print underlying command line always, not forcing floatoption of cli to be float, issue with mafft threads integer

Author: sinamajidian

read2tree/Aligner.py

@@ -292,9 +292,11 @@ def _align_worker(self, og_set):
             mafft_wrapper = Mafft(value.aa, datatype=DataType.PROTEIN)
             mafft_wrapper.options.options['--localpair'].set_value(True)
             mafft_wrapper.options.options['--maxiterate'].set_value(1000)
-            mafft_wrapper.options.options['--thread'].set_value(self.args.threads)
+            mafft_wrapper.options.options['--thread'].set_value(int(self.args.threads))
             logger.info("aligning OG {} with {} proteins".format(key, len(value.aa)))
             alignment = mafft_wrapper()
+            #logger.debug("MAFFT command line : {} {}".format(mafft_wrapper.cli.exe ,mafft_wrapper.command())) 
+
             codons = self._get_codon_dict_og(value)
             align = Alignment()
             align.aa = alignment

read2tree/wrappers/abstract_cli.py

@@ -212,7 +212,7 @@ def __call__(self, cmd=None, wait=False, **flags):
         if flags:
             cmd = ' '.join([cmd.strip(), _kwargs_to_args(flags, self._hyphen_policy)])
         self.cmd = '{} {}'.format(self.exe, cmd)
-        logger.debug('Running following command: {}'.format(self.cmd))
+        logger.info('Running following command: {}'.format(self.cmd))
 
         # spawn
         self.process = Popen(shlex.split(self.cmd),

read2tree/wrappers/options.py

@@ -99,7 +99,7 @@ def _type(self):
         return Real
 
     def get_value(self):
-        return float(self._value)
+        return self._value
 
 
 class StringOption(TypedValueOption):