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bp_load_gff(1p) [debian man page]

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

NAME

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

SYNOPSIS

	 % bp_load_gff.pl -d testdb -u user -p pw
	    --dsn 'dbi:mysql:database=dmel_r5_1;host=myhost;port=myport'
	       dna1.fa dna2.fa features1.gff features2.gff ...

DESCRIPTION

       This script loads a Bio::DB::GFF database with the features contained in a list of GFF files and/or FASTA sequence files.  You must use the
       exact variant of GFF described in Bio::DB::GFF.	Various command-line options allow you to control which database to load and whether to
       allow an existing database to be overwritten.

       This script uses the Bio::DB::GFF interface, and so works with all database adaptors currently supported by that module (MySQL, Oracle,
       PostgreSQL soon).  However, it is slow.	For faster loading, see the MySQL-specific bp_bulk_load_gff.pl and bp_fast_load_gff.pl scripts.

   NOTES
       If the filename is given as "-" then the input is taken from standard input. Compressed files (.gz, .Z, .bz2) are automatically
       uncompressed.

       FASTA format files are distinguished from GFF files by their filename extensions.  Files ending in .fa, .fasta, .fast, .seq, .dna and their
       uppercase variants are treated as FASTA files.  Everything else is treated as a GFF file.  If you wish to load -fasta files from STDIN,
       then use the -f command-line swith with an argument of '-', as in

	   gunzip my_data.fa.gz | bp_fast_load_gff.pl -d test -f -

       On the first load of a database, you will see a number of "unknown table" errors.  This is normal.

       About maxfeature: the default value is 100,000,000 bases.  If you have features that are close to or greater that 100Mb in length, then the
       value of maxfeature should be increased to 1,000,000,000, or another power of 10.

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

	  --dsn     <dsn>	Data source (default dbi:mysql:test)
	  --adaptor <adaptor>	Schema adaptor (default dbi::mysqlopt)
	  --user    <user>	Username for mysql authentication
	  --pass    <password>	Password for mysql authentication
	  --fasta   <path>	Fasta file or directory containing fasta files for the DNA
	  --create		Force creation and initialization of database
	  --maxfeature		Set the value of the maximum feature size (default 100 Mb; must be a power of 10)
	  --group		A list of one or more tag names (comma or space separated)
				 to be used for grouping in the 9th column.
	  --upgrade		Upgrade existing database to current schema
	  --gff3_munge		Activate GFF3 name munging (see Bio::DB::GFF)
	  --quiet		No progress reports
	  --summary		Generate summary statistics for drawing coverage histograms.
				  This can be run on a previously loaded database or during
				  the load.

SEE ALSO

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

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_LOAD_GFF(1p)

Check Out this Related Man Page

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

NAME

       bp_seqfeature_load.pl - Load GFF into a SeqFeature database

DESCRIPTION

       Pass any number of GFF or fasta format files (or GFF with embedded fasta) to load the features and sequences into a SeqFeature database.
       The database (and adaptor) to use is specified on the command line. Use the --create flag to create a new SeqFeature database.

SYNOPSIS

	bp_seqfeature_load.pl [options] gff_or_fasta_file1 [gff_or_fasta_file2 [...]]

       Try 'bp_seqfeature_load.pl --help' or '--man' for more information.

OPTIONS

       -d, --dsn
	   DBI data source (default dbi:mysql:test)

       -n, --namespace
	   The table prefix to use (default undef) Allows several independent sequence feature databases to be stored in a single database

       -s, --seqfeature
	   The type of SeqFeature to create... RTSC (default Bio::DB::SeqFeature)

       -a, --adaptor
	   The storage adaptor (class) to use (default DBI::mysql)

       -v, --verbose
	   Turn on verbose progress reporting (default true) Use --noverbose to switch this off.

       -f, --fast
	   Activate fast loading. (default 0) Only available for some adaptors.

       -T, --temporary-directory
	   Specify temporary directory for fast loading (default File::Spec->tmpdir())

       -i, --ignore-seqregion
	   If true, then ignore ##sequence-region directives in the GFF3 file (default, create a feature for each region)

       -c, --create
	   Create the database and reinitialize it (default false) Note, this will erase previous database contents, if any.

       -u, --user
	   User to connect to database as

       -p, --password
	   Password to use to connect to database

       -z, --zip
	   Compress database tables to save space (default false)

       -S, --subfeatures
	   Turn on indexing of subfeatures (default true) Use --nosubfeatures to switch this off.

       --summary
	   Generate summary statistics for coverage graphs (default false) This can be run on a previously loaded database or during the load. It
	   will default to true if --create is used.

       --noalias-target
	   Don't create an Alias attribute whose value is the target_id in a Target attribute (if the feature contains a Target attribute, the
	   default is to create an Alias attribute whose value is the target_id in the Target attribute)

       Please see http://www.sequenceontology.org/gff3.shtml for information about the GFF3 format. BioPerl extends the format slightly by adding
       a ##index-subfeatures directive. Set this to a true value if you wish the database to be able to retrieve a feature's individual parts
       (such as the exons of a transcript) independently of the top level feature:

	 ##index-subfeatures 1

       It is also possible to control the indexing of subfeatures on a case-by-case basis by adding "index=1" or "index=0" to the feature's
       attribute list. This should only be used for subfeatures.

       Subfeature indexing is true by default. Set to false(0) to save lots of database space and speed performance. You may use --nosubfeatures
       to force this.

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