def get_counts(alignment: AlignmentFile, chromosome: str, position: int, minimum_base_quality: int) -> Dict[str, int]:
coverage = alignment.count_coverage(contig=chromosome, start=position, stop=position + 1, quality_threshold=minimum_base_quality)
return {'A': coverage[0][0], 'C': coverage[1][0], 'G': coverage[2][0], 'T': coverage[3][0]}
def main(argv):
#parse reference file..?
#parse samtools header
bam = AlignmentFile(sys.argv[1])
observed = []
for read in bam.fetch():
if read.reference_name not in observed:
observed.append(read.reference_name)
ref_seqs = {}
for seq in SeqIO.parse(sys.argv[2], 'fasta'):
if seq.id in observed:
ref_seqs[seq.id] = str(seq.seq)
#count coverage
print(
"Subject\tReadcount\tCorrect_bases\tIncorrect_bases\tTotal_bases\tSubjlen\tCoverage\tPercent_ID"
)
for o in observed:
contig_counts = bam.count(o, start=0, end=len(ref_seqs[o]))
counts = bam.count_coverage(o, start=0, end=len(ref_seqs[o]))
pos_ids = []
trues = 0
falses = 0
total = 0
for ref_pos in range(0, len(ref_seqs[o])):
total += sum(counts[nt][ref_pos] for nt in range(4))
if total == 0:
continue
for ref_pos in range(0, len(ref_seqs[o])):
ref_allele = ref_seqs[o][ref_pos]
depth = sum(counts[nt][ref_pos] for nt in range(4))
count_a = counts[0][ref_pos]
count_c = counts[1][ref_pos]
count_g = counts[2][ref_pos]
count_t = counts[3][ref_pos]
values = [
o, ref_pos + 1, ref_allele, depth, count_a, count_c, count_g,
count_t
]
#if o == "protist-Blastocystis_sp_subtype_2-1079827at2759-S1":
#print(depth)
# print(ref_allele)
#print(count_a)
#print(count_c)
#print(count_g)
#print(count_t)
if depth > 0:
#now we calculate the percentage
not_n = True
if ref_allele == "A":
true = count_a
false = count_c + count_g + count_t
elif ref_allele == "C":
true = count_c
false = count_a + count_g + count_t
elif ref_allele == "G":
true = count_g
false = count_a + count_c + count_t
elif ref_allele == "T":
true = count_t
false = count_a + count_c + count_g
else:
#it's an n, skip it
not_n = False
#maybe just have it as an absolute. if there's one mismatch it's all wrong.
if not_n:
if false > 0:
falses += 1
else:
trues += 1
#trues += true
#falses += false
#ratio = true /(true + false)
#need the trues and positives for each ref_pos
#print('\t'.join(str(val) for val in values) + '\t' + str(ratio))
#pid = round(sum(pos_ids) / len(pos_ids) * 100, 2)
#print(o + '\t' + str(contig_counts) + '\t' + str(pid))
seqlen = len(ref_seqs[o])
# print(seqlen)
# print(trues)
# print(falses)
# print(o)
coverage = round(((trues + falses) / seqlen) * 100, 2)
if trues == 0 and falses == 0:
pid = 0
else:
pid = round((trues / (trues + falses)) * 100, 2)
print(o + '\t' + str(contig_counts) + '\t' + str(trues) + '\t' +
str(falses) + '\t' + str(trues + falses) + '\t' + str(seqlen) +
'\t' + str(coverage) + '\t' + str(pid))
