Program to calculate depth

calc_depth.py

+import pysam
+
+def calcul_depth(bamfile, seq, window_size=100):
+
+    samfile = pysam.AlignmentFile(bamfile, "rb")
+    seq_length = samfile.lengths[samfile.references.index(seq)]
+
+    for pos_start in range(0, seq_length, window_size):
+        pos_end = min(pos_start + window_size, seq_length)
+        window_depths = []
+
+        for pileupcolumn in samfile.pileup(seq, start=pos_start, stop=pos_end):
+            window_depths.append(pileupcolumn.n)
+
+        if window_depths:
+            avg_depth = sum(window_depths) / len(window_depths)
+            print(f"Profondeur moyenne pour la fenêtre {seq}:{pos_start}-{pos_end}: {avg_depth}")
+
+    samfile.close()
+
+bamfile_path = "/home/theo/dev/git/cnvCallerGPU/align.bam"
+sequence_of_interest = "chr21"
+calcul_depth(bamfile_path, sequence_of_interest, window_size=1000)