ENH: predict_traits passes, removed extraneous serializations

picrust/util.py

@@ -108,13 +108,8 @@ def convert_precalc_to_biom(precalc_in, ids_to_load=None,transpose=True,md_prefi
                      type='Gene table')
 
 
-def convert_biom_to_precalc(biom_in):
-    """Converts a biom file into a PICRUSt precalculated tab-delimited file """
-    if type(biom_in) in (str, unicode):
-        biom_table = parse_table(biom_in)
-    else:
-        biom_table = load_table(biom_in)
-
+def convert_biom_to_precalc(biom_table):
+    """Converts a biom table into a PICRUSt precalculated tab-delimited file """
     col_ids = biom_table.ids(axis='observation')
     row_ids = biom_table.ids()
 

scripts/predict_traits.py

@@ -376,7 +376,7 @@ def main():
         #convert to precalc (tab-delimited) format
 
         out_fh = open(opts.output_trait_table, 'w')
-        out_fh.write(convert_biom_to_precalc(biom_predictions.to_json('picrust')))
+        out_fh.write(convert_biom_to_precalc(biom_predictions))
         out_fh.close()
 
     #Write out variance information to file
@@ -404,7 +404,7 @@ def main():
             write_biom_table(biom_prediction_variances, variance_outfile)
         else:
             open(variance_outfile,'w').write(\
-                convert_biom_to_precalc(biom_prediction_variances.to_json('picrust')))
+                convert_biom_to_precalc(biom_prediction_variances))
 
 
     if confidence_intervals:
@@ -427,7 +427,7 @@ def main():
             write_biom_table(biom_prediction_upper_CI, upper_CI_outfile)
         else:
             open(upper_CI_outfile,'w').write(\
-                convert_biom_to_precalc(biom_prediction_upper_CI.to_json('picrust')))
+                convert_biom_to_precalc(biom_prediction_upper_CI))
 
         biom_prediction_lower_CI=biom_table_from_predictions({k:v['lower_CI'] for k,v in confidence_intervals.iteritems()},table_headers,\
           observation_metadata=None,\
@@ -444,7 +444,7 @@ def main():
             write_biom_table(biom_prediction_lower_CI, lower_CI_outfile)
         else:
             open(lower_CI_outfile,'w').write(\
-                convert_biom_to_precalc(biom_prediction_lower_CI.to_json('picrust')))
+                convert_biom_to_precalc(biom_prediction_lower_CI))
 
 
 if __name__ == "__main__":

tests/test_util.py

@@ -111,7 +111,7 @@ def test_convert_precalc_to_biom_value_error(self):
     def test_convert_biom_to_precalc(self):
         """ convert_biom_to_precalc as expected with valid input """
 
-        result = convert_biom_to_precalc(precalc_in_biom)
+        result = convert_biom_to_precalc(parse_biom_table(precalc_in_biom))
         self.assertEqual(result,precalc_in_tab)
 
     def test_biom_meta_to_string(self):