Flush before each maplot

ariaec/commands.py

@@ -64,7 +64,13 @@ class AriaEcCommand:
 
     def _update_logger(self, log):
         if log and hasattr(self.args, "output_directory"):
-            log.set_outdir(self.args.output_directory)
+            if not self.args.nolog:
+                # Don't generate log files
+                # TODO: get handler list from json file or customlogging object
+                logger.removeHandler("info_file_handler")
+                logger.removeHandler("error_file_handler")
+                logger.removeHandler("debug_file_handler")
+                log.set_outdir(self.args.output_directory)
             log.update_msg(self.args.command)
             log.welcome()
 
@@ -76,6 +82,8 @@ class AriaEcCommand:
                             type=str, help="Output directory")
         parser.add_argument("-c", "--conf", action=ReadableFile, dest="conf_file",
                             default=None, help="configuration file")
+        parser.add_argument("--nolog", action="store_true",
+                            default=False, help="Don't generate log files")
         # Create subcommands
         self._create_subparsers(parser.add_subparsers(dest="command"))
         return parser
@@ -173,6 +181,9 @@ class AriaEcCommand:
                             choices=self.contact_types, help="Infile(s) "
                                                              "contact "
                                                              "type(s)")
+        parser.add_argument("--merge", nargs="+", dest="merge",
+                            choices=self.contact_types,
+                            help="Merge given contact types with other maps")
         parser.add_argument("--nofilter", dest="nofilter", action="store_true",
                             default=None, help="Do not use contact list "
                                                "filter and select top n "
@@ -201,7 +212,6 @@ class AriaEcCommand:
         if self.args.output_directory:
             logger.info("Updating output directory")
             settings.infra = self.args.output_directory
-        settings.make_infra()
         return settings
 
     def run(self):

ariaec/conf/aria_ec.ini

@@ -61,7 +61,7 @@ cb_upper_bound:                             7.0
 ;                 separated by "+" character [pos]. If empty, use only position
 ;                 filter (avoid short range restraints)
 n_factor:                                   1.0
-contactfilter:                              pos
+contactfilter:                              all
 conservation_treshold:                      95
 position_treshold:                          5
 nd_beta:                                    0.99

ariaec/ecsettings.py

@@ -148,9 +148,9 @@ class AriaEcSettings(Settings):
             return self._scsc_min
 
     def make_infra(self):
-        logger.info("Making infrastructure in %s" % self.outdir)
+        logger.info("Making output directories")
         for direct in self.infra:
-            logger.debug("Making %s directory" % self.infra[direct])
+            logger.debug("Create %s directory" % self.infra[direct])
             if not os.path.exists(self.infra[direct]):
                 os.makedirs(os.path.abspath(self.infra[direct]))
 

ariaec/maplot.py

@@ -33,6 +33,8 @@ class AriaEcContactMap(object):
                                                 indent=4))
         logger.debug("Args:\n" + json.dumps(self.settings.contactmap.args,
                                             indent=4))
+        if not self.settings.contactmap.args.get("onlyreport", False):
+            self.settings.make_infra()
         # ----------------------------- Input -------------------------------- #
         if self.settings.contactmap.args.get("prefix"):
             self.outprefix = "_".join((get_filename(
@@ -92,11 +94,27 @@ class AriaEcContactMap(object):
                       for k in ('size_fig', 'plot_ext', 'plot_dpi')}
         outdir = self.settings.outdir
 
-        if self.settings.contactmap.config.get("save_fig"):
+        if self.settings.contactmap.config.get("save_fig") and not \
+                self.settings.contactmap.args.get("onlyreport", False):
             refmap.saveplot(outdir=outdir,
                             outprefix="_".join((self.outprefix, "pdb")),
                             **plotparams)
 
+        if self.settings.contactmap.args.get("merge", None):
+            # Combine merge maps with other maps
+            mergelist = self.settings.contactmap.args.get("merge")
+            for mergetype in mergelist:
+                if mergetype in self.allresmap:
+                    mergemaps = self.allresmap.pop(mergetype)
+                    mergecontactmap = mergemaps.get("contactmap")
+                    for mapt in self.allresmap.keys():
+                        if mapt != self.reftype:
+                            up_map = self.allresmap[mapt]["contactmap"]
+                            up_map[:] = up_map.add(mergecontactmap)
+                            mergekey = "%s_%s" % (mapt, mergetype)
+                            self.allresmap[mergekey] = {}
+                            self.allresmap[mergekey]["contactmap"] = up_map
+
         for mapt in self.allresmap.keys():
 
             prefix = "_".join((self.outprefix, mapt, self.reftype))
@@ -139,7 +157,9 @@ class AriaEcContactMap(object):
                           outdir=outdir,
                           plotag=not self.settings.contactmap.args.get(
                               "onlyreport"),
-                          plotdir=self.settings.infra.get("graphics", outdir))
+                          plotdir=self.settings.infra.get("graphics", outdir)
+                          if not self.settings.contactmap.args.get(
+                              "onlyreport") else self.settings.outdir)
             # Contact map comparison plot
             # TODO: elementwise error with compare method
             # Write cmp stats

ariaec/protmap.py

@@ -69,11 +69,7 @@ class Map(pd.DataFrame):
         self.sym = sym
         self.desc = desc
 
-    @staticmethod
-    def plotflush():
-        plt.clf()
-        plt.cla()
-        plt.close()
+
 
     def sortedset(self, human_idx=False):
         # Remove duplicate in sort_list
@@ -190,13 +186,18 @@ class ProteinMap(Map):
     def sequence(self):
         raise NotImplementedError
 
+    def plotflush(self):
+        plt.clf()
+        plt.cla()
+        plt.close()
+        self._maplot = None
+
     @property
     def maplot(self):
         # Contact map Plot
         if not self._maplot:
             # Flush matplot
             logger.debug("Build maplot")
-            self.plotflush()
             minticks = tickmin(self, shift=1)  # Nb graduations
 
             self._maplot = sns.heatmap(self, square=True, cbar=False,
@@ -636,7 +637,7 @@ class ResAtmMap(ProteinMap):
                     "Filtering values in matrix related to %s (%s)" %
                     (str(pair), str(treshold)))
                 if pair in (("SC", "SC"), ("sc", "sc")):
-                    # Use scsc_min to apply treshold only for selected atom
+                    # Use scsc_min to apply treshold updateonly for selected atom
                     # sidechain
                     idx_list = []
                     col_list = []

ariaec/setup.py

@@ -48,6 +48,7 @@ class AriaEcSetup:
                                                 indent=4))
         logger.debug("Args:\n" + json.dumps(self.settings.setup.args,
                                             indent=4))
+        self.settings.make_infra()
         # -------------------------------------------------------------------- #
         # ----------------------------- Input -------------------------------- #
         # -------------------------------------------------------------------- #