Merge pull request #134 from labgem/bugfix-sept-23

Bugfix sept 23

VERSION

@@ -1 +1 @@
-1.2.193
+1.2.193

ppanggolin/figures/draw_spot.py

@@ -647,7 +647,10 @@ def draw_spots(pangenome: Pangenome, output: Path, spot_list: str, disable_bar:
                          need_rgp=True, need_spots=True, need_modules=need_mod, disable_bar=disable_bar)
 
     if spot_list == 'all' or any(x == 'all' for x in spot_list):
-        logging.getLogger("PPanGGOLiN").debug("all is found in spot list, all spot are drawn.")
+        logging.getLogger("PPanGGOLiN").debug(f"'all' value is found in spot list, all spots are drawn.")
+        selected_spots = list(pangenome.spots)
+    elif spot_list == "synteny" or any(x == 'synteny' for x in spot_list):
+        logging.getLogger().debug(f"'synteny' value is found in spot list, all spots with more than 1 conserved synteny are drawn.")
         selected_spots = [s for s in pangenome.spots if len(s.get_uniq_ordered_set()) > 1]
     else:
         curated_spot_list = {'spot_' + str(s) if not s.startswith("spot_") else str(s) for s in spot_list}

ppanggolin/figures/drawing.py

@@ -91,7 +91,7 @@ def parser_draw(parser: argparse.ArgumentParser):
     optional.add_argument("--draw_spots", required=False, default=False, action="store_true",
                           help="draw plots for spots of the pangenome")
     optional.add_argument("--spots", required=False, default='all', nargs='+',
-                          help="a comma-separated list of spots to draw (or 'all' to draw all spots).")
+                          help="a comma-separated list of spots to draw (or 'all' to draw all spots, or 'synteny' to draw spots with different RGP syntenies).")
 
 
 if __name__ == '__main__':

ppanggolin/region.py

@@ -51,6 +51,7 @@ def __init__(self, name: str):
         self.starter = None
         self.stopper = None
         self.ID = Region.id_counter
+        self.spot = None
         Region.id_counter += 1
 
     def __str__(self):
@@ -133,6 +134,18 @@ def __getitem__(self, position: int) -> Gene:
         except KeyError:
             raise KeyError(f"There is no gene at position {position} in RGP {self.name}")
 
+    def add_spot(self, spot: Spot):
+        """Sets the spot of the RGP
+        
+        :param spot: spot to which the RGP is added
+
+        :raise TypeError: if the given spot is not a Spot.
+        """
+        if isinstance(spot, Spot):
+            self.spot = spot#only 1 spot possible
+        else:
+            raise TypeError(f"Unexpected class / type for {type(spot)} when adding it to a RGP")
+
     def __delitem__(self, position):
         """Remove the gene at the given position