fasuniq - Remove duplicate sequence records in a multifasta file or datastream.
fasuniq [options] [MULTIFASTA-FILE]
[MULTIFASTA-DATA-ON-STDIN] | fasuniq [options]
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
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.
Concatenate identifiers of repeated sequences in output
Use delimiter [string] to concatenate identifiers. Default is ":"
Removes duplicate sequences by matching on descriptions.
Removes duplicate sequences by matching on identifiers.
Print a brief help message and exit.
Print the manual page and exit.
Print version information and exit.
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.
Use [string] as the name of the logfile. Default is "FAST.log.txt".
Include comment [string] in logfile. No comment is saved by default.
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.
Specify the type of sequence on input (should not be needed in most cases, but sometimes Bioperl cannot guess and complains when processing data).
Use fastq format as input and output.
Remove duplicate sequences and append concatnated IDs of duplicate sequences to printed sequence:
fassort -s data1.fas | fasuniq -c
man perlre
perldoc perlre
Documentation on perl regular expressions.
man FAST
perldoc FAST
Introduction and cookbook for FAST
If you use FAST, please cite Lawrence et al. (2015). FAST: FAST Analysis of Sequences Toolbox. and Bioperl Stajich et al..
To install FAST, copy and paste the appropriate command in to your terminal.
cpanm
cpanm FAST
CPAN shell
perl -MCPAN -e shell install FAST
For more information on module installation, please visit the detailed CPAN module installation guide.