updated README section on gimme_taxa; fixed gimme_taxa header bug

README.md

@@ -196,22 +196,27 @@ file to pass in to it. It utilises the `ete3` toolkit, so refer to their site to
 if it's not already satisfied.
 
 You can query the database using a particular TaxID, or a scientific name. The primary function of the
-script is to return all the child taxa of the specified parent taxa. If specified with `-v` verbose
-flags however, the script will also print out some information about the lineages etc.
+script is to return all the child taxa of the specified parent taxa. The script has various options
+for what information is written in the output. 
 
 A basic invocation may look like:
 
 ```
-# Fetch all descendent taxa for Escherichia:
-python gimme_taxa.py -v -o ~/mytaxafile.txt -t 561
+# Fetch all descendent taxa for Escherichia (taxid 561):
+python gimme_taxa.py -o ~/mytaxafile.txt 561
 
-alternatively
+# Alternatively, just provide the taxon name
+python gimme_taxa.py -o all_descendent_taxids.txt Escherichia
 
-python gimme_taxa.py -v -o ~/mytaxafile.txt -n Escherichia
+# You can provide multiple taxids and/or names
+python gimme_taxa.py -o all_descendent_taxids.txt 561,Methanobrevibacter
 ```
 
-On first use, a small sqlite database will be created in your home directory. In future this can be
-updated by providing the `--update` flag.
+On first use, a small sqlite database will be created in your home directory
+by default (change the location with the `--database` flag). You can update this database
+by using the `--update` flag. Note that if the database is not in your home directory,
+you must specify it with `--database` or a new database will be created in your home
+directory.
 
 To see all help:
 ```

contrib/gimme_taxa.py

@@ -157,25 +157,28 @@ def main():
     # If names were provided in taxid list, convert to taxids
     args.taxid = args.taxid.replace('"', '').replace("'", '').split(',')
     args.taxid = name2taxid(args.taxid, ncbi)
-        
+
     # Output
     if args.outfile is None:
         outFH = sys.stdout
     else:
         outFH = open(args.outfile, 'w')
-
+    ## header
+    if args.taxon_info:
+        outFH.write('\t'.join(['name', 'taxid', 'rank', 'lineage']) + '\n')
+    elif not args.just_taxids:
+        outFH.write('\t'.join(['parent_taxid',
+                               'descendent_taxid',
+                               'descendent_name']) + '\n')
+    ## body
     for taxid in args.taxid:
         if args.taxon_info:
-            outFH.write('\t'.join(['name', 'taxid', 'rank', 'lineage']) + '\n')
             taxon_info(taxid, ncbi, outFH)
         else:
-            if not args.just_taxids:
-                outFH.write('\t'.join(['parent_taxid',
-                                       'descendent_taxid',
-                                       'descendent_name']) + '\n')
             desc_taxa(taxid, ncbi,  outFH, args.just_taxids)
 
     outFH.close()
 
+
 if __name__ == "__main__":
 	main()