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 varaible)
         -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>