Bug Fixe: remove duplicates in generated contact files

ariaec/maplot.py

@@ -3,6 +3,7 @@
 """
 from __future__ import absolute_import, division, print_function
 
+import sys
 import json
 import logging
 from .base import get_filename
@@ -73,9 +74,14 @@ class AriaEcContactMap(object):
                             outdir=self.settings.outdir)
             self.allresmap[fo.filetype] = fo.mapdict
 
+        try:
+            refmap = self.refmap["contactmap"]
+        except TypeError:
+            logger.error("First contact map should be a valid file")
+            sys.exit(1)
+
         nb_c = int(len(self.protein.aa_sequence.sequence) *
                    self.settings.setup.config.get("n_factor"))
-        refmap = self.refmap["contactmap"]
         plotparams = {k: self.settings.contactmap.config.get(k, None)
                       for k in ('size_fig', 'plot_ext', 'plot_dpi')}
 
@@ -86,7 +92,9 @@ class AriaEcContactMap(object):
 
             if mapt == self.reftype:
                 refmap.write_contacts("_".join((self.outprefix, mapt)),
-                                      outdir=outdir)
+                                      outdir=outdir,
+                                      scoremap=self.refmap.get("scoremap",
+                                                               None))
                 if self.settings.contactmap.config.get("save_fig"):
                     refmap.saveplot(outdir=outdir,
                                     outprefix="_".join((self.outprefix, mapt)),
@@ -121,6 +129,7 @@ class AriaEcContactMap(object):
             # TODO: only one function for output files
             # Write contact list in txt file
             cmpmap.write_contacts("_".join((self.outprefix, mapt)),
+                                  scoremap=scoremap,
                                   outdir=outdir)
             # Write cmp stats
             cmpmap.compare_contactmap(refmap, cmplist, prefix,

ariaec/protmap.py

@@ -216,9 +216,8 @@ class ProteinMap(Map):
     def contactset(self, human_idx=False):
         # Remove duplicate in contact_list
         if self.contact_list():
-            return sorted([(x, y) for x, y in set(sorted(x for x in
-                                                         self.contact_list(
-                                                             human_idx)))])
+            return sorted(set((tuple(sorted((x, y)))
+                               for x, y in self.contact_list(human_idx))))
         else:
             return None
 
@@ -316,7 +315,7 @@ class ProteinMap(Map):
             plt.plot(allfpr, alltpr, label='ROC curve (area = %0.2f)' % roc_auc)
             plt.plot([0, 1], [0, 1], 'k--')
             plt.xlim([0.0, 1.0])
-            plt.ylim([0.0, 1.05])
+            plt.ylim([0.0, 1.0])
             plt.xlabel('False Positive Rate')
             plt.ylabel('True Positive Rate')
             plt.title('Receiver operating characteristic %s vs. %s' % (
@@ -334,9 +333,9 @@ class ProteinMap(Map):
             plt.plot(allrec, allprec, label='Precision-Recall curve')
             plt.xlabel('Recall')
             plt.ylabel('Precision')
-            plt.ylim([0.0, 1.05])
+            plt.ylim([0.0, 1.0])
             plt.xlim([0.0, 1.0])
-            plt.title('Precision-Recall  {1} vs. {2}: AUC={0:0.2f}'.format(
+            plt.title('Precision-Recall {1} vs. {2}: AUC={0:0.2f}'.format(
                 aver_prec, map1name, map2name))
             plt.legend(loc="lower left")
             plt.savefig(plotpath)
@@ -430,7 +429,8 @@ class ProteinMap(Map):
                                             dmin)
                 print(msg, file=outfile)
 
-    def write_contacts(self, filename, outdir="", human_idx=True):
+    def write_contacts(self, filename, outdir="", human_idx=True,
+                       scoremap=None):
         filepath = "%s/%s.contact.txt" % (outdir, filename)
         logger.info("Generate contact file (%s)" % filepath)
         with open(filepath, 'w') as outfile:
@@ -439,8 +439,13 @@ class ProteinMap(Map):
             # for contact in sorted(contacts):
             for contact in self.contactset():
                 contact = sorted([contact[0] + offset, contact[1] + offset])
-                print("%d %d" % (contact[0], contact[1]), file=outfile)
-
+                if scoremap is not None:
+                    score = scoremap.iat[(int(contact[0]) - offset,
+                                          int(contact[1]) - offset)]
+                    print("%d %d %.4f" % (contact[0], contact[1], score),
+                          file=outfile)
+                else:
+                    print("%d %d" % (contact[0], contact[1]), file=outfile)
 
 class ResAtmMap(ProteinMap):
     """

ariaec/reader.py

@@ -153,12 +153,31 @@ class MapFile(RegexFile):
                 '(?P<hbscore>-?\d+\.?\d*)'),
             "score_field": "hbscore"
         },
-        "default": {
+        "default_1": {
+            "regex": re.compile(
+                '^\s*(?P<res1_nb>\d+)\s+(?P<res2_nb>\d+)\s+'
+                '(?P<resn1>\w+)\s+'
+                '(?P<resn2>\w+)\s+'
+                '(?P<score>[\w\d\.\+\-]+)'),
+            "score_field": "score"
+        },
+        "default_2": {
+            "regex": re.compile(
+                '^\s*(?P<res1_nb>\d+)\s+(?P<res2_nb>\d+)\s+'
+                '(?P<score>[\w\d\.\+\-]+)'),
+            "score_field": "score"
+        },
+        "default_3": {
             "regex": re.compile(
                 '^\s*(?P<res1_nb>\d+)\s+(?P<res2_nb>\d+)\s+'
                 '(?P<resn1>\w+)\s+'
                 '(?P<resn2>\w+)\s+'),
-            "score_field": ""
+            "score_field": None
+        },
+        "default_4": {
+            "regex": re.compile(
+                '^\s*(?P<res1_nb>\d+)\s+(?P<res2_nb>\d+)\s+'),
+            "score_field": None
         }
     }
     check_type = True
@@ -210,6 +229,11 @@ class MapFile(RegexFile):
             # Check first and second line of file
             for index, line in enumerate(infile):
                 match = self.types[self.filetype].get("regex").match(line)
+                # TODO: DRY rule !!
+                def1match = self.types["default_1"]["regex"].match(line)
+                def2match = self.types["default_2"]["regex"].match(line)
+                def3match = self.types["default_3"]["regex"].match(line)
+                def4match = self.types["default_4"]["regex"].match(line)
                 if match:
                     logger.debug("Format type correct")
                     return [
@@ -217,6 +241,34 @@ class MapFile(RegexFile):
                         self.filetype,
                         self.types[self.filetype].get("score_field")
                     ]
+                elif def1match:
+                    logger.debug("Format type correct")
+                    return [
+                        self.types["default_1"].get("regex"),
+                        self.filetype,
+                        self.types["default_1"].get("score_field")
+                    ]
+                elif def2match:
+                    logger.debug("Format type correct")
+                    return [
+                        self.types["default_2"].get("regex"),
+                        self.filetype,
+                        self.types["default_2"].get("score_field")
+                    ]
+                elif def3match:
+                    logger.debug("Format type correct")
+                    return [
+                        self.types["default_3"].get("regex"),
+                        self.filetype,
+                        self.types["default_3"].get("score_field")
+                    ]
+                elif def4match:
+                    logger.debug("Format type correct")
+                    return [
+                        self.types["default_4"].get("regex"),
+                        self.filetype,
+                        self.types["default_4"].get("score_field")
+                    ]
                 if index > 2:
                     logger.error("Error reading %s file." % self.filetype)
                     # Remove contact file

ariaec/setup.py

@@ -167,7 +167,8 @@ class AriaEcSetup:
         for maptype in self.allresmap:
             self.allresmap[maptype].get("contactmap").write_contacts(
                 "_".join((self.outprefix, maptype, "filtered")),
-                self.settings.infra.get("others"))
+                self.settings.infra.get("others"), scoremap=self.allresmap[
+                    maptype].get("scoremap"))
             if self.allresmap[maptype]["alldistmap"] is not None:
                 self.allresmap[maptype]["alldistmap"].to_csv(
                     "%s/%s.distmap.csv" % (self.settings.infra.get("others"),