Merge pull request #9433 from mvdbeek/fix_twobitfile_reading

[20.01] Fix TwoBitFile handle not opened in binary mode

lib/galaxy/visualization/genomes.py

@@ -392,7 +392,7 @@ class Genomes(object):
 
         # Read and return reference data.
         try:
-            twobit = TwoBitFile(open(twobit_file_name))
+            twobit = TwoBitFile(open(twobit_file_name, 'rb'))
             if chrom in twobit:
                 seq_data = twobit[chrom].get(int(low), int(high))
                 return GenomeRegion(chrom=chrom, start=low, end=high, sequence=seq_data)

tools/extract/extract_genomic_dna.py

@@ -222,7 +222,7 @@ def __main__():
                 continue
         elif seq_path and os.path.isfile(seq_path):
             if not(twobitfile):
-                twobitfile = bx.seq.twobit.TwoBitFile(open(seq_path))
+                twobitfile = bx.seq.twobit.TwoBitFile(open(seq_path, 'rb'))
             try:
                 if options.gff and interpret_features:
                     # Create sequence from intervals within a feature.