This is the command bp_fetchp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use bp_fetchp online using onworks.net services
