default prints the first 10 sequence records.

Options specific to fashead: -n, --number=<integer> the number of sequence records to print -a, --annotate annotate sequence records with source filename in descriptions -j, --join=<string> use <string> to join annotation in descriptions

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

fashead 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 [integer], --records=[integer] --number=[integer]

The number of sequence records to print. Must be a positive integer. Defaults to 10.

-a, --annotate

Annotate sequence descriptions with file names if and when input is being processed from files.

-j, --join=[string]

Use [string] to append filenames in descriptions. Use "\t" to indicate a tab-character.

-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

use fastq format as input and output.

EXAMPLES

Print the first 10 sequences:

cat data.fas | fashead -n 10 > data.dna.fas

Print the first 5 sequences:

cat data.fas | fashead -n 5 > data.dna.fas

Print the first 5 sequences with file name added to the description:

cat data.fas | fashead -a -n 5 > data.dna.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. and Bioperl Stajich et al..