fix bug of .gz

BigDataBiology · Jun 17, 2020 · 427434c · 427434c
1 parent b3c629e
commit 427434c
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/gmgc_mapper/main.py b/gmgc_mapper/main.py
@@ -69,9 +69,13 @@ def gene_prediction(fasta_input, output, tmpdirname):
 
     if os.path.splitext(fasta_input)[1] == '.bz2':
         with bz2.BZ2File(fasta_input) as ifile:
-            open(tmpdirname + '/input.fasta', "wb+").write(output_file.read())
+            open(tmpdirname + '/input.fasta', "wb+").write(ifile.read())
         fasta_input = tmpdirname + '/input.fasta'
 
+    if os.path.splitext(fasta_input)[1] == '.gz':
+        with bz2.BZ2File(fasta_input) as ifile:
+            open(tmpdirname + '/input.fasta', "wb+").write(ifile.read())
+        fasta_input = tmpdirname + '/input.fasta'
 
     subprocess.check_call(
             ['prodigal',