Provided by: bioperl_1.7.8-1_all bug

NAME - fetches sequences from bioperl indexed databases

 -fmt GCG swiss:ROA1_HUMAN


       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, or to fetch sequences
       from the NCBI website

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


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


       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


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

       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)


       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


       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.


       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).


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       is much appreciated.
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       Ewan Birney <>