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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 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>

perl v5.20.2                      2015-09-15                       BP_FETCH(1)

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