Bio::Tools::Blast::Run::LocalBlast.pm - Bioperl module for running Blast analyses locally.
use Bio::Tools::Blast::Run::LocalBlast qw(&blast_local); &blast_local( %named_parameters);
See blast_local() for a description of available parameters.
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.
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:
that accepts a Bio::Tools::Blast.pm object + named parameters as specified by blast_local().
a list of names of files containing the raw Blast reports.
in the arrays @Blast_dbn_local and @Blast_dbp_local.
@Blast_dbn_local
@Blast_dbp_local
The generic version of this module provides some rudimentary logic, but feel free to customize as necessary.
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.
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.
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
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.
vsns-bcd-perl@lists.uni-bielefeld.de - General discussion vsns-bcd-perl-guts@lists.uni-bielefeld.de - Technically-oriented discussion http://bio.perl.org/MailList.html - About the mailing lists
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/
Steve A. Chervitz, sac@genome.stanford.edu
Bio::Tools::Blast::Run::LocalBlast.pm, 0.01
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.
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.
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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.