Updated the CHANGELOG.md and README.md

CHANGELOG.md

@@ -91,6 +91,10 @@ Removed the following entries
 9. Chichiri,"6,14,24","z4,z24",-,,H,TRUE,enterica
 10. II 4:a:z39,"1,4,12,[27]",a,z39,,B,FALSE,salamae
 
+### New fields 
+- Added `antigenic_formula` field that aggregates the O, H1 and H2 antigen values in a single location for convenience
+- Added `--list-of-serovars` option allowing user to provide a single column text file listing all serovars of interest to match against the SISTR prediction. This could be useful for cases when only a certain list of serovars could be reported
+
 # 1.1.1
 
 * Fixed issue with sorting of BLAST results (causing cgMLST types to be different between BLAST versions). Pull request #43.

README.rst

@@ -138,7 +138,7 @@ These are the external dependencies required for ``sistr_cmd``:
 - Python (>= v2.7 OR >= v3.4)
 - BLAST+ (>= v2.2.30)
 - MAFFT (>=v7.271 (2016/1/6))
-- `Mash v1.0+ <https://github.com/marbl/Mash/releases>`_ [optional]
+- `Mash v2.0+ <https://github.com/marbl/Mash/releases>`_ [optional]
 
 Python Dependencies
 -------------------
@@ -219,6 +219,11 @@ If you run ``sistr -h``, you should see the following usage info:
 	                        serovar prediction results.
 	  -t THREADS, --threads THREADS
 	                        Number of parallel threads to run sistr_cmd analysis.
+	  -l LIST_OF_SEROVARS, --list-of-serovars LIST_OF_SEROVARS
+                        	A path to a single column text file containing list of
+                        	serovar(s) to check serovar prediction against. Report
+                        	predicted serovar is Y (present) and N (absent) in the
+                        	list
 	  -v, --verbose         Logging verbosity level (-v == show warnings; -vvv ==
 	                        show debug info)
 	  -V, --version         show program's version number and exit

sistr/src/serovar_prediction/__init__.py

@@ -133,6 +133,8 @@ def __init__(self, blast_runner):
 
     def search_for_wzx(self):
         self.wzx_prediction = self.get_antigen_gene_blast_results(self.wzx_prediction, WZX_FASTA_PATH)
+        #'blast_results', 'is_missing', 'is_perfect_match', 'is_trunc', 'serogroup', 'top_result'
+        #print( self.wzx_prediction.top_result); raise Exception()
         if not self.wzx_prediction.is_missing and not self.wzx_prediction.top_result is None :
             top_result = self.wzx_prediction.top_result
             top_result_pident = top_result['pident']
@@ -379,7 +381,7 @@ def get_serovar(df, sg, h1, h2, spp):
 
         df_prediction = df[(b_spp & b_sg & b_h1 & b_h2)]
 
-        logging.debug(f"Antigen to serovar dataframe filtered {spp} {sg} {h1} {h2}:\n{df_prediction}\n")
+        logging.debug(f"Antigen to serovar dataframe filtered spp={spp} sg={sg} h1={h1} h2{h2}\n Total of {df_prediction.shape[0]} serovar hits:\n{df_prediction}\n")
         logging.debug('Rough antigenic serovar(s) prediction for subspecies %s sg=%s:h1=%s:h2=%s is %s serovar(s)', spp, sg, h1, h2, list(df_prediction['Serovar']))
         if df_prediction.shape[0] > 0:
             return '|'.join(list(df_prediction['Serovar']))