corrections et ajouts dans les statistiques de transfert

ClassSegFeat.py

@@ -7,6 +7,10 @@ class Segment:
         self.chr=chr
         self.start=int(start)
         self.stop=int(stop)
+
+        # segments précedent et suivant.
+        # séquence.
+        # cf odgi objets
         
         self.size=self.stop-self.start+1
         
@@ -30,6 +34,8 @@ class Feature:
         self.childs=childs # liste of childs features (exons, cds, etc)
         self.parent=parent
         self.segments_list=seg # list of oriented segment on which the feature is (-s1/+s1, depending on the strand)
+
+        self.note=""
         
     def __str__(self):
         if self.parent=="":

main.py

 import Functions as fct
 
 # creates segments and features for the intersect between the graph for chr10 and the gff of IRGSP
-intersect_path='/home/nina/annotpangenome/align_genes/intersect_segments-features_chr10.bed'
+intersect_path='/home/nina/annotpangenome/align_genes/intersect_segments-genes_chr10.bed'
+#intersect_path='/home/nina/annotpangenome/align_genes/intersect_reel_genes_chr10.bed'
 fct.create_seg_feat(intersect_path)
 
 # outputs the gff of the graph for chr10
@@ -11,11 +12,14 @@ fct.graph_gff(output_file)
 
 gff="new_graph_chr10.gff"
 
-if 1==0:
+genome = 'ac'
+
+if genome=='ac': # transfer grom graph to azucena
     pos_seg="seg_coord/AzucenaRS1_chromosome10.bed"
-    out="azucena_chr10_all.gff"
+    #out="azucena_chr10_all.gff"
+    out="azucena_chr10.gff"
 
-if 1==1:
+if genome=='nb': # transfer from graph to nipponbare
     out="nb_chr10_all.gff"
     pos_seg="seg_coord/IRGSP-1_0_Chr10.bed"