allow passage of stderr handle in run_and_print

allow passage of stderr handle in run_and_print, defaulting to stdout redirection as before if not specified

test/integration/test_intrahost.py

@@ -100,7 +100,7 @@ class TestSnpEff(TestCaseWithTmp):
  def capsys(self, capsys):
  self.capsys = capsys
 
- @unittest.skipIf(True, "test is marked to be skipped")
+ #@unittest.skipIf(True, "test is marked to be skipped")
  def test_snpeff(self):
  temp_dir = tempfile.gettempdir()
  input_dir = util.file.get_test_input_path(self)

tools/snpeff.py

@@ -43,7 +43,7 @@ def __init__(self, install_methods=None, extra_genomes=None):
  def version(self):
  return "4.1"
 
- def execute(self, command, args, JVMmemory=None, stdin=None, stdout=None): # pylint: disable=W0221
+ def execute(self, command, args, JVMmemory=None, stdin=None, stdout=None, stderr=None): # pylint: disable=W0221
  if not JVMmemory:
  JVMmemory = self.jvmMemDefault
 
@@ -59,7 +59,7 @@ def execute(self, command, args, JVMmemory=None, stdin=None, stdout=None): #
  ] + args
 
  _log.debug(' '.join(tool_cmd))
- return util.misc.run_and_print(tool_cmd, stdin=stdin, buffered=True, silent=("databases" in command), check=True)
+ return util.misc.run_and_print(tool_cmd, stdin=stdin, stderr=stderr, buffered=True, silent=("databases" in command), check=True)
 
  def has_genome(self, genome):
  if not self.known_dbs:
@@ -109,7 +109,9 @@ def create_db(self, accessions, emailAddress=None, JVMmemory=None):
  self.execute('build', args, JVMmemory=JVMmemory)
 
  def available_databases(self):
- command_ps = self.execute("databases", args=[])
+ # do not capture stderr, since snpEff writes 'Picked up _JAVA_OPTIONS'
+ # which is not helpful for reading the stdout of the databases command
+ command_ps = self.execute("databases", args=[], stderr=subprocess.DEVNULL)
 
  split_points = []
  keys = ['Genome', 'Organism', 'Status', 'Bundle', 'Database']

util/misc.py

@@ -229,6 +229,9 @@ def run_and_print(args, stdout=None, stderr=None,
  This is useful for nose, which has difficulty capturing stdout of
  subprocess invocations.
  '''
+
+ stderr = stderr or subprocess.STDOUT
+
  if loglevel:
  silent = False
  if not buffered:
@@ -238,7 +241,7 @@ def run_and_print(args, stdout=None, stderr=None,
  args,
  stdin=stdin,
  stdout=subprocess.PIPE,
- stderr=subprocess.STDOUT,
+ stderr=stderr,
  env=env,
  cwd=cwd,
  timeout=timeout,
@@ -268,7 +271,7 @@ def run_and_print(args, stdout=None, stderr=None,
  raise(e)
  else:
  result = run(args, stdin=stdin, stdout=subprocess.PIPE,
- stderr=subprocess.STDOUT, env=env, cwd=cwd,
+ stderr=stderr, env=env, cwd=cwd,
  timeout=timeout, check=check)
  if not silent and not loglevel:
  print(result.stdout.decode('utf-8'))
@@ -281,7 +284,7 @@ def run_and_print(args, stdout=None, stderr=None,
  'CompletedProcess', ['args', 'returncode', 'stdout', 'stderr'])
 
  process = subprocess.Popen(args, stdin=stdin, stdout=subprocess.PIPE,
- stderr=subprocess.STDOUT, env=env,
+ stderr=stderr, env=env,
  cwd=cwd)
  output = []
  while process.poll() is None: