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package FAST; |
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use 5.10.1; |
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use strict; |
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use Carp; |
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use warnings FATAL => 'all'; |
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our $VERSION = '1.05'; |
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our $DEF_FORMAT = "fasta"; |
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our $DEF_LOGNAME = "FAST.log.txt"; |
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our $DEF_JOIN_STRING = " "; |
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our $DEF_SPLIT_REGEX = ' '; |
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sub log { |
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my ($logname, $DATE, $COMMAND, $comment, $fromSTDIN) = @_; |
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unless ($logname and $DATE and $COMMAND) { |
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carp join "","FAST::log: logname, DATE, or COMMAND undefined; logging not possible.\n"; |
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return; |
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} |
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open (LOG, ">>$logname") or carp "FAST::log: cannot open logfile $logname\n"; |
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if (*LOG) { |
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if (!$fromSTDIN) { |
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print LOG "\n# FAST $VERSION $DATE "; |
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print LOG "$comment" if ($comment); |
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print LOG "\n"; |
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print LOG "$COMMAND" |
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} |
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else { |
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print LOG " | $COMMAND" |
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} |
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close LOG; |
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} |
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} |
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=head1 NAME |
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FAST - FAST Analysis of Sequences Toolbox |
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=head1 VERSION |
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Version 1.03 |
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=head1 SYNOPSIS |
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The Fast Analysis of Sequences Toolbox (FAST) is a set of UNIX |
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utilities (for example fasgrep, fascut, fashead and fastr) that |
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extends the UNIX toolbox paradigm to bioinformatic sequence |
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records. Modeled after the UNIX textutils (such as grep, cut, head, |
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tr, etc), FAST workflows are designed for "inline" (serial) processing |
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of flatfile biological sequence record databases per-sequence, rather |
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than per-line, through UNIX pipelines. The default data exchange |
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format is multifasta (specifically, a restriction of BioPerl FastA |
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format). FASTQ format is supported. FAST is designed for learnability, |
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interoperability, interface consistency, rapid prototyping, fine-tuned |
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control, and reproducibility. FAST tools expose the power of Perl and |
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BioPerl to users in an easy-to-learn command-line paradigm. |
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=head1 UTILITIES |
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FAST 1.0x contains the following utilities. Each has its own man page. |
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=over 4 |
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=item B |
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select sites based on site variation and gap-content |
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=item B |
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calculate molecular population genetic statistics |
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=item B |
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tally/annotate codon usage |
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=item B |
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tally/annotate monomer frequencies |
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=item B |
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convert sequences to or from from fasta format |
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=item B |
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select/reorder sequence records based on index lists/ranges |
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=item B |
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filter sequence records based on numerical values |
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=item B |
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filter sequence records based on perl regular expressions |
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=item B |
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filter leading sequence records |
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=item B |
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annotate sequence lengths |
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=item B |
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concatenate sequence records |
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=item B |
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reverse complement nucleotide sequences and alignments |
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=item B |
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sort sequence records |
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=item B |
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transform sequence records using regex-based substitutions |
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=item B |
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filter trailing sequence records |
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=item B |
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filter sequence records based on NCBI taxonomy IDs or names |
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=item B |
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sort sequence records based on NCBI taxonomy IDs or names |
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=item B |
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transform sequence records by character, degap, strict |
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=item B |
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remove duplicate sequence records from sorted data |
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=item B |
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tally sequences and characters |
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=item B |
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translate gapped and ungapped sequences and alignments |
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=item B |
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select sites by regex matching of features in a GenBank file |
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=item B |
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print sequences by regex matching to features in a GenBank file |
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=back |
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=head1 AUTHORS |
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David H. Ardell, C<< >> |
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and members of the Ardell Laboratory |
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and other contributors including: |
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Travis Lawrence |
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Dana Carper |
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Katherine Amrine |
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Kyle Kauffman |
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Claudia Canales |
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=head1 BUGS |
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Please report any bugs or feature requests to C, or through |
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the web interface at L. I will be notified, and then you'll |
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automatically be notified of progress on your bug as I make changes. |
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=head1 ACKNOWLEDGEMENTS |
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=head1 LICENSE AND COPYRIGHT |
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Copyright 2015 David H. Ardell. |
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This program is free software; you can redistribute it and/or modify it |
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under the terms of the the Artistic License (2.0). You may obtain a |
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copy of the full license at: |
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L |
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Any use, modification, and distribution of the Standard or Modified |
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Versions is governed by this Artistic License. By using, modifying or |
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distributing the Package, you accept this license. Do not use, modify, |
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or distribute the Package, if you do not accept this license. |
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If your Modified Version has been derived from a Modified Version made |
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by someone other than you, you are nevertheless required to ensure that |
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your Modified Version complies with the requirements of this license. |
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This license does not grant you the right to use any trademark, service |
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mark, tradename, or logo of the Copyright Holder. |
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This license includes the non-exclusive, worldwide, free-of-charge |
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patent license to make, have made, use, offer to sell, sell, import and |
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otherwise transfer the Package with respect to any patent claims |
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licensable by the Copyright Holder that are necessarily infringed by the |
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Package. If you institute patent litigation (including a cross-claim or |
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counterclaim) against any party alleging that the Package constitutes |
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direct or contributory patent infringement, then this Artistic License |
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to you shall terminate on the date that such litigation is filed. |
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Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER |
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AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. |
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THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR |
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PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY |
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YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR |
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CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR |
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CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE, |
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EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
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=cut |
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1; # End of FAST |