print the params into header (from dvklopfenstein)

goatools/go_enrichment.py

@@ -99,9 +99,8 @@ def run_study(self, study):
 
         pop_n, study_n = len(self.pop), len(study)
 
-        #Uncomment these to cause tests/test_enrichment_fdr.py to pass:
-        #study_count = 0
-        #pop_count   = 0
+        # Init study_count and pop_count to handle empty sets
+        study_count = pop_count = 0
         for term, study_count in list(term_study.items()):
             pop_count = self.term_pop[term]
             p = fisher.pvalue_population(study_count, study_n,
@@ -160,6 +159,9 @@ def update_results(self, method, corrected_pvals):
             rec.__setattr__("p_"+method, val)
 
     def print_summary(self, min_ratio=None, indent=False, pval=0.05):
+        # Header contains parameters
+        print("# min_ratio={0} pval={1}".format(min_ratio, pval))
+
         # field names for output
         print("\t".join(GOEnrichmentRecord()._fields))
 

goatools/version.py

@@ -1 +1 @@
-__version__ = "0.5.3"
+__version__ = "0.5.4"

scripts/find_enrichment.py

@@ -129,5 +129,3 @@ def check_bad_args(args):
     g = GOEnrichmentStudy(pop, assoc, obo_dag, alpha=opts.alpha,
                           study=study, methods=methods)
     g.print_summary(min_ratio=min_ratio, indent=opts.indent, pval=opts.pval)
-    print('pval={}'.format(opts.pval))
-    print('min_ratio={}'.format(min_ratio))