line1 = True

with open(yank_loc, mode="r") as yank:

yank_lines = list()

for line in yank:

if line1:

index_dict = pc_toolbox.read_yank_titles(line)

line1 = False

else:

lsplit = line.strip().split()

if not lsplit == []:

yank_info = YankInfo(start=lsplit[index_dict['start']],

end=lsplit[index_dict['end']],

chro=lsplit[index_dict['chr']],

lz=lsplit[index_dict['lz']],

ID=lsplit[index_dict['id']],

pos=lsplit[index_dict['pos']],

p=lsplit[index_dict['p']])

yank_lines.append(yank_info)

hit_dict = dict()

with open(hit_dict_loc) as hitty:

for line in hitty:

lsplit = line.strip().split()

if not lsplit == []:

hit_dict[lsplit[0]] = lsplit[1:]

print hit_dict

'''Reads arguments from the command line and assigns values to globals

Keyword arguments:

argv -- commandline arguments (?)

'''

global outfolder, ccfolder, yank_loc, single, ldfolder, freq_loc

global out_flag, user_script_loc, build, horse_args, hit_dict_loc

out_flag = ''

yank_loc = None

build = 'hg19'

ccfolder = None

outfolder = None

user_script_loc = None

horse_args = list()

single = False

ldfolder = LDFOLDER

freq_loc = FREQ_LOC

hit_dict_loc = HIT_DICT_LOC

try:

opts, args = getopt.getopt(argv, "ho:s:f:",

["help","outfolder=","script=","flag=",

"ccfolder=","yank=","build=","single",

"freq=","ldfolder=","multihits="])

except getopt.GetoptError:

usage()

sys.exit(2)

for opt, arg in opts:

if opt in ("-h","--help"):

usage()

sys.exit()

elif opt in ("-f","--flag"):

out_flag = '_'+arg

elif opt in ("-s","--script", "--build"):

horse_args.extend((opt,arg))

#user_script_loc = arg

elif opt in ("-o","--outfolder"):

outfolder = arg

elif opt in ("multihits"):

hit_dict_loc = arg

elif opt in ("--ccfolder"):

ccfolder = arg

elif opt in ("--ldfolder"):

ldfolder = arg

elif opt in ("--freq"):

freq_loc = arg

elif opt in ("--single"):

horse_args.append('--single')

single = True

elif opt in ("--yank"):

global outfolder, ccfolder, yank_loc, ldfolder, freq_loc

global out_flag, user_script_loc, build, horse_args, hit_dict_loc

cl_arguments(argv)

hit_dict = read_hit_dict(hit_dict_loc)

yank_lines_list = read_yank(yank_loc)

## region_out = '/home/jkb4y/work/data/Region_Lists/hg19/T1D_regions_hg19_05242012_sigsOnly.txt'

## new_regionlist = open(region_out, mode = "w")

## new_regionlist.write('\t'.join(['gene_chr','Chr_band',

## 'region_start','region_end',

## 'gene_symbol','band_title','region_id'])+'\n')

for info in yank_lines_list:

if not float(info.p) > 3.5e-7:

chromosome = info.chro

start = info.start

end = info.end

lz = info.lz

ID = info.ID

band_title = info.ID.replace('_z','').replace('_a','').replace('_b','')

## new_regionlist.write('\t'.join([chromosome, ID, start,

## end, '.',band_title,ID])+'\n')

assoc_name = ID + '_~0_SNPsOut.assoc.logistic'

assoc_loc = os.path.join(ccfolder, 'chr{0}'.format(chromosome),assoc_name)

cmd_list = ['--region-id',ID,'--chromosome',chromosome,

'--start',start,'--end',end,

#'--snpstar',lz,

'--assoc',assoc_loc]#'--build', build,

#'--script',user_script_loc,'--outfolder',outfolder]

if single:

if not 'Singles' in outfolder:

print("in if statement")

new_out = os.path.join(outfolder, 'Singles')

if not os.path.exists(new_out):

os.makedirs(new_out)

outfolder = new_out

cmd_list.extend(['--outfolder',outfolder])

cmd_list.extend(['--ldfolder',ldfolder,'--freq',freq_loc])

cmd_list.extend(horse_args)

hit_index = 1

if ID in hit_dict:

for snp in hit_dict[ID]:

cmd_list_prime = []

cmd_list_prime.extend(cmd_list)

if hit_index == 1:

cmd_list_prime.extend(['--hit1',','.join(hit_dict[ID])])

cmd_list_prime.extend(['--snpstar',snp,'--multi', hit_index])

print cmd_list_prime

testsigs_workhorse.main(cmd_list_prime)

hit_index = hit_index + 1

else:

cmd_list.extend(['--snpstar',lz])

print cmd_list