faslen -- annotate sequence lengths to descriptions
faslen [MULTIFASTA-FILE...]
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
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.
Output data in a table to standard output. By default, length data is annotated into descriptions.
Use [string] to append length data in descriptions. Use with argument "\t" to indicate a tab-character.
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 "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.
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.
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
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.