#!/usr/bin/env python
"""
2008-10-01
example to call DrawSNPRegion as an API
"""
import sys, os, math
sys.path.insert(0, os.path.expanduser('~/lib/python'))
sys.path.insert(0, os.path.join(os.path.expanduser('~/script')))
from variation.src.DrawSNPRegion import DrawSNPRegion
instance = DrawSNPRegion(db_user='******', db_passwd='', hostname='papaya.usc.edu', database='stock_250k', input_fname='/tmp/dumb', output_dir='/tmp', debug=0)
gene_annotation_picklef = '/Network/Data/250k/tmp-yh/at_gene_model_pickelf'
LD_info_picklef = '/Network/Data/250k/tmp-yh/call_method_17_LD_m0.2_n0.1_m40000'
#LD_info_picklef = None
LD_fname = '/Network/Data/250k/tmp-yh/call_method_17_LD_m0.2.tsv' #optional
phenotype_method_id = 1
chromosome, start, stop = 2, 9588685-40000, 9588685+40000
output_fname = '/tmp/SNP_2_9588685'
center_snp_position = 9588685
instance.drawSNPRegion(gene_annotation_picklef, LD_info_picklef, phenotype_method_id, chromosome, start, stop, \
output_fname, center_snp_position=center_snp_position, LD_fname=LD_fname,\
which_LD_statistic=2, call_method_id=17, min_MAF=0.1)
