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FAST-1.0
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FAST --- Fast Analysis of Sequences Toolbox

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 pipelines. The default data exchange format is multifasta (specifically, a restriction of BioPerl FastA format). FAST is designed for learnability, interoperability, interface consistency, rapid prototyping, fine-tuned control, and reproducibility. FAST tools expose the power of Perl and BioPerl to users in an easy-to-learn command-line paradigm.

UTILITIES

FAST 1.0 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 position | | 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 | | gbfcut | select sequences by regex match on features in a GenBank file | | gbfalncut | select sites by regex match on features in a GenBank file |

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 records | | fastr | transform sequence records by character, degap | | fassub | transform sequence records by regex-based substitutions |

Analysis

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

INSTALLATION

To install this module, run the following commands:

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

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).

VERSION AND CHANGES

1.0 -- First public release

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.