From 0aae0f692e786a3794b3f232be2f99ac6ef842c1 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 10 Feb 2009 16:30:17 +0000
Subject: [PATCH] writing out sequence files
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9794 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
docs/chado/overview.shtml | 18 ++++++++++++++++++
1 file changed, 18 insertions(+)
diff --git a/docs/chado/overview.shtml b/docs/chado/overview.shtml
index 4535b3891..2ee11cbb5 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>
+
--
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