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 eliminates redundant sequence records from the input. A redundant record is one in which a specific data field tests equal as a string against the same field in one or more records that immediately follow it in the input multifasta file or datastream. By default the actual sequences are compared, optionally identifiers or descriptions may be tested for equality. The data on input must be sorted with respect to the data being compared using, for example, fassort -s. Only one field in sequence records is tested. By default, the last matching sequence record in a series of matches is the one printed. Identifiers of adjacent duplicate sequence records can be concatenated to the printed sequence using the --concat option. The count of redundant records may be annotated into sequence descriptions with the --count option.

Options specific to fasuniq: -i, --identifier test for string equality on identifiers -d, --description test for string equality on descriptions -c, --count annotate descriptions with counts of duplicates -j, --join=<string> use <string> as delimiter when appending count data, default " " --concat:<string> concatenate identifiers of duplicate records using ":" by default or <string>

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

-d, --description

Removes duplicate sequences by matching on descriptions.

-i, --identifier

Removes duplicate sequences by matching on identifiers.

-c, --count

Annotate the number of redundant records into descriptions.

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

Use <string> to append count data to sequence record descriptions. Use with argument "\t" to indicate a tab-character.

--concat, --concat=[string]

Concatenate identifiers of repeated sequences in output. Use delimiter [string] to concatenate identifiers. If none given, default is ":"

-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 --concat

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..