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# Author: Lei Yan
# Create Date: 2014-01-21
# Last Update Date: 2014-01-24
# import
import sys
import os
import re
import MySQLdb
import ConfigParser
def main(argv):
# load configuration from configuration file
config = ConfigParser.ConfigParser()
config.read(argv[1])
genofile = config.get('configuration', 'genofile')
# parse genofile
genotypes = []
file_geno = open(genofile, 'r')
for line in file_geno:
line = line.strip()
if line.startswith('#'):
continue
if line.startswith('@'):
continue
cells = line.split()
if line.startswith("Chr"):
strains = cells[4:]
continue
genotype = {}
genotype['chr'] = cells[0]
genotype['locus'] = cells[1]
genotype['cm'] = cells[2]
genotype['mb'] = cells[3]
genotype['values'] = cells[4:]
genotypes.append(genotype)
print "get %d strains:\t%s" % (len(strains), strains)
print "load %d genotypes" % len(genotypes)
# phenotypes
# main
if __name__ == "__main__":
main(sys.argv)
print "exit successfully"
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