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BP_FETCH(1)	      User Contributed Perl Documentation	   BP_FETCH(1)

NAME
       bp_fetch.pl - fetches sequences from bioperl indexed databases

SYNOPSIS
	 bp_fetch.pl swiss:ROA1_HUMAN

	 bp_fetch.pl net::genbank:JX295726

	 bp_fetch.pl net::genpept:ROA1_HUMAN

	 bp_fetch.pl ace::myserver.somewhere.edu,21000:X56676

	 bp_fetch.pl -fmt GCG swiss:ROA1_HUMAN

DESCRIPTION
       Fetches sequences using the DB access systems in	Bioperl. The most
       common use of this is to	bp_fetch sequences from	bioperl	indices	built
       using bpindex.pl, or to fetch sequences from the	NCBI website

       The format for retrieving sequences is delibrately like the GCG/EMBOSS
       format like the following:

	 db:name

       with the	potential of putting in	a 'meta' database type,	being

	 meta::db:name

       The meta	information can	be one of three	types

	 local - local indexed flat file database
	 net   - networked http: based database
	 ace   - ACeDB database

       This information	defaults to 'local' for	database names with no meta db
       information

OPTIONS
	 -fmt  <format>	- Output format
			  Fasta	(default), EMBL, Raw, swiss or GCG
	 -acc		- string is an accession number, not an
			  id.

       options only for	expert use

	 -dir  <dir>	- directory to find the	index files
			 (overrides BIOPERL_INDEX environment variable)
	 -type <type>	- type of DBM file to open
			 (overrides BIOPERL_INDEX_TYPE environment variable)

ENVIRONMENT
       bp_index	and bp_fetch coordinate	where the databases lie	using the
       environment variable BIOPERL_INDEX. This	can be overridden using	the
       -dir option. The	index type (SDBM or DB_File or another index file) is
       controlled by the BIOPERL_INDEX_TYPE variable. This defaults to
       SDBM_File

USING IT YOURSELF
       bp_fetch	is a wrapper around the	bioperl	modules	which support the
       Bio::DB::BioSeqI	abstract interface. These include:

	 Author		 Code

	 James Gilbert - Fasta indexer,	Abstract indexer
	 Aaron Mackay  - GenBank and GenPept DB	access
	 Ewan Birney   - EMBL .dat indexer
	 Many people   - SeqIO code

       These modules can be used directly, which is far	better than using this
       script as a system call or a pipe to read from. Read the	source code
       for bp_fetch to see how it is used.

EXTENDING IT
       bp_fetch	uses a number of different modules to provide access to
       databases. Any module which subscribes to the Bio::DB::BioSeqI
       interface can be	used here. For flat file indexers, this	is best	done
       by extending Bio::Index::Abstract, as is	done in	Bio::Index::EMBL and
       Bio::Index::Fasta. For access to	other databases	you will need to roll
       your own	interface.

       For new output formats, you need	to add a new SeqIO module. The easiest
       thing is	to look	at Bio::SeqIO::Fasta and figure	out how	to hack	it for
       your own	format (call it	something different obviously).

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://github.com/bioperl/bioperl-live/issues

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

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

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | ENVIRONMENT | USING IT YOURSELF | EXTENDING IT | FEEDBACK | AUTHOR

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