++ed by:
TSIBLEY

1 PAUSE user
1 non-PAUSE user.

David H. Ardell

NAME

FAST - FAST Analysis of Sequences Toolbox

VERSION

Version 1.03

SYNOPSIS

The Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX utilities (for example fasgrep, fascut, fashead and fastr) that extends the UNIX toolbox paradigm to bioinformatic sequence records. 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). FASTQ format is supported. 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 1.0x contains the following utilities. Each has its own man page.

alncut select sites based on site variation and gap-content
alnpi calculate molecular population genetic statistics
fascodon tally/annotate codon usage
fascomp tally/annotate monomer frequencies
fasconvert convert sequences to or from from fasta format
fascut select/reorder sequence records based on index lists/ranges
fasfilter filter sequence records based on numerical values
fasgrep filter sequence records based on perl regular expressions
fashead filter leading sequence records
faslen annotate sequence lengths
faspaste concatenate sequence records
fasrc reverse complement nucleotide sequences and alignments
fassort sort sequence records
fassub transform sequence records using regex-based substitutions
fastail filter trailing sequence records
fastax filter sequence records based on NCBI taxonomy IDs or names
fastaxsort sort sequence records based on NCBI taxonomy IDs or names
fastr transform sequence records by character, degap, strict
fasuniq remove duplicate sequence records from sorted data
faswc tally sequences and characters
fasxl translate gapped and ungapped sequences and alignments
gbfalncut select sites by regex matching of features in a GenBank file
gbfcut print sequences by regex matching to features in a GenBank file

AUTHORS

David H. Ardell, <dhard at cpan.org> and members of the Ardell Laboratory and other contributors including: Travis Lawrence Dana Carper Katherine Amrine Kyle Kauffman Claudia Canales

BUGS

Please report any bugs or feature requests to bug-fast at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=FAST. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

Copyright 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.