Bio::Tools::Blast::Run::LocalBlast(3)

NAME
Bio::Tools::Blast::Run::LocalBlast.pm - Bioperl module for running Blast analyses locally.

SYNOPSIS
    use Bio::Tools::Blast::Run::LocalBlast qw(&blast_local);
    &blast_local( %named_parameters);
See the blast_local manpage() for a description of available parameters.

INSTALLATION
This module is included with the central Bioperl distribution:

   http://bio.perl.org/Core/Latest
   ftp://bio.perl.org/pub/DIST
Follow the installation instructions included in the README file.

DESCRIPTION
Bio::Tools::Blast::Run::LocalBlast.pm contains methods and data necessary for running Blast sequence analyses on a local machine. This module must be customized for a specific site.

The basic requirements are that it conform to this minimal API:

1 Export a method called the blast_local manpage()
    that accepts a Bio::Tools::Blast.pm object + named parameters as specified by the blast_local manpage().

2 The the blast_local manpage() method should return
    a list of names of files containing the raw Blast reports.

3 Exporting arrays containing a list of available databases
    in the arrays "@Blast_dbn_local" and "@Blast_dbp_local".

The generic version of this module provides some rudimentary logic, but feel free to customize as necessary.

  Script Files
Sometimes it is convenient to write an executable shell script for running a set of Blasts on a local machine. This script can be saved and re-executed as necessary or saved for documentation purposes. This module could provide a convenient way to consolidate the logic necessary for producing such script files or perhaps stubs of script file that could be further modified for Blast-ing specific datasets.

DEPENDENCIES
Bio::Tools::Blast::Run::LocalBast.pm is used by Bio::Tools::Blast.pm The development of this is linked with the Blast.pm module and should be updated along with that module.

SEE ALSO
 Bio::Tools::Blast.pm                    - Blast object.
 Bio::Tools::Blast::Run::postclient.pl   - Script for accessing remote server.
 Bio::Tools::Blast::Run::Webblast.pm     - Utility module for running Blasts remotely.
 Bio::Tools::Blast::HTML.pm              - Blast HTML-formating utility class.
 Bio::Seq.pm                             - Biosequence object
 http://bio.perl.org/Projects/modules.html  - Online module documentation
 http://bio.perl.org/Projects/Blast/        - Bioperl Blast Project
 http://bio.perl.org/                       - Bioperl Project Homepage

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

    bioperl-l@bioperl.org          - General discussion
    http://bio.perl.org/MailList.html             - About the mailing lists

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

    bioperl-bugs@bio.perl.org
    http://bio.perl.org/bioperl-bugs/

AUTHOR
Steve A. Chervitz, sac@genome.stanford.edu

VERSION
Bio::Tools::Blast::Run::LocalBlast.pm, 0.01

COPYRIGHT
Copyright (c) 1998 Steve A. Chervitz. All Rights Reserved. This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

APPENDIX
Methods beginning with a leading underscore are considered private and are intended for internal use by this module. They are not considered part of the public interface and are described here for documentation purposes only.

  blast_local
 Usage     : @files = blast_local($blast_object,  %namedParameters);
           : This method is exported.
 Purpose   : Run a local Blast analysis on one or more sequences.
           : This method defines the API for your LocalBlast.pm module.
 Returns   : Array containing a list of filenames of the Blast reports.
 Argument  : $blast_object = object ref for a Bio::Tools::Blast.pm object.
           : %named parameters: (PARAMETER TAGS CAN BU UPPER OR LOWER CASE)
           : These are some basic parameters. Supply more as desired.
           :
           :   -SEQS       => ref to an array of Bio::Seq.pm objects.
           :   -SEQ_FILES  => ref to an array of strings containing full-path file names.
           :   -PROG       => name of blast program (blastp, blastx, etc.)
           :   -DATABASE   => name of database (see below.)
           :   -EXPECT     => expect value cutoff
           :   -FILTER     => sequence complexity filter ('default' or 'none')
           :   -MATRIX     => substitution scoring matrix (blast1 only for NCBI server)
           :   -DESCR      => integer, number of on-line descriptions (V, 100)
           :   -ALIGN      => integer, number of alignments (B, 100)
           :   -GAP        => 'on' or 'off'
           :   -OUT_DIR    => output directory to store blast result files
           :
 Throws    : Exception if:
           :   - Cannot obtain parameters by calling _rearrange() on the
           :     first argument, which should be a Bio::Tools::Blast.pm object ref.
           :   - No sequences are provided (objects or files).
           :   - Sequence type is incompatible with Blast program type.
           :   - Database name is not one of the valid names.
 Comments  :
  -------------------------------------------------------------
  Available programs: blastn, blastx, blastp, tblastn, tblastx
  -------------------------------------------------------------
  Available local databases are:
   LIST YOUR LOCAL DATABASES HERE.
    These are exported by this module in the @Blast_dbp_local
    and @Blast_dbn_local arrays.
  -------------------------------------------------------------
  Available substitution scoring matrices:
    (Here are the standard ones)
    BLOSUM: 100,90,85,80,75,70,65,62,60,55,50,45,40,35,30
    PAM:    500,490,480,470,460,450,440,430,420,410,400,390,380,370,360,350
            340,330,320,310,300,290,280,270,260,250,240,230,220,210,200,190,
            180,170,160,150,140,130,120,110,100,90,80,70,60,50,40,30,20,10
    OTHER: DAYHOFF, GONNET, IDENTITY, MATCH
    These are exported by this module in the @Blast_matrix_local
  -------------------------------------------------------------
  Available sequence complexity filters:
       SEG, SEG+XNU, XNU, dust, none.
See Also : _set_options(), _validate_options(), _blast_seqs(), _blast_files(), Bio::Tools::Blast.pm