NAME

get_ensembl_annotation.pl

A script to retrieve Ensembl annotation and write it out as GFF3.

SYNOPSIS

get_ensembl_annotation.pl [--options...] --species <text>

  Options:
  --species <text>
  --out <filename>
  --(no)chromo
  --(no)protein
  --(no)rna
  --(no)miscrna
  --(no)snrna
  --(no)snorna
  --(no)mirna
  --(no)rrna
  --(no)trna
  --(no)cds
  --(no)utr
  --codon
  --ucsc
  --group <text>
  --host <host.address>
  --port <integer>
  --user <text>
  --pass <text>
  --printdb
  --version
  --help

OPTIONS

The command line flags and descriptions:

--species <text>

Enter the species name for the database to connect to. Common aliases, e.g. human, may be acceptable. This is typically provided in the format as "genus_species", e.g. "homo_sapiens". Check the EnsEMBL website for the species databases available, or print the list using the --printdb option below.

--out <filename>

Specify the output filename. By default, it uses the species name. An extension will be added if necessary.

--(no)chromo

Boolean flag to indicate whether to write (or not) features for the toplevel chromosomes/scaffolds/contigs/sequences in the database. The default is true.

--no(protein)

Boolean flag to indicate whether or not to collect protein-coding genes from the database. The default is true.

--(no)rna

Boolean flag to indicate whether or not to collect all non-coding RNA genes, including misc_RNA, snRNA, snoRNA, rRNA, tRNA, miRNA, and piRNA, from the database. This option may be superseded by setting the individual RNA options. For example, setting both --rna and --notrna will collect all RNA types except tRNAs. The default is true.

--(no)miscrna

Boolean flag to indicate whether or not to collect miscellenaeous noncoding RNA genes. The default is true.

--(no)snrna

Boolean flag to indicate whether or not to collect small nuclear RNA (snRNA) genes. The default is true.

--(no)snorna

Boolean flag to indicate whether or not to collect small nucleolar RNA (snoRNA) genes. The default is true.

--(no)mirna

Boolean flag to indicate whether or not to collect micro RNA (miRNA) genes. The default is true.

--(no)rrna

Boolean flag to indicate whether or not to collect ribosomal RNA (rRNA) genes. The default is true.

--(no)trna

Boolean flag to indicate whether or not to collect transfer RNA (tRNA) genes. The default is true.

--(no)cds

Boolean flag to indicate whether or not to include CDS information for mRNA transcripts and genes. Default is true.

--(no)utr

Boolean flag to indicate whether or not to include UTR features for mRNA transcripts and genes. Default is true.

--codon

Boolean flag to indicate whether or not to include start and stop codons for mRNA transcripts and genes. Default is false.

--ucsc

Boolean flag to prefix chromosome names with 'chr' in the style of UCSC genome annotation. Only coordinate systems of type 'chromosome' are changed, not scaffolds, contigs, etc. Default is false.

--group <text>

Specify the name of the database group with which to connect. The default value is 'core'. See EnsEMBL documentation for more information.

--host <host.address>

Specify the Internet address of the EnsEMBL public MySQL database host. The default value is 'ensembldb.ensembl.org'.

--port <integer>

Specify the IP port address for the MySQL server. Default is 5306.

--user <text>

Specify the user name with which to connect to the EnsEMBL public database. The default value is 'anonymous'.

--pass <text>

Specify the password to use when connecting to the database. The default value is none.

--printdb

Print all of the available database names, species, and groups from the connected EnsEMBL database. The program will exit after printing the list.

--version

Print the version number.

--help

Display this POD documentation.

DESCRIPTION

This program will connect to the public EnsEMBL MySQL database and retrieve the latest genome annotation for a given species. It will generate a GFF3 annotation file suitable for loading into a Bio::DB database or genome browser. The GFF3 features generated are multi-level nested gene->mRNA->CDS features. It will optionally generate features for the top-level sequences (chromosomes, contigs, scaffolds, etc.) and non-coding RNA genes (snRNA, tRNA, rRNA, etc.).

Note that EnsEMBL releases new Perl API modules with each database release. If you do not see the latest genome version (compared to what is available on the web), you should update your EnsEMBL Perl modules. The API version should be printed at the beginning of execution.

REQUIREMENTS

This program requires EnsEMBL's Perl API modules to connect to their public MySQL servers. It is not available through CPAN, unfortunately, but you can find installation instructions at http://www.ensembl.org/info/docs/api/api_installation.html.

DATABASE ACCESS

If you having difficulties connecting, check the server and port numbers at http://www.ensembl.org/info/data/mysql.html.

To connect to the Ensembl Genomes public mysql server rather than the default, please specify the host as "mysql.ebi.ac.uk" and port 4157. See http://www.ensemblgenomes.org/info/data_access for up to date information.

AUTHOR

 Timothy J. Parnell, PhD
 Howard Hughes Medical Institute
 Dept of Oncological Sciences
 Huntsman Cancer Institute
 University of Utah
 Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0.