Fixed: python 3 byte decoding error from cython

KarchinLab · Oct 4, 2016 · 85f2c16 · 85f2c16
1 parent 0e10271
commit 85f2c16
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/prob2020/console/annotate.py b/prob2020/console/annotate.py
@@ -398,7 +398,7 @@ def main(opts):
     # save indels
     if opts['maf']:
         with open(opts['output'], 'a') as handle:
-            mywriter = csv.writer(handle, delimiter='\t')
+            mywriter = csv.writer(handle, delimiter='\t', lineterminator='\n')
             for maf_lines in indel.simulate_indel_maf(indel_df, bed_dict,
                                                       opts['num_iterations'],
                                                       opts['seed']):

diff --git a/prob2020/python/permutation.py b/prob2020/python/permutation.py
@@ -613,7 +613,7 @@ def maf_permutation(context_counts,
             # append results
             maf_line = [gene_name, strand, chrom, genome_coord[k], genome_coord[k],
                         ref_nuc, mysomatic_base, base_context[k], dna_change,
-                        protein_change, var_class[k]]
+                        protein_change, var_class[k].decode()]
             maf_list.append(maf_line)
 
     return maf_list