syntax modifications (report file name)

ariaec/commands.py

@@ -79,7 +79,7 @@ class AriaEcCommand:
                                                  u"restraints toolbox",
                                      formatter_class=argp.ArgumentDefaultsHelpFormatter)
         parser.add_argument("-o", "--output", dest="output_directory",
-                            type=str, help="Output directory")
+                            type=str, help="Output directory", required=True)
         parser.add_argument("-c", "--conf", action=ReadableFile, dest="conf_file",
                             default=None, help="configuration file")
         parser.add_argument("--nolog", action="store_true",

ariaec/maplot.py

@@ -127,7 +127,7 @@ class AriaEcContactMap(object):
 
         for mapname, mapt, mapath in self.allresmap.keys():
 
-            prefix = "_".join((mapname, self.refname))
+            prefix = "_".join((mapname, self.refname)).replace(".", "_")
 
             if mapname == self.refname:
                 if not self.settings.contactmap.args.get("onlyreport", False):

ariaec/protmap.py

@@ -312,8 +312,8 @@ class ProteinMap(Map):
 
     def report(self, cmpmap, scoremap=None, outprefix="", outdir="", plotdir="",
                plot_ext="pdf", plotag=True):
-        reportpath = "%s/%s.report" % (outdir, outprefix)
-        logger.info("Generate report file (%s)" % reportpath)
+        reportpath = "%s/%s.mapreport" % (outdir, outprefix)
+        logger.info("Generate map report file (%s)" % reportpath)
         with open(reportpath, 'w') as reportf:
             y_true = list(self.values.astype(int).flat)
             y_pred = list(cmpmap.values.astype(int).flat)

ariaec/test/__init__.py

 """
                         ARIA EC test module
 """
+
+# TODO
+# Essayer de faire au moins un test par fonction/methode
+#
+# setup.py
+#   - run

bin/ec2aria.py

@@ -6,10 +6,7 @@
 """
 from __future__ import absolute_import, division, print_function
 
-# TODO: PLMContact object
-# TODO: PLMContactsList object
 # TODO: replace all aria_ec ref into script name
-# TODO: nc factor function
 # TODO: Utiliser scikit-bio pour traiter les sequences biologiques
 
 import logging