Adding some modification (reference dict)

non_align_bam.py

@@ -9,15 +9,23 @@ for read in samfile:
 samfile.close()
 non_align.close()
 
+total_sequence_non_alignées = 0
 non_align_file = pysam.AlignmentFile("/home/theo/non_align.bam", "rb")
 
-total = 0
+reference = non_align_file.references
+reference_dict = {reference: i for i, reference in enumerate(reference)}
+
+print("Index\tChromosome")
+for chromosome, index in reference_dict.items():
+    print(f"{index}\t{chromosome}")
+
 for read in non_align_file:
-    #print(read)
-    #print(f"Chromosome: {read.reference_name}")
-    #print(f"Position: {read.reference_start}")
-    #print(f"Non aligné: {read.is_unmapped}")
-    total += 1
-print(f"Total de sequences non alignées : {total}")    
+    print(read)
+    chr_name = reference[read.reference_id]
+    position = read.reference_start + 1
+    print(f"Chromosome: {chr_name}")
+    print(f"Position: {position}")
+    print(f"Non aligné: {read.is_unmapped}")
+    total_sequence_non_alignées += 1
+print(f"Total de sequences non alignées : {total_sequence_non_alignées}")    
 non_align_file.close()
-