Commit 097eb6a5 authored by Theo Serralta's avatar Theo Serralta

Adding test file

parent a9713966
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()
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