updated manual

Updated manual and some minor intro to the script. Adding the command
-db.

.gitignore

@@ -0,0 +1,2 @@
+
+FUNGuild_DB.txt

FUNGuild_v1.0.py

@@ -15,17 +15,18 @@
     You should have received a copy of the GNU General Public License
     along with this program.  If not, see <http://www.gnu.org/licenses/>.
 	
-This script assigns functional information to the OTUs in the user's OTU table. The OTU table needs to have a column named 'taxonomy', which contains information from a reference database (such as UNITE - https://unite.ut.ee/). It is required that the first line of the OTU table to be the header, without any additional comments. Some programs, such as single_rarefaction.py in Qiime will add an additional row of comments before the header, and this has to be removed before using the FunGuild script. The script will try to recognized the delimiter in the user's OTU table, but comma (.csv) or tab (.txt) delimiter formats are recommended.
+This script assigns functional information to the OTUs in the user's OTU table. The OTU table needs to have a column named 'taxonomy', which contains information from a reference database (such as UNITE - https://unite.ut.ee/). It is required that the first line of the OTU table to be the header, without any additional comments. Some programs, such as QIIME will add an additional row of comments before the header, and this has to be removed before using the FunGuild script. The script will try to recognized the delimiter in the user's OTU table, but comma (.csv) or tab (.txt) delimiter formats are recommended.
 
 The functional database is fetched from http://www.stbates.org/funguild_db.php
 
-Script usage: FunGuild.py [-h] [-otu OTU_file] [-m] [-u]
+Script usage: FunGuild.py [-h] [-otu OTU_file] [-db] [-m] [-u]
 
 optional arguments:
   -h, --help       Show this help message and exit
   -otu OTU         Path and file name of the OTU table. The script will try to
                    detect the delimiters in the file, but tab or csv are
                    preferred formats.
+  -db              Database to use ('fungi' or 'nematode') [default:fungi]
   -m, --matched    Ask the script to output an otu table containing only OTUs
   		   for which functional assignments have been made
   -u, --unmatched  Ask the script to output an otu table containing only OTUs
@@ -42,6 +43,8 @@
 
 Care should be taken in managing directories as existing files will be overwritten without notice if matching file names (e.g., user_otu_table.matched.txt) are generated by the script.
 
+By using the -db option, you will call the database for your group of organism. Currently we have 'fungi' and 'nematode' but more databases will be added in the future. The default is 'fungi'.
+
 All output tables are sorted according to the sum total number of sequences corresponding to each OTU (rank OTU abundance).
 
 ###################################################################################
@@ -51,7 +54,7 @@
 
 The algorithm used by FunGuild was first developed by Scott T. Bates in R to assign functions to any fungal taxon and to indicate a probability for the assignment.
 
-The current FunGuild script has been developed by Zewei Song in python in order to improve performance and cross-platform compatibility.
+The current FunGuild script has been developed by Zewei Song in python in order to improve functionality, performance and cross-platform compatibility.
 ###################################################################################
 
 Zewei Song