/ 
FAST-1.06
River stage zero No dependents
/ faslen

NAME

faslen -- annotate sequence lengths to descriptions

SYNOPSIS

faslen [MULTIFASTA-FILE...]

DESCRIPTION

faslen takes sequence or alignment data on input, computes sequence lengths, and annotates sequence record descriptions with their lengths in the format "length:<value>." All sequence characters get counted, including gap characters. Identifiers and lengths may optionally be printed in a table to STDOUT.

Options specific to faslen: -t, --table print lengths with ids in a table -j, --join=<string> use <string> to join data

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

faslen 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

-t, --table

Output data in a table to standard output. By default, length data is annotated into descriptions.

-j, --join=[string]

Use [string] to append length data in descriptions. Use with argument "\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 "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

Print length of all sequences:

    faslen sequences.fas > measured.fas

Print tab-delimited table of lengths:

    faslen -tj "\t" sequences.fas

Filtering sequences to have length >= 300:

    faslen sequences.fas | fasfilter -t length 300..

Sorting sequences by length:

    faswc sequences.fas | fassort -t length

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..