def _draw_chrom_dividers(self, x_axis):
if self.chrom == 0:
if x_axis == 'cm_cumulative':
genome_offset = genome_cm_offset()
else:
genome_offset = genome_bp_offset()
offset = genome_offset[:NUM_CHROMOSOMES]
for chr_offset in offset[1:]: P.plot([chr_offset, chr_offset], [-0.1, 1.1], c='k', linestyle=':')
def bp_cumulative(self):
'''cM axis offset for aligning multiple chromosomes.'''
offset = genome_bp_offset()[:NUM_CHROMOSOMES]
return self.snp.info['base_pair'] + offset[self.snp.info['chrom'] - 1]
Are they near centromeres?
Created on December 9, 2013
@author: Oren Livne <*****@*****.**>
============================================================
'''
import impute as im, os, numpy as np
from scipy import ndimage
from impute.plot.plots import genome_bp_offset
####################################################################################
if __name__ == '__main__':
proband, parent = 579, 1403 # 248, 547#80, 547
data = os.environ['OBER_OUT'] + '/validation/affy'
stats = im.imputation.impute_stats.Stats.load(data + '/stats.npz')
chrom = stats.snp.info['chrom']
x = stats.cm_edge_dist
y = stats.cm_cumulative
c = stats.snp.call_rate_imputed_full
k = np.argsort(x)
cs = ndimage.median_filter(c, 20)
dip = np.where((cs[k] < 0.58) & (x[k] > 70))[0]
kd = k[dip]
i = np.argsort(chrom[k[dip]])
genome_offset = genome_bp_offset()[:22]
for z in zip(chrom[kd][i], stats.snp.info['base_pair'][kd][i], stats.snp.info['base_pair'][kd][i] + genome_offset[chrom[kd][i] - 1], x[kd][i], y[kd][i]):
print '%-2d %-10d %-12d %-9.3f %-9.3f' % (z)
