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FAST --- Fast Analysis of Sequences Toolbox

Version 1.6. Apr 21, 2015

The FAST Analysis of Sequences Toolbox (FAST) is a set of Unix tools (for example fasgrep, fascut, fashead and fastr) for sequence bioinformatics modeled after the Unix textutils (such as grep, cut, head, tr, etc). FAST workflows are designed for "inline" (serial) processing of flatfile biological sequence record databases per-sequence, rather than per-line, through Unix command pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FAST tools expose the power of Perl and BioPerl for sequence analysis to non-programmers in an easy-to-learn command-line paradigm.

You do not need to know Perl or BioPerl to use FAST.

UTILITIES

FAST 1.6 contains the following utilities. Each has its own man page. FAST utilities may be classifed as for annotation, selection, transformation, and analysis.

Annotation

Program Description
faslen annotate sequence lengths
fascodon tally/annotate codon usage
fascomp tally/annotate monomer frequencies
fasxl translate gapped and ungapped sequences and alignments
fasrc reverse complement nucleotide sequences and alignments

Selection

Program Description
fasgrep select sequence records by perl regular expressions
fasfilter select sequence records by numerical values
fastax select sequence records by NCBI Taxonomy IDs or names
fascut select/reorder sequence record data by sequential ranges
fasuniq remove duplicate sequence records from sorted data
fashead select leading sequence records
fastail select trailing sequence records
alncut select sites based on variation and gap-content content
gbfcut select sequences by regex match on features in a GenBank features
gbfalncut select sites by regex match on features in a GenBank features

Transformation

Program Description
fasconvert convert sequences to or from from fasta format
fassort sort sequence records
fastaxsort sort sequence records by NCBI Taxonomy IDs or names
faspaste concatenate sequence record data
fastr transform sequence records by characters and alphabets
fassub transform sequence records by regex-based substitutions

Analysis

Program Description
faswc tally sequences and characters
alnpi tally molecular population genetic statistics

PREREQUISITES

FAST has some Perl dependencies. Once posted to CPAN, the easiest way to install FAST with its dependencies will be by executing this command:

perl -MCPAN -e 'install FAST'

You can also follow INSTALLATION instructions below, but you may need to first run these commands to install FAST dependencies:

perl -MPCAN -e 'install Sort::Key'
perl -MCPAN -e 'install Sort::MergeSort'
perl -MCPAN -e 'install Bit::Vector'
perl -MCPAN -e 'install Test::More'
perl -MCPAN -e 'install Test::Script::Run'

INSTALLATION

To install this module, run the following:

perl Makefile.PL
make
make test
(sudo) make install

If you haven't installed perl-based software on your system before, or you are having problems, please see more detailed notes in INSTALL.

GETTING STARTED

perldoc fasgrep
man fasgrep
perldoc FAST

Some usage examples in the man pages refer to data that ships with FAST, in the installation package under t/data. Run these examples with these data to get started right away using FAST.

DOCUMENTATION

Installation generates a man page for each utility. From the installation directory, additional resources are in ./doc, particularly the FAST_Cookbook

SUPPORT

You can also look for information at:

RT, CPAN's request tracker (report bugs here):

http://rt.cpan.org/NoAuth/Bugs.html?Dist=FAST

AnnoCPAN, Annotated CPAN documentation:

http://annocpan.org/dist/FAST

CPAN Ratings:

http://cpanratings.perl.org/d/FAST

Search CPAN:

http://search.cpan.org/dist/FAST/

CITING

If you use FAST please, cite the FAST project (Lawrence et al. 2015) and Bioperl (Stajich et al. 2005).

If you publish work that cites data provided in this FAST installer, please cite the authors of this data accordingly. For example, if you use the tRNAdb-CE data provided in this installer, please cite: Abe T, Inokuchi H, Yamada Y, Muto A, Iwasaki Y and Ikemura T (2014) tRNADB-CE: tRNA gene database well-timed in the era of big sequence data. Front. Genet. 5:114. doi: 10.3389/fgene.2014.00114

VERSION AND CHANGES

1.0 -- First public release

LICENSE AND COPYRIGHT

Copyright (C) 2015 David H. Ardell

This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). You may obtain a copy of the full license at: http://www.perlfoundation.org/artistic_license_2_0

Any use, modification, and distribution of the Standard or Modified Versions is governed by this Artistic License. By using, modifying or distributing the Package, you accept this license. Do not use, modify, or distribute the Package, if you do not accept this license. If your Modified Version has been derived from a Modified Version made by someone other than you, you are nevertheless required to ensure that your Modified Version complies with the requirements of this license. This license does not grant you the right to use any trademark, service mark, tradename, or logo of the Copyright Holder. This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed. Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.