def test_window():
#bam_fn = os.path.join(os.path.dirname(__file__), '../timing/window_example.bed')
bam_fn = os.path.join(os.path.dirname(__file__), '../timing/example.bam')
iterable = genomicfeatures.BAMFile(bam_fn)
#iterable = genomicfeatures.BEDFile(bam_fn)
w = genomicfeatures.Window(iterable, windowsize=100, debug=0)
windowsize = w.windowsize
c = 0
for i in w:
c += 1
#if c > 50000:
# break
center, low_reads, high_reads = i
genomicfeatures.dups_score(low_reads, high_reads, center, windowsize)
fn = 'example.bam'
interval_file = genomicfeatures.BAMFile(os.path.join(this_dir, fn))
fout = open('test.bedgraph','w')
fout.write('track type=bedGraph name=score_test\n')
debug = 0
limit = 100000
if 1:
#window = genomicfeatures.Window(interval_file, debug=debug, limit=35, halfwidth=72)
windowsize = 72
window = genomicfeatures.Window(interval_file, debug=debug, windowsize=windowsize)
c = 0
for w in window:
center, low_reads, high_reads = w
c += 1
if limit is not None:
if c > limit:
break
score = genomicfeatures.dups_score(low_reads, high_reads, center, windowsize=windowsize)
#center = w[0].start + window.halfwidth
if debug:
print ' %s =========>output:' % c, center, score,
print [i.start for i in reads]
fout.write('\t'.join([ low_reads[0].chrom, str(center), str(center+1), str(score)])+'\n')
fout.flush()
fout.close()
