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.
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.
|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|
|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|
|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|
|faswc||tally sequences and characters|
|alnpi||tally molecular population genetic statistics|
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'
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.
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.
Installation generates a man page for each utility. From the installation directory, additional resources are in ./doc, particularly the FAST_Cookbook
You can also look for information at:
RT, CPAN's request tracker (report bugs here):
AnnoCPAN, Annotated CPAN documentation:
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.