bp_fetch.pl - fetches sequences from bioperl indexed databases
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
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
-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)
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).
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.
[email protected] - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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
Ewan Birney <
[email protected]>