mlist = line.strip().split('\t')

chro=mlist[manifest_indices['chr']].replace('X','23').replace('Y','24').replace('XY','23')

name=mlist[manifest_indices['name']]

pos=mlist[manifest_indices['pos']]

gbuild=mlist[manifest_indices['build']]

if 36 <= float(gbuild) < 37:

hgbuild = 'hg18'

elif 37 <= float(gbuild) < 38:

#elif gbuild == '37':

hgbuild = 'hg19'

else:

hgbuild = 'ERROR'

manifest_info = ManifestInfo(name=name,build=hgbuild,chro=chro,pos=pos)

dict_loc = locate_manifest_dict(manifest_loc)

manifest_dict = open(dict_loc, mode="w")

with open(manifest_loc, mode = "r") as manifest:

line1 = True

for mline in manifest:

if line1:

m_indices = read_manifest_titles(mline)

line1 = False

else:

m_info = read_manifest(m_indices,mline)

manifest_dict.write('\t'.join(m_info) +'\n')

title_list = line.strip().split('\t')

chr_col = title_list.index(CHR_TITLE)

name_col = title_list.index(IM_TITLE)

pos_col = title_list.index(POS_TITLE)

build_col = title_list.index(BUILD_TITLE)

manifest_indices = {'chr':chr_col, 'name':name_col,

'pos':pos_col,'build':build_col}

#global meta

manifest_dict = dict()

with open(manifest_dict_loc, mode="r") as mannie:

for m in mannie:

m_list = m.strip().split()

minfo = ManifestInfo._make(m_list)

ref = minfo.name

manifest_dict[ref]=minfo

(basepath, ext) = os.path.splitext(table_loc)

orig_rename = basepath + '~'

new_loc = str(rename_as_necessary(orig_rename, ext)) + ext

output_loc = new_loc

with open(table_loc, mode="r") as table:

output = open(output_loc, mode="w")

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

error_list = list()

for line in table:

line_list = line.strip().split()

snp = line_list[index_dict['snp']]

if manifest_dict[snp].build == build:

line_list[index_dict['chr']]= manifest_dict[snp].chro.replace('X','23').replace('Y','24').replace('XY','23')

line_list[index_dict['pos']]= manifest_dict[snp].pos

elif snp in ['rs9279834','rs10636228','rs17510415',

'rs17539100','rs17510360','rs5743293','rs35768562']:

line_list[index_dict['pos']]= str(int(line_list[index_dict['pos']])+1)

else:

try:

if build == 'hg18':

line_list[index_dict['chr']]= annot_dict[snp].hg18_chr.replace('X','23').replace('Y','24').replace('XY','23')

line_list[index_dict['pos']]= annot_dict[snp].hg18_pos

else:

line_list[index_dict['chr']]= annot_dict[snp].hg19_chr.replace('X','23').replace('Y','24').replace('XY','23')

line_list[index_dict['pos']]= annot_dict[snp].hg19_pos

except KeyError:

error_list.append(list(line_list))

output.write('\t'.join(line_list)+'\n')

output.close()

base, ext = os.path.splitext(new_loc)

error_loc = base + '_NAMEERRORS.txt'

efile = open(error_loc,mode="w")

efile.write('\t'.join(['CHR','RS','cM','POS'])+'\n')

for error in error_list:

efile.write('\t'.join(error)+'\n')

KeyInfo = namedtuple("KeyInfo","im,rs,hg18_chr,hg18_pos,hg19_chr,hg19_pos,mbuild")

key = open(key_loc, mode="w")

title_list = ['imchip_id','rs_id','hg18_chr','hg18_pos','hg19_chr','hg19_pos','manifest_build']

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

with open(table_loc, mode="r") as table:

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

error_list = list()

for line in table:

line_list = line.strip().split()

im = line_list[index_dict['snp']]

mbuild = manifest_dict[im].build

rs = 'NA'

hg18_chr = 'NA'

hg19_chr = 'NA'

hg18_pos = 'NA'

hg19_pos = 'NA'

print mbuild

if mbuild == 'hg18':

hg18_chr = manifest_dict[im].chro

hg18_pos = manifest_dict[im].pos

try:

hg19_chr = annot_dict[im].hg19_chr

hg19_pos = annot_dict[im].hg19_pos

rs = annot_dict[im].rs

except KeyError:

rs = 'NA'

hg19_chr = 'NA'

hg19_pos = 'NA'

## error_list.append(list(line_list))

## error_list.extend(mbuild)

line_list.append(mbuild)

error_list.append(list(line_list))

elif im in ['rs9279834','rs10636228','rs17510415',

'rs17539100','rs17510360','rs5743293','rs35768562']:

hg18_chr = line_list[index_dict['chr']]

hg18_pos = str(int(line_list[index_dict['pos']])+1)

hg19_chr = 'NA'

hg19_pos = 'NA'

rs = im

elif mbuild == 'hg19':

hg19_chr = manifest_dict[im].chro

hg19_pos = manifest_dict[im].pos

try:

hg18_chr = annot_dict[im].hg18_chr

hg18_pos = annot_dict[im].hg18_pos

rs = annot_dict[im].rs

except KeyError:

line_list.append(mbuild)

error_list.append(list(line_list))

rs = 'NA'

hg18_chr = 'NA'

hg18_pos = 'NA'

keyinfo = KeyInfo(im=im,rs=rs,hg18_chr=hg18_chr,

hg18_pos=hg18_pos, hg19_chr=hg19_chr,

hg19_pos=hg19_pos,mbuild=mbuild)

key.write('\t'.join(keyinfo)+'\n')

key.close()

base, ext = os.path.splitext(table_loc)

error_loc = base + '_KEYERRORS.txt'

efile = open(error_loc,mode="w")

efile.write('\t'.join(['CHR','RS','cM','POS','A1','A2','manifest_build'])+'\n')

for error in error_list:

efile.write('\t'.join(error)+'\n')

'''

Determines if the desired new name for the input map file already exists,

and, if so, chooses another name.

Args:

new_orig -- target to which to map file could be moved

ext -- extension of the map file

Returns:

next_rename -- target name to which the original map file can

be saved without overwriting any other file

'''

next_rename = new_orig

if os.path.exists(new_orig + ext):

print( '''There is already a file named {0}, which means that map_adapt has

already been run on this map file. To avoid overwriting the contents of {0},

the contents of the new output file will be written to: '''.format(new_orig + ext))

if new_orig[-1].isdigit():

pieces = new_orig.rpartition('~')

up1 = int(pieces[2])+ 1

next_rename = pieces[0]+'~'+ str(up1)

print(next_rename + ext)

next_rename = rename_as_necessary(next_rename, ext)

else:

next_rename = new_orig + '1'

print(next_rename + ext)

next_rename = rename_as_necessary(next_rename, ext)

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

Keyword arguments:

argv -- commandline arguments (?)

'''

global manifest_loc, build, table_loc

manifest_loc = None

#manifest_loc = MANIFEST_LOC

build = BUILD

table_loc = TABLE_LOC

try:

opts, args = getopt.getopt(argv, "h",

["help","manifest=","build=","table="])

except getopt.GetoptError:

usage()

sys.exit(2)

for opt, arg in opts:

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

usage()

sys.exit()

elif opt in ("--table"):

table_loc = arg

elif opt in ("--manifest"):

manifest_loc = arg

elif opt in ("--build"):

global manifest_loc, table_loc, build

cl_arguments(argv)

if manifest_loc is not None:

print("WRITING MANIFEST DICT!")

write_manifest_dict(manifest_loc)

dict_loc = locate_manifest_dict()

manifest_dict = build_manifest_dict(dict_loc)

annot_dict_loc = fix_it.locate_annot_dict(build)

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

fix_table(table_loc, build, manifest_dict, annot_dict)

key_loc = locate_table_key(table_loc)