Rename motif search max_genes argument, add test

motifsearch/search.py

@@ -105,7 +105,7 @@ def read_data(self):
             seq = regex.sub(r"\*$", "", seq)
             self.peptides.update({peptide_id: seq})
 
-    def motif(self, scope, search_text, max_genes = 500, context = 25):
+    def motif(self, scope, search_text, max_gene_details = 500, context = 25):
         """Search all peptides of the regular expression 'search_text'
 returning an array like:
     [
@@ -144,7 +144,7 @@ def add_match(peptide_id, peptide_matches, seq):
             pep_res = []
             pep_res_count = 0
             for m in patt.finditer(seq, timeout=2):
-                if len(peptide_matches) >= max_genes:
+                if len(peptide_matches) >= max_gene_details:
                     pep_matches = {
                         'peptide_id': peptide_id
                     }

motifsearch/tests.py

@@ -72,3 +72,17 @@ def test_one_gene(self):
         self.assertEqual(len(result[0]['matches']), 1)
         self.assertEqual(result[0]['matches'][0]['end'], 14)
         self.assertEqual(result[0]['matches'][0]['before'], 'MASTFSQS')
+
+    def test_max_genes(self):
+        result = self._search.motif('all', 'F', max_gene_details = 999)
+        count = 0
+        for res in result:
+            if 'matches' in res:
+                count += 1
+        self.assertEqual(count, 5)
+        result = self._search.motif('all', 'F', max_gene_details = 2)
+        count = 0
+        for res in result:
+            if 'matches' in res:
+                count += 1
+        self.assertEqual(count, 2)