creating new program to isolate aligned sequences

align_bam.py

+import pysam
+samfile = pysam.AlignmentFile("/home/theo/dev/git/cnvCallerGPU/3544.bam", "rb")
+
+align = pysam.AlignmentFile("align.bam", "wb", header = samfile.header)
+
+for read in samfile:
+    if read.is_mapped:
+        align.write(read)
+samfile.close()
+align.close()
+
+total_sequences_alignées = 0
+align_file = pysam.AlignmentFile("/home/theo/dev/git/cnvCallerGPU/align.bam", "rb")
+
+reference = 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 align_file:
+    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_sequences_alignées += 1
+print(f"Total de sequences alignées : {total_sequences_alignées}")    
+align_file.close()