mpl.close()
has_mpl = True
except:
has_mpl = False
from pysam import Samfile
if __name__ == "__main__":
window_size = int(10e3)
mel = Samfile('analysis/on_mel/mel_gdna_bowtie2_dedup.bam')
sim = Samfile('analysis/on_mel/sim_gdna_bowtie2_dedup.bam')
posns = []
mel_covs = []
sim_covs = []
prog = 0
pbar = ProgressBar(max_value=sum(mel.lengths) + 1)
for r, l in zip(mel.references, mel.lengths):
for start in range(0, l, window_size):
posns.append('{}_{}'.format(r, start))
mel_covs.append(sum(sum(i) for i in
mel.count_coverage(r, start, start+window_size)))
sim_covs.append(sum(sum(i) for i in
sim.count_coverage(r, start, start+window_size)))
prog += l
pbar.update(prog)
pbar.finish()
(pd.DataFrame(index=posns, data={'mel':mel_covs, 'sim':sim_covs})
.to_csv('analysis/on_mel/melsim_cov.tsv', sep='\t')
)
