faswc - tally sequences and sequence characters
faswc [OPTION]... [MULTIFASTA-FILE...]
faswc takes sequence or alignment data on input and outputs tallies of sequences and/or sequence characters directly to STDOUT (in analogy to wc). If a list of files are given as arguments to faswc, tallies are calculated by file as well as in total. If input is over STDIN, only totals are output.
Options specific to faswc: -s, --sequences tally sequences only -c, --characters tally characters only
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 =head1 INPUT AND OUTPUT
faswc 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 tallies of sequences only by file and/or in total.
Output tallies of sequence characters only by file and/or in total.
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.
Count the number of sequences in data1.fas and data2.fas and the total:
faswc -s data1.fas data2.fas
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. Bioinformatics 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.