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::SeqIO::MultiFile(3pm)				User Contributed Perl Documentation				Bio::SeqIO::MultiFile(3pm)

NAME

       Bio::SeqIO::MultiFile - Treating a set of files as a single input stream

SYNOPSIS

	  $seqin = Bio::SeqIO::MultiFile( '-format' => 'Fasta',
					  '-files'  => ['file1','file2'] );
	  while((my $seq = $seqin->next_seq)) {
	      # do something with $seq
	  }

DESCRIPTION

       Bio::SeqIO::MultiFile provides a simple way of bundling a whole set of identically formatted sequence input files as a single stream.

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://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/projects/bioperl/

AUTHOR - Ewan Birney
       Email birney@ebi.ac.uk

APPENDIX

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

   next_seq
	Title	: next_seq
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   next_primary_seq
	Title	: next_primary_seq
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   _load_file
	Title	: _load_file
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   _set_file
	Title	: _set_file
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   _current_seqio
	Title	: _current_seqio
	Usage	: $obj->_current_seqio($newval)
	Function:
	Example :
	Returns : value of _current_seqio
	Args	: newvalue (optional)

   _format
	Title	: _format
	Usage	: $obj->_format($newval)
	Function:
	Example :
	Returns : value of _format
	Args	: newvalue (optional)

perl v5.14.2							    2012-03-02						Bio::SeqIO::MultiFile(3pm)

Linux and UNIX Man Pages

bp_index(1p) [debian man page]

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