fastme: if alignment in phylip already exists do not redo it

genomeAPCAT/tree_module/fastme_func.py

@@ -31,6 +31,11 @@ def convert2phylip(infile, outfile):
     Input alignment is in fasta format. Input of fastME must be in Phylip-relaxed format.
     Convert it here.
     """
+    if os.path.isfile(outfile):
+        logger.info("Phylip alignment file already existing.")
+        logger.warning(("The Phylip alignment file {} already exists. The program "
+                        "will use it instead of re-converting {}.").format(outfile, infile))
+        return
     logger.info("Converting fasta alignment to PHYLIP-relaxed format.")
     with open(infile, 'r') as input_handle, open(outfile, 'w') as output_handle:
         alignments = AlignIO.parse(input_handle, "fasta")

genomeAPCAT/utils.py

@@ -191,8 +191,10 @@ def run_cmd(cmd, error, eof=False, **kwargs):
     if not "stderr" in kwargs:
         kwargs["stderr"] = None
     try:
-        retcode = subprocess.call(shlex.split(cmd), stdout=kwargs["stdout"],
+        call = subprocess.Popen(shlex.split(cmd), stdout=kwargs["stdout"],
                                   stderr=kwargs["stderr"])
+        call.wait()
+        retcode = call.returncode
     except OSError:
         logger.error(error + ": " + "{} does not exist".format(cmd))
         if eof:
@@ -203,7 +205,7 @@ def run_cmd(cmd, error, eof=False, **kwargs):
         logger.error(error)
         if eof:
             sys.exit(retcode)
-    return retcode
+    return call
 
 
 def plot_distr(values, limit, outfile, title, text):