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Adding mean coverage to qc.py #79

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Adding mean coverage to qc.py #79

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19 changes: 17 additions & 2 deletions bin/qc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,17 @@ def get_covered_pos(pos_depth, min_depth):

return counter

def get_mean_coverage(pos_depth):
counter = 0
sum_of_depths = 0

for con,pos,depth in pos_depth:
sum_of_depths = sum_of_depths + int(depth)
counter = counter + 1

mean_coverage =round(sum_of_depths / counter,2)
return mean_coverage

def get_N_positions(fasta):
n_pos = [i for i, letter in enumerate(fasta.seq.lower()) if letter == 'n']

Expand Down Expand Up @@ -120,9 +131,12 @@ def go(args):
depth_covered_bases = get_covered_pos(depth_pos, depth)

pct_covered_bases = depth_covered_bases / ref_length * 100

## Number of aligned reads calculaton
num_reads = get_num_reads(args.bam)

## Mean coverage calculation
mean_coverage = get_mean_coverage(depth_pos)

# Unknown base calcs
fasta = SeqIO.read(args.fasta, "fasta")
Expand All @@ -146,8 +160,9 @@ def go(args):
'pct_covered_bases' : "{:.2f}".format(pct_covered_bases),
'longest_no_N_run' : largest_N_gap,
'num_aligned_reads' : num_reads,
'fasta': args.fasta,
'fasta' : args.fasta,
'bam' : args.bam,
'mean_coverage' : mean_coverage,
'qc_pass' : qc_pass}


Expand Down