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Bio-Grep-v0.8.2
River stage zero No dependents
++
/ bgrep

NAME

bgrep - Wrapper for several suffix array tools

VERSION

This document describes bgrep version 0.8.2

SYNOPSIS

  # to create a database
  bgrep --backend Vmatch --database Data.fa --datapath data --createdb

  # to search
  bgrep [ Options ] --query_file Query.fa --database Data.fa  --datapath data

    --query_file    A Fasta file with the query sequences.
    --database      A Fasta database.

OPTIONS

--help

Brief help message.

--man

Full documentation

--backend b

The back-end tool. Agrep, GUUGle, Hypa and Vmatch are supported.

--mismatches n

The number of mismatches.

--editdistance n

The allowed edit distance.

--insertions n

The number of insertions.

--deletions n

The number of deletions.

--query_length n

Report all matches of length of at least n.

--reverse_complement

Searches for the reverse complement.

--direct_and_rev_com

Searches for direct matches and the reverse complement.

--upstream n

Display n nucleotides/AAs upstream the match.

--downstream n

Display n nucleotides/AAs downstream the match.

--sort s

Sets sort mode to s.

--maxhits n

Display only the n (best) hits.

--datapath p,

Generate suffix arrays in path p. Default is 'data'

--showdesc n,

Vmatch only (see manual). Is faster because it extracts all data directly out of the vmatch output. Otherwise, vsubseqselect is called for every hit.

--hxdrop n

Vmatch only (see manual). Specifies the xdrop value for hamming distance extension.

--exdrop n

Vmatch only (see manual). Specifies the xdrop value for edit distance extension.

DESCRIPTION

Bio-Grep is a collection of Perl modules for searching in Fasta files. It is programmed in a modular way. There are different backends available. You can filter search results.

bgrep is an example of how to use this library.

BUGS AND LIMITATIONS

No bugs have been reported.

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

SEE ALSO

perldoc Bio::Grep

AUTHOR

Markus Riester, <mriester@gmx.de>

LICENCE AND COPYRIGHT

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

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 LICENCE, 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.