script_fichier_BAM.py

import pysam
nb_seq=0
samfile = pysam.AlignmentFile("/home/theo/Documents/alternance/Projet Alternance/dijex8000.bam", "rb")
for read in samfile.fetch("chrY"):
    print(read)
    nb_seq+=1
print(nb_seq)
samfile.close()

#for pileupcolumn in samfile.pileup("chr1", 1):
#    print("\ncoverage at base %s = %s" % (pileupcolumn.pos, pileupcolumn.n))
 #   for pileupread in pileupcolumn.pileups:
  #      if not pileupread.is_del and not pileupread.is_refskip:
            # query position is None if is_del or is_refskip is set.
   #         print('\tbase in read %s = %s' %
                 # (pileupread.alignment.query_name, #pileupread.alignment.query_sequence[pileupread.query_position]))

#samfile.close()