bp_fetch(1p) [debian man page]

BP_FETCH(1p)						User Contributed Perl Documentation					      BP_FETCH(1p)

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 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://redmine.open-bio.org/projects/bioperl/

AUTHOR

       Ewan Birney <birney@ebi.ac.uk>

perl v5.14.2							    2012-03-02							      BP_FETCH(1p)

Check Out this Related Man Page

Bio::SeqIO::ace(3pm)					User Contributed Perl Documentation				      Bio::SeqIO::ace(3pm)

NAME

       Bio::SeqIO::ace - ace sequence input/output stream

SYNOPSIS

       Do not use this module directly.  Use it via the Bio::SeqIO class.

DESCRIPTION

       This object can transform Bio::Seq objects to and from ace file format.	It only parses a DNA or Peptide objects contained in the ace file,
       producing PrimarySeq objects from them.	All other objects in the files will be ignored.  It doesn't attempt to parse any annotation
       attatched to the containing Sequence or Protein objects, which would probably be impossible, since everyone's ACeDB schema can be
       different.

       It won't parse ace files containing Timestamps correctly either.  This can easily be added if considered necessary.

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 one
       of the Bioperl mailing lists.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHORS - James Gilbert
       Email: jgrg@sanger.ac.uk

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   next_seq
	Title	: next_seq
	Usage	: $seq = $stream->next_seq()
	Function: returns the next sequence in the stream
	Returns : Bio::Seq object
	Args	: NONE

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq(@seq)
	Function: writes the $seq object into the stream
	Returns : 1 for success and 0 for error
	Args	: Bio::Seq object(s)

perl v5.14.2							    2012-03-02						      Bio::SeqIO::ace(3pm)

Linux and UNIX Man Pages

bp_fetch(1p) [debian man page]

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