bp_index(1p) [debian man page]

BP_INDEX(1p)						User Contributed Perl Documentation					      BP_INDEX(1p)

NAME

       bp_index.pl - indexes files for use by bp_fetch.pl

SYNOPSIS

       bp_index.pl index_name file1 file2 etc.

DESCRIPTION

       bp_index.pl builds a bioperl index for the sequence files given in the argument list, under the index name. For example

	  bp_index.pl nrdb /data/nrdb/nrdb.fasta

       would build an index called 'nrdb' as the index name for the file nrdb.fasta, and

	  bp_index.pl -fmt EMBL swiss /data/swiss/*.dat

       would build an index called swiss for all the files in /data/swiss which end in .dat which are in EMBL format.

       The indexes are built using the Bio/Index/* modules, in particular, Bio::Index::EMBL and the Bio::Index::Fasta modules. Any script which
       uses these modules can use the index. A good example script is bp_fetch which fetches sequences and pipes them to STDOUT, for example

	  bp_fetch swiss:ROA1_HUMAN

       gets the ROA1_HUMAN sequence from the swiss index and writes it as fasta format on STDOUT.

OPTIONS

	 -fmt  <format>   - Fasta (default), swiss or EMBL
	 -dir  <dir>	  - directory where the index files are found
			    (overrides BIOPERL_INDEX environment variable)

       Options for expert use

	 -type <db_type>  - DBM_file type.
			    (overrides BIOPERL_INDEX_TYPE environment variable)
	 -v		  - report every index addition (debugging)

ENVIRONMENT

       bp_index and bp_fetch coordinate where the databases lie using the enviroment variable BIOPERL_INDEX. This can be overridden using the -dir
       option. There is no default value, so you must use the -dir option or set BIOPERL_INDEX.

       The DB type is coordinated with BIOPERL_INDEX_TYPE which if it is not there, defaults to whatever the bioperl modules have installed, which
       itself defaults to SDBM_File.

USING IT YOURSELF

       bp_index.pl is a script that drives the Index modules. If you want to use this script heavily in your work, if it is Perl based, it is
       almost certainly better to look at the code in this script and copy it across (probably you will be more likely to want to use the bp_fetch
       code).

EXTENDING IT

       bp_index is just a wrapper around James Gilbert's excellent Index modules found in bioperl

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 the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

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

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ewan Birney
       Ewan Birney <birney@ebi.ac.uk>

perl v5.14.2							    2012-03-02							      BP_INDEX(1p)

Check Out this Related Man Page

Bio::Index::SwissPfam(3pm)				User Contributed Perl Documentation				Bio::Index::SwissPfam(3pm)

NAME

       Bio::Index::SwissPfam - Interface for indexing swisspfam files

SYNOPSIS

	   use Bio::Index::SwissPfam;
	   use strict;

	   my $Index_File_Name = shift;
	   my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name,
						'-write_flag' => 'WRITE');
	   $inx->make_index(@ARGV);

	   use Bio::Index::SwissPfam;
	   use strict;

	   my $Index_File_Name = shift;
	   my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name);

	   foreach my $id (@ARGV) {
	       my $seq = $inx->fetch($id); # Returns stream
		    while( <$seq> ) {
			if(/^>/) {
			      print;
				 last;
			}
		    }
	   }

DESCRIPTION

       SwissPfam is one of the flat files released with Pfam. This modules provides a way of indexing this module.

       Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing SwissPfam files.
       Only retrieves FileStreams at the moment. Once we have something better (ie, an object!), will use that. Heavily snaffled from Index::Fasta
       system of James Gilbert. Note: for best results 'use strict'.

FEED_BACK
   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://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   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 the
       web:

	 https://redmine.open-bio.org/project/bioperl

AUTHOR - Ewan Birney
APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   _index_file
	 Title	 : _index_file
	 Usage	 : $index->_index_file( $file_name, $i )
	 Function: Specialist function to index swisspfam format files.
		   Is provided with a filename and an integer
		   by make_index in its SUPER class.
	 Example :
	 Returns :
	 Args	 :

   fetch
	 Title	 : fetch
	 Usage	 : $index->fetch( $id )
	 Function: Returns a Bio::Seq object from the index
	 Example : $seq = $index->fetch( 'dJ67B12' )
	 Returns : Bio::Seq object
	 Args	 : ID

perl v5.14.2							    2012-03-02						Bio::Index::SwissPfam(3pm)

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bp_index(1p) [debian man page]

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