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BLASTaid-v0.0.2
River stage zero No dependents
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/ BLASTaid

NAME

BLASTaid - A simple interface for byte indexing a WU-BLAST multi-part report for faster access.

VERSION

This document describes BLASTaid version 0.0.2

SYNOPSIS

    BLASTaid --report <file> --index <file> (opt: --query OR --list)

    EX: BLASTaid --report "report.blast" --index "/tmp/report.index" --query "gi|71143145|ref|NM_006300.2|"
    EX: BLASTaid --report "report.blast" --index "/tmp/report.index" --list "queries.fof"

DESCRIPTION

This script is a simple interface to the BLASTaid.pm module and aids in accessing specific reports from longer, multi part WU-BLAST (http://blast.wustl.edu/) alignments reports. Depending on parameters and starting input, BLAST reports may be several gigabytes in size. Extremely large files can prove to be problematic and rate-limiting in post-process analysis. BLASTaid takes a multi-part BLAST report and creates a byte index. Specific reports may be pulled directly from the larger set by jumping directly to the entry via the byte-index. The index file need only be created one time per BLAST report... the script automatically uses a supplied index file if it already exists. A user may also also loop through a list of queries in the report in a systematic way by invoking the --list option. Retrieval is always based around QUERY name, as this should be a unique value in the BLAST report. When BLASTaid makes QUERY names, it takes the first section of the BLAST report's "Query=" line before any white space.

The index file has the following associated format:

 [ID]            [BYTE POS.]     [ALIGNMENTS?]   [TYPE]          [QUERY NAME]
 1               0               TRUE            BLASTN          gi|45238847|ref|NM_000945.3|
 2               24552           TRUE            BLASTN          gi|71143145|ref|NM_006300.2|
 3               177083          TRUE            BLASTN          gi|56121814|ref|NM_030957.2|

INTERFACE

The following options are supported:

--report

report: Path/name of the WU-BLAST report to parse and index. [REQUIRED]

--index

index: Path/name of the byte index file to be written--or possibly already exists, in which case it will be loaded. [REQUIRED]

--query

query: Specific query name (as it appears in the byte index file) used to return a single report. [OPTIONAL]

--list

list: Path/name of a file which lists a number of queries to return reports for. Should be one query per line, as follows. [OPTIONAL]

 gi|45238847|ref|NM_000945.3|
 gi|71143145|ref|NM_006300.2|
 gi|56121814|ref|NM_030957.2|
 ...

CONFIGURATION AND ENVIRONMENT

BLASTaid requires no configuration files or environment variables. This distribution supplies the perl script "BLASTaid", which is a command line interface for BLASTaid.pm's main functions. The default installation is /usr/bin/. If you are installing on a Windows based system, please manually place the BLASTaid script somewhere in your perl path.

DEPENDENCIES

This script requires the BLASTaid.pm module.

INCOMPATIBILITIES

None reported.

BUGS AND LIMITATIONS

No bugs have been reported. This script is limited to parsing WU-BLAST style reports--it does not currently support NCBI or other formats.

Please report any bugs or feature requests to bug-blastaid@rt.cpan.org, or through the web interface at http://rt.cpan.org.

AUTHOR

Todd Wylie

<perldev@monkeybytes.org>

http://www.monkeybytes.org

LICENSE AND COPYRIGHT

Copyright (c) 2006, Todd Wylie <perldev@monkeybytes.org>. All rights reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See perlartistic.

DISCLAIMER OF WARRANTY

BECAUSE THIS SOFTWARE IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE SOFTWARE, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE SOFTWARE "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE SOFTWARE IS WITH YOU. SHOULD THE SOFTWARE PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR, OR CORRECTION.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE SOFTWARE AS PERMITTED BY THE ABOVE LICENSE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE SOFTWARE (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE SOFTWARE TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

NOTE

This software was written using the latest version of GNU Emacs, the extensible, real-time text editor. Please see http://www.gnu.org/software/emacs for more information and download sources.