FAST --- FAST Analysis of Sequences Toolbox
Version 1.0. February, 2015
INTRODUCTION
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 1.0 contains the following utilities. Each has its own man
page. FAST utilities may be classifed as for annotation, selection,
transformation, and analysis.
annotation
----------
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
---------
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 GenBank features
gbfalncut -- select sites by regex match on GenBank features
transformation
--------------
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
--------
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:
(sudo) 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:
(sudo) perl -MPCAN -e 'install Sort::Key'
(sudo) perl -MCPAN -e 'install Sort::MergeSort'
(sudo) perl -MCPAN -e 'install Bit::Vector'
(sudo) perl -MCPAN -e 'install Pod::Usage'
To complete the optional "make test" step below, try installing also:
(sudo) perl -MCPAN -e 'install Test::More'
(sudo) perl -MCPAN -e 'install Test::Script::Run'
INSTALLATION
To install this module, please run the following:
perl Makefile.PL
make
make test
(sudo) make install
On some Windows systems, "make test" will fail. The "make test" step
is optional.
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)
AnnoCPAN, Annotated CPAN documentation
CPAN Ratings
Search CPAN
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:
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