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Update normalize.py #157

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6 changes: 3 additions & 3 deletions maxatac/analyses/normalize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ def run_normalization(args):
3) Find the genomic min and max values by looping through each chromosome
5) Loop through each chromosome and minmax normalize the values based on the genomic values.

:param args: signal, output_dir, chromosome_sizes, chromosomes, max_percentile, method, blacklist
:param args: signal, output_dir, chromosome_sizes, chromosomes, max_percentile, method, blacklist, max_zooms

:return: A minmax normalized bigwig file
"""
Expand Down Expand Up @@ -83,7 +83,7 @@ def run_normalization(args):
with pyBigWig.open(args.signal) as input_bw, pyBigWig.open(output_filename, "w") as output_bw:
header = [(x, chromosome_length_dictionary[x]) for x in sorted(args.chromosomes)]

output_bw.addHeader(header)
output_bw.addHeader(header, maxZooms = args.max_zooms)

# For every chromosome in header, perform normalization
for chrom_name, chrom_length in header:
Expand Down Expand Up @@ -115,7 +115,7 @@ def run_normalization(args):
ends=chrom_length,
span=1,
step=1,
values=normalized_signal.tolist()
values=normalized_signal.astype(np.float16).tolist()
)

# Measure time of averaging
Expand Down