bp_seqfeature_load.pl man page on DragonFly

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BP_SEQFEATURE_LOAD(1) User Contributed Perl DocumentationBP_SEQFEATURE_LOAD(1)

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.

       -N, --nosummary
	   Do not generate summary statistics to save some space and load time
	   (default if --create is not specified, use this option to
	   explicitly turn off summary statistics when --create is specified)

       --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 v5.20.2			  2015-09-15		 BP_SEQFEATURE_LOAD(1)
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