title_list = line.strip().split()

assoc_chr_col = title_list.index(ASSOC_CHR_TITLE)

p_col = title_list.index(ASSOC_P_TITLE)

snp_col = title_list.index(ASSOC_SNP_TITLE)

position_col = title_list.index(ASSOC_POS_TITLE)

assoc_indices = {'chr':assoc_chr_col, 'p':p_col,

'snp':snp_col,

'pos':position_col,'pvalcol':ASSOC_P_TITLE,'markercol':ASSOC_SNP_TITLE}

print("Index Dict:")

print assoc_indices

line1=True

im_list = list()

with open(list_file, mode="r") as listy:

for line in listy:

line_list = line.strip().split()

if line1:

line1=False

continue

elif len(line_list)>1:

im = line_list[IM_INDEX]

im_list.append(im)

im_snp_list = list()

listy = open(list_loc,mode="r")

for line in listy:

snp = line.strip()

im_snp = annot_dict[snp].name

im_snp_list.append(im_snp)

try:

info =annot_dict[im_name]

return info

except KeyError:

head, tail = os.path.split(assoc_loc)

line1 = True

super_assoc = os.path.join(outfolder, tail + '.JB')

superass = open(super_assoc, mode="w")

with open(assoc_loc, mode="r") as assoc:

for aline in assoc:

lsplit = aline.strip().split()

if line1:

index_dict = read_assoc_titles(aline)

lsplit.extend(['rs_name','hg18_pos', 'hg19_pos','annotation', 'intersect'])

line1 = False

else:

im = lsplit[index_dict['snp']]

intersect = 'no'

if im in intersect_list:

intersect = 'yes'

try:

rs = annot_dict[im].rs

hg18 = annot_dict[im].hg18_pos

hg19 = annot_dict[im].hg19_pos

annot = annot_dict[im].annot

except KeyError:

rs = 'NA'

hg18 = 'NA'

hg19 = 'NA'

annot = 'no-annotation'

lsplit.extend([rs,hg18,hg19,annot, intersect])

superass.write('\t'.join(lsplit) +'\n')

index_dict = {'chr':0,'pos':3,'snp':1}

out = open(out_file, mode="w")

out.write('\t'.join(title_list)+'\n')

with open(map_file, mode="r") as mappy:

for line in mappy:

line_list = line.strip().split()

im=line_list[index_dict['snp']]

info = look_up_snp(im, annot_dict)

intersect = 'no'

if info is not None:

if info.name in intersect_list:

intersect = 'yes'

out.write('\t'.join([im,info.rs, info.hg18_pos, info.hg19_pos,

info.lz,intersect]) +'\n')

else:

out.write('\t'.join([im,im,line_list[index_dict['pos']],

'??','chr16:'+line_list[index_dict['pos']],

intersect])+'\n')

build = BUILD

#list_file = LIST_FILE

out_file = OUT_FILE

outfolder = '/home/jkb4y/work/data/Joe/HapMapCorrect/'

#map_file = MAP_FILE

intersect_loc = INTERSECT_LOC

assoc_loc = ASSOC_LOC

title_list = ['imchip_name','rs_name','hg18_pos','hg19_pos','hg18_lz','intersect']

annot_dict_loc = fix_it.locate_annot_dict(build)

annot_dict = fix_it.build_annot_dict('MAP',annot_dict_loc)

intersect_annot_loc = fix_it.locate_annot_dict('hg19')

intersect_annot_dict = fix_it.build_annot_dict('LOG',intersect_annot_loc)

#im_list = old_read_list(list_file)

intersect_list = read_list(intersect_loc, intersect_annot_dict)

#map_and_key(map_file, out_file, annot_dict, intersect_list)

## index_dict = {'chr':0,'pos':3,'snp':1}

## out = open(out_file, mode="w")

## out.write('\t'.join(title_list)+'\n')

## with open(map_file, mode="r") as mappy:

## for line in mappy:

## line_list = line.strip().split()

## im=line_list[index_dict['snp']]

## info = look_up_snp(im, annot_dict)

## intersect = 'no'

##

## if info is not None:

##

## if info.name in intersect_list:

## intersect = 'yes'

## out.write('\t'.join([im,info.rs, info.hg18_pos, info.hg19_pos,

## info.lz,intersect]) +'\n')

##

## else:

## out.write('\t'.join([im,im,line_list[index_dict['pos']],

## '??','chr16:'+line_list[index_dict['pos']],

## intersect])+'\n')

## out.close()