NAME

fasuniq - Remove duplicate sequence records in a multifasta file or datastream.

SYNOPSIS

fasuniq [options] [MULTIFASTA-FILE]

[MULTIFASTA-DATA-ON-STDIN] | fasuniq [options]

DESCRIPTION

fasuniq removes duplicate sequence records in a multifasta file or datastream. The sequences should be sorted such as output from fassort -s. Only the sequence data itself must be identical, not identifiers or descriptions. By default, the first matching sequence record in a series of matches (including identifier and description) is the one printed. IDs of adjacent duplicate sequence records can be concatenated to the printed sequence using the -c, --concat option.

Options specific to fasuniq: -c, --concat concatenate identifiers -d, --delimiter=<string> use <string> between identifers [:] -D, --description match on description -I, --id match on identifiers

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

fasuniq 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 file or on STDIN. Output occurs to STDOUT. The FAST utility fasconvert can reformat other formats to and from multifasta.

OPTIONS

-c, --concat

Concatenate identifiers of repeated sequences in output

-d [string], --delim=[string]

Use delimiter [string] to concatenate identifiers. Default is ":"

-D --description

Removes duplicate sequences by matching on descriptions.

-I --id

Removes duplicate sequences by matching on identifiers.

-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

Remove duplicate sequences and append concatnated IDs of duplicate sequences to printed sequence:

fassort -s data1.fas | fasuniq -c

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..