5.4. Coverage module example

from sequana import SequanaCoverage, sequana_data

bedfile = sequana_data("JB409847.bed")

Reading input BED file

gc = SequanaCoverage(bedfile)
0it [00:00, ?it/s]
1it [00:00, 122.55it/s]

Select a chromosome (first and only one in that example)

chrom = gc[0]
print(chrom)
Chromosome length:      19795
Sequencing depth (DOC):                    931.31
Sequencing depth (median):                 988.00
Breadth of coverage (BOC) (percent):        96.60
Coverage standard deviation:        237.15
Coverage coefficient variation:       0.25

Compute running median and zscore telling the algorithm that the chromosome is circular.

chrom.running_median(n=5001, circular=True)
chrom.compute_zscore()
print(chrom.get_centralness())
0.8684516291992928

Plotting

chrom.plot_coverage()
plot coverage

Total running time of the script: (0 minutes 0.747 seconds)

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