use raw name when no binomial nomenclature is found

wdingx · Mar 16, 2018 · 5cbd58d · 5cbd58d
1 parent f634deb
commit 5cbd58d
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/scripts/sf_extract_metadata.py b/scripts/sf_extract_metadata.py
@@ -12,8 +12,10 @@ def organism_format(raw_data):
         """"""
         #Pseudomonas putida ND6
         #[Pseudomonas syringae] pv. tomato str. DC3000
-        new_tag=raw_data.replace('[','').replace(']','').split(' ')[:2]
-        new_tag=new_tag[0][:1]+'.'+new_tag[1]
+        new_tag=raw_data
+        if ' ' in raw_data: #Binomial nomenclature
+            new_tag=raw_data.replace('[','').replace(']','').split(' ')[:2]
+            new_tag=new_tag[0][:1]+'.'+new_tag[1]
         return new_tag
     from Bio import SeqIO
     with open('%s%s'%(path,'metainfo.tsv'), 'wb') as writeseq: