fix and test for close of --output file after first input file

ChangeLog

@@ -1,3 +1,8 @@
+2015-10-25  Titus Brown  <[email protected]>
+
+   * scripts/normalize-by-median.py,tests/test_normalize_by_median.py: test
+   and fix for close of --output file after first input file.
+
 2015-10-05  Michael R. Crusoe  <[email protected]>
 
    * lib/magic: add file extensions, one media type, and a better comment

scripts/normalize-by-median.py

@@ -400,7 +400,7 @@ def main():  # pylint: disable=too-many-branches,too-many-statements
                     write_record(record, outfp)
 
             log_info('output in {name}', name=describe_file_handle(outfp))
-            if not is_block(outfp):
+            if not args.single_output_file:
                 outfp.close()
 
     # finished - print out some diagnostics.

tests/test_normalize_by_median.py

@@ -847,3 +847,14 @@ def test_diginorm_basic_functionality_5():
                         'b/1', 'b/2',
                         'c/1', 'c/2',
                         'd/1', 'd/2']), seqs
+
+
+def test_normalize_by_median_outfile_closed_err():
+    infile1 = utils.get_test_data('paired-mixed.fa.pe')
+    infile2 = utils.get_test_data("test-abund-read-2.fa")
+    outfile = utils.get_temp_filename('outfile_xxx')
+    script = 'normalize-by-median.py'
+    args = ['-o', outfile, infile1, infile2]
+    (status, out, err) = utils.runscript(script, args)
+    assert status == 0, (out, err)
+    assert os.path.exists(outfile)