ajout de commentaires

ClassSegFeat.py

@@ -3,7 +3,7 @@ class Segment:
         self.id=id
         self.features=feature # list of the features on this segment. if thre feature is on the + strand, it will be named '+feature_id', else '-feature_id'
 
-        # position on the reference genome
+        # position on the original genome
         self.chr=chr
         self.start=int(start)
         self.stop=int(stop)
@@ -15,7 +15,7 @@ class Segment:
         self.size=self.stop-self.start+1
         
     def __str__(self):
-        return f"id={self.id}, position sur nipponbare={self.chr}:{self.start}-{self.stop}, size={self.size}, features={self.features}"
+        return f"id={self.id}, position on the original genome={self.chr}:{self.start}-{self.stop}, size={self.size}, features={self.features}"
 
 
 class Feature:
@@ -23,7 +23,7 @@ class Feature:
         self.id=id
         self.type=type
         
-        # position on the reference genome
+        # position on the original genome
         self.chr=chr
         self.start=int(start)
         self.stop=int(stop)
@@ -39,7 +39,7 @@ class Feature:
         
     def __str__(self):
         if self.parent=="":
-            return f"id={self.id}, type={self.type}, segments={self.segments_list}, position sur la référence={self.chr}:{self.start}-{self.stop}, childs={self.childs}, annotation={self.annot}"
+            return f"id={self.id}, type={self.type}, segments={self.segments_list}, position on the original genome={self.chr}:{self.start}-{self.stop}, childs={self.childs}, annotation={self.annot}"
         else:
-            return f"id={self.id}, type={self.type}, segments={self.segments_list}, position sur la référence={self.chr}:{self.start}-{self.stop}, parent={self.parent}, childs={self.childs}, annotation={self.annot}"
+            return f"id={self.id}, type={self.type}, segments={self.segments_list}, position on the original genome={self.chr}:{self.start}-{self.stop}, parent={self.parent}, childs={self.childs}, annotation={self.annot}"
  
\ No newline at end of file

main.py

@@ -14,7 +14,7 @@ gff="new_graph_chr10.gff"
 
 genome = 'ac'
 
-if genome=='ac': # transfer grom graph to azucena
+if genome=='ac': # transfer from graph to azucena
     pos_seg="seg_coord/AzucenaRS1_chromosome10.bed"
     #out="azucena_chr10_all.gff"
     out="azucena_chr10.gff"
@@ -23,5 +23,6 @@ if genome=='nb': # transfer from graph to nipponbare
     out="nb_chr10_all.gff"
     pos_seg="seg_coord/IRGSP-1_0_Chr10.bed"
 
+# outputs the gff of a genome for the chr10
 fct.genome_gff(pos_seg,gff,out)