bp_meta_gff(1p) [debian man page]

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

NAME

       bp_meta_gff.pl - Get/set Bio::DB::GFF meta-data

SYNOPSIS

	 # set the following meta data values
	 % bp_meta_gff.pl -d testdb tag1=value1 tag2=value2

	 # get the indicated meta data value
	 % bp_meta_gff.pl -d testdb tag1 tag2

DESCRIPTION

       This script gets or sets metadata in a Bio::DB::GFF database.  Not all adaptors support this operation!	To set a series of tags, pass a
       set of tag=value pairs to the script.  To get the contents of a series of tags, pass the bare tag names.

       The output from the get operation will be an easily parseable set of tag=value pairs, one per line.

COMMAND-LINE OPTIONS
       Command-line options can be abbreviated to single-letter options.  e.g. -d instead of --database.

	  --database <dsn>	Mysql database name (default dbi:mysql:test)
	  --adaptor <adaptor>	Mysql adaptor (default dbi::mysqlopt)
	  --user    <user>	Username for mysql authentication
	  --pass    <password>	Password for mysql authentication

SEE ALSO

       Bio::DB::GFF

AUTHOR

       Lincoln Stein, lstein@cshl.org

       Copyright (c) 2002 Cold Spring Harbor Laboratory

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.  See DISCLAIMER.txt for
       disclaimers of warranty.

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

BP_GENBANK2GFF(1p)					User Contributed Perl Documentation					BP_GENBANK2GFF(1p)

NAME

       bp_genbank2gff.pl - Load a Bio::DB::GFF database from GENBANK files.

SYNOPSIS

	 % bp_genbank2gff.pl -d genbank -f localfile.gb
	 % bp_genbank2gff.pl -d genbank --accession AP003256
	 % bp_genbank2gff.pl --accession AP003256 --stdout

DESCRIPTION

       This script loads a Bio::DB::GFF database with the features contained in a either a local genbank file or an accession that is fetched from
       genbank.  Various command-line options allow you to control which database to load and whether to allow an existing database to be
       overwritten.

       The database must already have been created and the current user must have appropriate INSERT and UPDATE privileges.  The --create option
       will initialize a new database with the appropriate schema, deleting any tables that were already there.

COMMAND-LINE OPTIONS
       Command-line options can be abbreviated to single-letter options.  e.g. -d instead of --database.

	  --create		   Force creation and initialization of database
	  --dsn       <dsn>	   Data source (default dbi:mysql:test)
	  --user      <user>	   Username for mysql authentication
	  --pass      <password>   Password for mysql authentication
	  --proxy     <proxy>	   Proxy server to use for remote access
	  --stdout		   direct output to STDOUT
	  --adaptor   <adaptor>    adaptor to use (eg dbi::mysql, dbi::pg, dbi::oracle)   --viral		   the genome you are loading is viral (changes tag
					choices)
	  --source    <source>	   source field for features ['genbank']
	   EITHER --file	   Arguments that follow are Genbank/EMBL file names
	   OR --gb_folder	   What follows is a folder full of gb files to process    OR --accession	   Arguments that follow are genbank accession numbers
					(not gi!)
	   OR --acc_file	   Accession numbers (not gi!) in a file (one per line, 				no punc.)
	   OR --acc_pipe	   Accession numbers (not gi!) from a STDIN pipe (one
					per line)

SEE ALSO

       Bio::DB::GFF, bulk_load_gff.pl, load_gff.pl

AUTHOR

       Scott Cain, cain@cshl.org

       Copyright (c) 2003 Cold Spring Harbor Laboratory

       This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.  See DISCLAIMER.txt for
       disclaimers of warranty.

perl v5.14.2							    2012-03-02							BP_GENBANK2GFF(1p)