diff --git a/docs/chado/overview.shtml b/docs/chado/overview.shtml index 4535b3891f0fb65151836cae501333c968da0176..2ee11cbb50e20b1ea79efaa38af61df90dff78ce 100644 --- a/docs/chado/overview.shtml +++ b/docs/chado/overview.shtml @@ -13,6 +13,7 @@ <li><a href="#WRITE">Writing To The Database</a> <li><a href="#GENEBUILDER">Opening the Standalone Gene Builder</a> <li><a href="#COMMUNITY+ANNOTATION">Community Annotation</a> +<li><a href="#WRITING-SEQUENCE-FILES">Writing Out Sequence Files</a> </ul> <a NAME="CONNECT"></a><h2>Connecting to a Chado Database</h2> The following java flags are used when running Artemis when connecting to a @@ -261,3 +262,20 @@ For a read only connection -Dread_only is specified on the command line: If the corresponding feature in the database has changed by another user it will ask whether to continue with the commit process. + <a NAME="WRITING-SEQUENCE-FILES"></a><h3>Writing Out Sequence Files</h3> + Artemis can write out EMBL and GFF files from the database. An option is given to + optionally flatten the gene model to just a CDS feature. Also an option is given to ignore + any obsolete features. For EMBL it uses mappings for conversion of the keys and qualifiers. + These mappings are stored in the 'etc/key_mapping' and 'etc/qualifier_mapping' + files. + <p> + A script (etc/write_db_entry) is also provided as a means of writing out multiple + sequences from the database. The script takes the following options: + <pre> +-h show help +-f [y|n] flatten the gene model, default is y +-i [y|n] ignore obsolete features, default is y +-s space separated list of sequences to read and write out +-o [EMBL|GFF] output format, default is EMBL + </pre> +