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bp_fetch.1p

Langue: en

Autres versions - même langue

Version: 2008-06-24 (ubuntu - 07/07/09)

Section: 1 (Commandes utilisateur)

NAME

bp_fetch.pl - fetches sequences from bioperl indexed databases

SYNOPSIS

   bp_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>
>> Balance du cafe en intraveineuse.
> Mais c'est une tentative d'assassinat !
Si tu mets de l'arsenic dedans, ça marche encore mieux.
-+- AGDV in GFA : "Conseil technique made in fmbl" -+-