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

NAME - indexes files for use by

SYNOPSIS index_name file1 file2 etc.

DESCRIPTION builds a bioperl index for the sequence files given in the
       argument	list, under the	index name. For	example nrdb /data/nrdb/nrdb.fasta

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

	 -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)

       bp_index	and bp_fetch coordinate	where the databases lie	using the
       environment 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 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).

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

   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.			- General discussion	- 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

AUTHOR - Ewan Birney
       Ewan Birney <>

perl v5.32.0			  2019-12-07			   BP_INDEX(1)


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