Christopher Fields > BioPerl-1.6.921 > bp_seqfeature_load.pl

Download:
BioPerl-1.6.921.tar.gz

Annotate this POD

CPAN RT

New  12
Open  4
View/Report Bugs
Source   Latest Release: BioPerl-1.6.924

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.

syntax highlighting: