Created a program for unaligned sequences

non_align_bam.py

+import pysam
+samfile = pysam.AlignmentFile("/home/theo/dev/git/cnvCallerGPU/3544.bam", "rb")
+
+non_align = pysam.AlignmentFile("non_align.bam", "wb", header = samfile.header)
+
+for read in samfile:
+    if read.is_unmapped:
+        non_align.write(read)
+samfile.close()
+non_align.close()
+
+non_align_file = pysam.AlignmentFile("/home/theo/non_align.bam", "rb")
+
+total = 0
+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}")    
+non_align_file.close()
+