changed default cutoff to 8 in contactdef. We want to give the highest...

changed default cutoff to 8 in contactdef. We want to give the highest precision values as in CASD...

ariaec/commands.py

@@ -184,10 +184,9 @@ class AriaEcCommand:
         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 "
-                                               "contacts")
+        parser.add_argument("--filter", dest="nofilter", action="store_true",
+                            default=False, help="Use contact list filter "
+                                                "and top n contacts selection")
         parser.add_argument("--onlyreport", dest="onlyreport",
                             action="store_true",
                             default=False, help="Generate only report file")

ariaec/conf/aria_ec.ini

@@ -6,10 +6,9 @@ scsc_min_file:
 ariaproject_template:
 
 [contactdef]
-; Contact definition section used to define contactmap from pdb file. This
-; threshold is volontary low since it define the base if other cutoff are
-; given (ca_ca, ...)
-default_cutoff:                             5.0
+; Contact definition section used to define contactmap from pdb file.
+; Decrease this threshold if using other cutoff (ca_ca, ...)
+default_cutoff:                             8.0
 ; Add contact cutoff folowwing the syntax atm1_atm2
 ;ca_ca:                                      7.0
 ;cb_cb:                                      7.0

ariaec/maplot.py

@@ -47,11 +47,9 @@ class AriaEcContactMap(object):
         # Load Sequence file
         self.protein.set_aa_sequence(self.settings.contactmap.args.get("seq", None))
         # Load secondary structure prediction file
-        ss_file = self.settings.main.config["ss_dist_file"] if \
-            self.settings.main.config["ss_dist_file"] else None
         self.protein.set_sec_struct(self.settings.contactmap.args.get("sspred",
                                                                       None),
-                                    ss_file,
+                                    ssdist_filename=self.settings.ssdist,
                                     ssidx=self.settings.contactmap.args.get(
                                         "ssidx", False))
         # ---------------------------- Processing ---------------------------- #
@@ -72,7 +70,7 @@ class AriaEcContactMap(object):
                 self.reftype = fo.filetype
                 self.refname = fo.filename if type(self.outprefix) != list \
                     else self.outprefix[idx]
-            if not self.settings.contactmap.args.get("nofilter"):
+            if self.settings.contactmap.args.get("filter"):
                 self.filter(fo.mapdict, fo.filetype, fo.contactlist,
                             self.protein, clashlist=fo.clashlist,
                             outprefix=self.outprefix[idx] if type(
@@ -158,7 +156,7 @@ class AriaEcContactMap(object):
 
             # TODO: only one function for output files
             # Write contact list in txt file
-            refmap.report(cmpmap, scoremap=scoremap, outprefix=prefix,
+            refmap.report(cmpmap, scoremap=scoremap,
                           outdir=outdir,
                           plotag=not self.settings.contactmap.args.get(
                               "onlyreport"),

ariaec/protmap.py

@@ -312,7 +312,9 @@ class ProteinMap(Map):
 
     def report(self, cmpmap, scoremap=None, outprefix="", outdir="", plotdir="",
                plot_ext="pdf", plotag=True):
-        reportpath = "%s/%s.mapreport" % (outdir, outprefix)
+        filename = ".".join((outprefix, "mapreport")) if outprefix else \
+            "mapreport"
+        reportpath = "%s/%s" % (outdir, filename)
         logger.info("Generate map report file (%s)" % reportpath)
         with open(reportpath, 'w') as reportf:
             y_true = list(self.values.astype(int).flat)