From 77c094d2af404de86d6d38e5ba1187900e6414cb Mon Sep 17 00:00:00 2001
From: Anton Nekrutenko <anton@bx.psu.edu>
Date: Wed, 6 Feb 2008 18:59:00 +0000
Subject: [PATCH] readme.txt for taxonomy scripts

---
 scripts/taxonomy/readme.txt | 49 +++++++++++++++++++++++++++++++++++++
 scripts/taxonomy/tax.py     |  2 +-
 2 files changed, 50 insertions(+), 1 deletion(-)
 create mode 100644 scripts/taxonomy/readme.txt

diff --git a/scripts/taxonomy/readme.txt b/scripts/taxonomy/readme.txt
new file mode 100644
index 00000000000..6ce0cc0ce5e
--- /dev/null
+++ b/scripts/taxonomy/readme.txt
@@ -0,0 +1,49 @@
+How to prepare NCBI taxonomy for Galaxy Metagenomic Toolkit
+-----------------------------------------------------------
+
+1. run runTest.sh
+   If this script produces NO messages -> everything is OK
+   
+2. run processRaxonomy.sh
+   This script does several things:
+   - downloads taxonomy dump tarball from NCBI ftp site
+   - downloads very large gi2taxId files for nucleotide and protein entries of GenBank
+   - runs a series of 3 python scripts on these files
+   - creates a sqlite database called taxonomy.db (you can use sqlite to explore this database)
+   - this database is used by /tools/metag/tax.py tool to convert gi's into full taxonomic representation
+   
+3. move taxonomy.db into /static/taxonomy/
+
+Taxonomy ranks
+--------------
+
+These scripts consider the following taxonomic ranks:
+
+ 1      root
+ 2      superkingdom
+ 3      kingdom
+ 4      subkingdom
+ 5      superphylum
+ 6      phylum
+ 7      subphylum
+ 8      superclass
+ 9      class
+10      subclass
+11      superorder
+12      order
+13      suborder
+14      superfamily
+15      family
+16      subfamily
+17      tribe
+18      subtribe
+19      genus
+20      subgenus
+21      species
+22      subspecies
+
+Problems?
+---------
+   E-mail to anton@bx.psu.edu
+   
+
diff --git a/scripts/taxonomy/tax.py b/scripts/taxonomy/tax.py
index 133b44216a8..fb6213916fd 100644
--- a/scripts/taxonomy/tax.py
+++ b/scripts/taxonomy/tax.py
@@ -9,7 +9,7 @@ usage: %prog taxonomy_db gi_list_file out_file
     gi_list_file - user's input containing gi's in the column specified by option -c
 
     taxonomy_db - database containing collapsed NCBI taxonomy generated by prepareTaxonomy.sh script 
-    distributed with Galaxy. See prepareTaxonomy.readme for information on how to generate
+    distributed with Galaxy. See readme.txt for information on how to generate
     necessary files
     
 """