group mutations follow same general mutation format

vector-engineering · Jan 18, 2022 · 3ab374d · 3ab374d
1 parent 5755610
commit 3ab374d
Show file tree

Hide file tree

Showing 2 changed files with 22 additions and 9 deletions.
diff --git a/services/server/cg_server/query/group_mutation_frequencies.py b/services/server/cg_server/query/group_mutation_frequencies.py
@@ -18,8 +18,10 @@ def query_group_mutation_frequencies(conn, req):
         table_name = "{group}_frequency_{mutation_type}_mutation".format(
             group=group, mutation_type=mutation_type
         )
-        mutation_table_name = "{mutation_type}_mutation".format(mutation_type=mutation_type)
-        mutation_cols = ["pos", "ref", "alt", "mutation_name"]
+        mutation_table_name = "{mutation_type}_mutation".format(
+            mutation_type=mutation_type
+        )
+        mutation_cols = ["pos", "ref", "alt", "mutation_name", "mutation_str"]
         if mutation_type == "gene_aa":
             mutation_cols = ["gene",] + mutation_cols
         elif mutation_type == "protein_aa":
@@ -55,7 +57,7 @@ def query_group_mutation_frequencies(conn, req):
 
         res = pd.DataFrame.from_records(
             cur.fetchall(),
-            columns=["name", "count", "fraction", "mutation_id",] + mutation_cols,
+            columns=["name", "count", "fraction", "mutation_id"] + mutation_cols,
         )
 
     # print(res)

diff --git a/src/components/GroupReport/MutationList.js b/src/components/GroupReport/MutationList.js
@@ -6,8 +6,13 @@ import { format } from 'd3-format';
 
 import { config } from '../../config';
 import { getAllGenes, getAllProteins } from '../../utils/gene_protein';
+import { formatMutation } from '../../utils/mutationUtils';
 import { reds, mutationColorArray } from '../../constants/colors';
-import { ASYNC_STATES, PLOT_DOWNLOAD_OPTIONS } from '../../constants/defs.json';
+import {
+  ASYNC_STATES,
+  PLOT_DOWNLOAD_OPTIONS,
+  DNA_OR_AA,
+} from '../../constants/defs.json';
 
 import GroupSearch from './GroupSearch';
 import EmptyPlot from '../Common/EmptyPlot';
@@ -261,17 +266,16 @@ const MutationListContent = observer(() => {
       // Unique mutations
       .filter(
         (v, i, a) =>
-          a.findIndex(
-            (element) => element.mutation_name === v.mutation_name
-          ) === i
+          a.findIndex((element) => element.mutation_str === v.mutation_str) ===
+          i
       )
       .map((featureMutation) => {
         // Find fractional frequencies for each group
         const freqs = [];
         groupDataStore.selectedGroups.forEach((group) => {
           const matchingMutation = groupFeatureMutations.find(
             (mut) =>
-              mut.mutation_name === featureMutation.mutation_name &&
+              mut.mutation_str === featureMutation.mutation_str &&
               mut.name === group
           );
           // 0 if the mutation record isn't found
@@ -281,7 +285,13 @@ const MutationListContent = observer(() => {
         });
 
         return {
-          mutation_name: featureMutation.mutation_name,
+          // mutation_name: featureMutation.mutation_name,
+          mutation_name: formatMutation(
+            featureMutation.mutation_str,
+            groupDataStore.groupMutationType === 'dna'
+              ? DNA_OR_AA.DNA
+              : DNA_OR_AA.AA
+          ),
           pos: featureMutation.pos,
           ref: featureMutation.ref,
           alt: featureMutation.alt,
@@ -342,6 +352,7 @@ const MutationListContent = observer(() => {
         groupDataStore.groupMutationType === 'dna'
           ? mut.mutation_name
           : mut.mutation_name.split(':')[1];
+
       rowItems.push(
         <MutationListRow
           key={`group-mut-${feature.name}-${mut.mutation_name}`}