本文整理汇总了Python中pybedtools.BedTool.count方法的典型用法代码示例。如果您正苦于以下问题：Python BedTool.count方法的具体用法？Python BedTool.count怎么用？Python BedTool.count使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类pybedtools.BedTool的用法示例。
在下文中一共展示了BedTool.count方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: comp_score
# 需要导入模块: from pybedtools import BedTool [as 别名]
# 或者: from pybedtools.BedTool import count [as 别名]
def comp_score(self, gap_penalty):
'''compute_score_given_gap_penalty'''
if gap_penalty in self.__cache:
return self.__cache[gap_penalty]['score']
gb = self.orig_bins.scale_neg_scores(gap_penalty)
observed_result = gb.max_segments()
mc_res = MonteCarlo.run_simulation(gb.chrom_scores,
niter=self.mc_trials, nprocs=self.nprocs)
tester = IntervalTest(observed_result, mc_res)
segments = [segment for (segment, pval) in tester.pvalues()
if pval < self.pval_lim]
if len(segments) == 0:
# no potential peaks found
log.notice('''Gap penalty of %.2f gives a score of 0.0 \
(0 potential peaks with 0.00MB coverage)''' % gap_penalty)
self.__cache[gap_penalty] = {'score': 0.00}
return 0.0
# TODO use bx.python instead of pybedtools
peaks_sb = StringIO.StringIO()
tester.segments_to_bedstream(segments, peaks_sb)
peaks = BedTool(peaks_sb.getvalue(), from_string=True)
d = self.count_stats(self.bins_bedtool.intersect(peaks))
d['gap-penalty'] = gap_penalty
try:
d['peak_EIB_ratio'] = d['EIB'] / float(d['EIB'] + d['DIB'])
except ZeroDivisionError:
# no peaks found
d['peak_EIB_ratio'] = 0.0
d['global_EIB_coverage'] = d['EIB'] / float(self.genome_wide_stats['EIB'])
d['score'] = d['peak_EIB_ratio']**5 * d['global_EIB_coverage']
peak_cov = sum(x.end - x.start for x in peaks) / 1e6
log.notice('''Gap penalty of %.2f gives a score of %.3f \
(%d potential peaks with %.2fMB coverage)''' % (gap_penalty, d['score'], peaks.count(), peak_cov))
self.__cache[gap_penalty] = d
return d['score']示例2: main
# 需要导入模块: from pybedtools import BedTool [as 别名]
# 或者: from pybedtools.BedTool import count [as 别名]
def main():
error_site = BedTool('/home/kwoklab-user/Error_exome_all.bed')
# protein_coding_site = BedTool('/home/kwoklab-user/Shared_resources/gemini/data/gencode15.protein_coding.20130131.hg19.bed')
gemini_data_dir = "/home/kwoklab-user/Shared_resources/gemini/data"
dbsnp_137_site = BedTool('/home/kwoklab-user/Shared_resources/gemini/data/dbsnp.137.vcf.gz')
#https://code.google.com/p/discovering-cse/
cse_site = BedTool('/home/kwoklab-user/Shared_resources/gemini/data/cse-hiseq-8_4-2013-02-20.bed.gz')
# gms_site = BedTools( path.join(gemini_data_dir, 'GRCh37-gms-mappability.vcf.gz'))
rmsk_site = BedTool(path.join(gemini_data_dir, 'hg19.rmsk.bed.gz'))
segdup_site = BedTool(path.join(gemini_data_dir, 'hg19.segdup.bed.gz'))
clinvar_site = BedTool(path.join(gemini_data_dir,'clinvar_20130118.vcf.gz'))
dgv_site = BedTool(path.join(gemini_data_dir,'hg19.dgv.bed.gz'))
CpG_site = BedTool(path.join(gemini_data_dir,'hg19.CpG.bed.gz'))
print "total error sites %d" % error_site.count()
print "error in cse site %d" % (error_site+cse_site).count()
print "error in dbsnp137 site %d" %(error_site+dbsnp_137_site).count()
print "errors in repeat mask region %d" % (error_site+rmsk_site).count()
print "errors in segdup %d" % (error_site+segdup_site).count()
print "errors in Clinvar %d" % (error_site+clinvar_site).count()
print "errors in dgv %d" % (error_site+dgv_site).count()
print "errors in CpG %d" % (error_site+CpG_site).count()示例3: BedTool
# 需要导入模块: from pybedtools import BedTool [as 别名]
# 或者: from pybedtools.BedTool import count [as 别名]
split_num = 100
split_region_list = [[]*5]
print split_region_list
bed = BedTool('/Users/huangzhibo/workitems/10.testData/testPlatformTJ/bed/test.bed')
bed = BedTool(bed.sort().merge().window_maker(b=bed.fn, w=100))
bed.all_hits()
# x = BedTool().window_maker(genome='hg38', w=1000000)
bed.saveas('/Users/huangzhibo/workitems/10.testData/testPlatformTJ/bed/test_w100.bed')
split_num = bed.count() if bed.count() < split_num else split_num
print bed.count()/split_num
# print bed.split(10, 'out')
# print x
n = 0
for region in bed:
# print region.length
print str(region).strip()
n += 1
print n