Allow rna parsing to accept U and T as valid input characters

uw-ipd · Sep 19, 2022 · 0f69706 · 0f69706
1 parent 776c556
commit 0f69706
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/network/parsers.py b/network/parsers.py
@@ -111,6 +111,11 @@ def parse_fasta(filename,  maxseq=10000, rna_alphabet=False, dna_alphabet=False)
     for i in range(alphabet.shape[0]):
         msa[msa == alphabet[i]] = i
 
+    # also accept 'U' in rna_alphabet
+    if rna_alphabet:
+        msa[msa == "U"] = 30
+
+
     #print ((msa>40).nonzero()) 
     #print (msa_orig[6788])