fix: Allow lower-case bases in sequence validation

AntonelliLab · Jun 24, 2020 · 1aa9065 · 1aa9065
1 parent 53798b8
commit 1aa9065
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/src/common/typecheckAlignment.js b/src/common/typecheckAlignment.js
@@ -21,10 +21,10 @@ export const getFinalDataType = (dataTypes) => {
 
 // Valid characters taken from Standard-RAxML (axml.c)
 const reInvalidBinary = /[^01-?]/g;
-const reInvalidDNA = /[^ABCDGHKMRSTUVWYNOX?-]/g;
-const reInvalidAA = /[^ARNDCQEGHILKMFPSTWYVBZX*?-]/g;
-const reInvalidGeneric = /[^0123456789ABCDEFGHIJKLMNOPQRSTU?-]/g;
-const reInvalidMixed = /[^0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ*?-]/g;
+const reInvalidDNA = /[^ABCDGHKMRSTUVWYNOX?-]/gi;
+const reInvalidAA = /[^ARNDCQEGHILKMFPSTWYVBZX*?-]/gi;
+const reInvalidGeneric = /[^0123456789ABCDEFGHIJKLMNOPQRSTU?-]/gi;
+const reInvalidMixed = /[^0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ*?-]/gi;
 
 export function findInvalidCharacter(code, dataType) {
   // Returns the index of the invalid character if found, else -1

diff --git a/static/example-files/phylip/test_lower_case_bases.txt b/static/example-files/phylip/test_lower_case_bases.txt
@@ -0,0 +1,6 @@
+      5    20
+Turkey     AAGCTNGGGC ATTTCAGGGT
+Salmo_gair aagccttggc AGTGCAGGGT
+H_Sapiens  ACCGGTTGGC CGTTCAGGGT
+Chimp      AAACCCTTGC CGTTACGCTT
+Gorilla    AAACCCTTGC CGGTACGCTT