ref_dict = dict()

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

line1 = True

for line in yank:

line_list = line.strip().split()

if line1:

yank_indices = pc_toolbox.read_yank_titles(line)

line1 = False

else:

ref_dict[line_list[yank_indices["id"]]] = (line_list[yank_indices["lz"]],line_list[yank_indices["im"]])

print(lz_cmd)

os.chdir(outfolder)

p = subprocess.Popen(lz_cmd, bufsize = 0, executable=None,stdin=None,

stdout=None,stderr=None, preexec_fn=None,close_fds=False,

shell=False,cwd=None,env=None, universal_newlines=False,

startupinfo=None, creationflags=0)

sys.stdout.flush()

p.wait()

global altref, altannot

altref = False

altannot = False

yank_loc = "/home/jkb4y/cphgdesk_share/Projects/IMCHIP/Intersect_SNP_list/eurmeta_10172012/RegionYank/eurmeta_yank.tbl"

#region_loc = '/home/jkb4y/work/data/Region_Lists/hg19/T1D_regions_hg19_09202012.txt'

#region_loc = '/home/jkb4y/work/data/Region_Lists/hg19/T1D_regions_hg19_09202012_chr19_20_21_22_23.txt'

region_loc = '/home/jkb4y/work/data/Region_Lists/hg19/achilleas_all_09202012.txt'

#region_loc = '/home/jkb4y/work/data/Region_Lists/hg19/achilleas_chr21_22_23_09202012.txt'

#region_loc = '/home/jkb4y/work/data/Region_Lists/hg19/MHC_zoom.txt'

#assoc_loc = '/home/jkb4y/ubs/work/results/July2012/ModelComparison/AA_cov_12_nosex.assoc.logistic'

assoc_loc = '/home/jkb4y/ubs/work/results/July2012/ModelComparison/AA_cov_12_nosex_SIlz.assoc.logistic'

#outfolder = '/home/jkb4y/ubs/work/results/July2012/RegionGraphs/RefTopUK'

#outfolder = '/home/jkb4y/cphgdesk_share/Projects/IMCHIP/July2012/RegionGraphs/MHC'

#outfolder = '/home/jkb4y/ubs/work/results/July2012/RegionGraphs/RefTopUK_expand_0.2'

#outfolder = '/home/jkb4y/ubs/work/results/July2012/RegionGraphs/SI_Annot_expansion_0.1'

outfolder = '/home/jkb4y/ubs/work/results/July2012/RegionGraphs/Achilleas_regions'

outfolder = '/home/jkb4y/cphgdesk_share/Projects/IMCHIP/July2012/RegionGraphs/Achilleas_regions_expansion_0.1'

#assoc_loc = fix_it.locate_fixed_table(assoc_loc, build="hg19",table_type = "assoc")

regions = pc_toolbox.create_bp_region_list(region_loc)

expansion = int(.1e6)

ref_dict = make_ref_dict(yank_loc)

print ref_dict

for region in regions:

prefix = region.ID + '_AA'

cache_folder = os.path.join(outfolder, 'ld_caches')

if not os.path.exists(cache_folder):

os.makedirs(cache_folder)

ld_cache = os.path.join(cache_folder, 'chr{0}_ld_cache.db'.format(region.chro))

lz_args = ["locuszoom", "--metal", assoc_loc,

'--chr',region.chro, '--start',str(region.start - expansion),

'--end',str(region.end + expansion),'--pvalcol','P','--markercol','EXTREME_LZ',

"--pop","AFR",'--build','hg19','--source','1000G_Nov2010',

'--prefix', prefix,

#'annotCol=annotation','annotPch=24,25,22,23,21',

#'annotOrder=splice,nonsyn,coding,utr,no-annotation',

'--plotonly','--verbose','--no-date','--delim','whitespace','ymax=5',

'--cache',ld_cache]

if altannot:

lz_args.extend([#'prelude=./altannot_prelude.R',

'postlude=/home/jkb4y/h4t1/programs/plink_python/aa_postlude.R',

'refsnpTextColor=transparent',

'annotCol=SI_annotation',

'annotPch=8,21','annotOrder=SI,none'])

else:

lz_args.extend(['annotCol=annotation','annotPch=24,25,22,23,21',

'annotOrder=splice,nonsyn,coding,utr,no-annotation'])

## if refsnp in ['rs75793288'] and not altref:

## lz_args.extend(['--no-ld'])

#if region.title in ['20p13'] and not altref:

# lz_args.extend(['--no-ld'])

if region.ID in ['1p21.2_y','1q23.3_b_y','12p13.33_y'] and not altref:

lz_args.extend(['--no-ld'])

if int(region.chro) > 22:

lz_args.extend(['--no-ld'])

if region.title not in ['6p21.32'] and altref:

refsnp = ref_dict[region.ID][0]

if refsnp in ['rs75793288','rs3216815','rs12416116']:

lz_args.extend(['--no-ld'])

title = "{0}: AA population, refsnp {1}".format(region.ID, refsnp)

lz_args.extend(["--refsnp",refsnp,'title={0}'.format(title)])

else:

lz_args.extend(['title={0}'.format(region.ID)])

if region.ID in ['20p13']:

lz_args.extend(['--no-ld'])

if region.ID in ['6p21.32']:

lz_args.extend(['rfrows=7'])