fasuniq - Remove duplicate sequence records in a multifasta file or datastream.
fasuniq [options] [MULTIFASTA-FILE]
[MULTIFASTA-DATA-ON-STDIN] | fasuniq [options]
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
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.
Removes duplicate sequences by matching on descriptions.
Removes duplicate sequences by matching on identifiers.
Annotate the number of redundant records into descriptions.
Use <string> to append count data to sequence record descriptions. Use with argument "\t" to indicate a tab-character.
Concatenate identifiers of repeated sequences in output. Use delimiter [string] to concatenate identifiers. If none given, default is ":"
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 --concat
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.