BP_FETCH(1) User Contributed Perl Documentation BP_FETCH(1)NAMEbp_fetch.pl - fetches sequences from bioperl indexed databases
SYNOPSISbp_fetch.pl swiss:ROA1_HUMAN
bp_fetch.pl net::genbank:X47072
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 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
enviroment 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:
http://bugzilla.open-bio.org/
AUTHOR
Ewan Birney <birney@ebi.ac.uk>
perl v5.14.1 2011-07-22 BP_FETCH(1)
