'''

Determine if the SNP position falls between the start and end positions of

the region.

Args:

position -- SNP position

left_endpoint -- start of region

right_endpoint -- end of region

'''

if left_endpoint <=position and position <= right_endpoint:

return True

else:

print('''

USAGE: assoc_yank.py [FLAG] OBJECT

FLAG DESCRIPTION CURRENT DEFAULT

-o, --outfile pathname of output file {0}

-a, --assoc pathname of association file {1}

-f, --freq pathname of frequency file {2}

-m, --map path of unadapted map file {3}

-r, --region-list pathname of region list file {4}

--bp-form unit used to define region {5}

choices: mb, kb, bp

-h, --help display this usage string

''' Determine if reference gene symbol is appropriate for dictionary use,

and change where appropriate.

Args:

gene_symbol -- gene_symbol listed in the region list

chromosome -- chromosome listed in region list

Returns:

new_symbol -- symbol to be used in dictionary

'''

new_symbol = gene_symbol

if gene_symbol=='0' or gene_symbol =='No' or gene_symbol == 'no' or gene_symbol == 'NA':

new_symbol = 'nogene-'+ chromosome

elif gene_symbol=='multiple' or gene_symbol=='Multiple':

new_symbol = 'multiple-'+chromosome

title_list = line.split()

chr_col = title_list.index(ASSOC_CHR_TITLE)

p_col = title_list.index(P_TITLE)

snp_col = title_list.index(SNP_TITLE)

pos_col = title_list.index(POSITION_TITLE)

or_col = title_list.index(OR)

stat_col = title_list.index(STAT)

a1_col = title_list.index(A1)

assoc_indices = {'chr':chr_col, 'p':p_col,'snp':snp_col,'pos':pos_col,

'stat':stat_col,'OR':or_col,'a1':a1_col}

'''

Read file containing regional information and create a dictionary holding

that information.

Args:

region_loc -- filepath of file containing region information

position_form -- string ('kb' or 'mb')describing units used in region file

Returns:

gene_region_dict -- dictionary of region information

'''

#create a dictionary to hold the regional information

gene_region_dict = {}

standardizer = 1

if position_form == 'mb':

standardizer = 1e6

elif position_form == 'kb':

standardizer = 1e3

with open(region_loc, mode='r') as region_file:

line1 = True

for line in region_file:

if line1:

reg_indices = pc_toolbox.read_regional_titles(line)

line1 = False

else:

line_list = line.strip().split()

gene_sym = line_list[reg_indices['sym']]

chr_num = line_list[reg_indices['chr']]

line_list[reg_indices['sym']]=correct_gene_sym(gene_sym,chr_num)

gene_region_dict.update({line_list[reg_indices['sym']]

:[int(chr_num),

int(float(line_list[reg_indices['start']])*standardizer),

int(float(line_list[reg_indices['end']])*standardizer)]})

line1 = True

old_p = 1

old_out=[]

reg_chr, reg_start, reg_end = gene_region_dict[gene_name]

assoc_counter = 0

multi_counter = 1

sig_list = []

blank_dict = {'chr':'--','start':'--','end':'--','sym':'--','snp':'--',

'lz':'--','pval':'--','stat':'--','OR':'NA','aa1':'NA',

'pos':'--','notes':'--','maf':'NA','ma1':'NA','ma2':'NA'}

order_list = ['chr','start','end','sym','snp','lz','pval','stat','OR',

'aa1','maf','ma1','ma2','notes']

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

for line in assoc:

if line1:

assoc_indices = read_assoc_titles(line)

assoc_counter = 1

line1 = False

else:

line_list = line.strip().split()

snp_pos = int(line_list[assoc_indices['pos']])

if not line_list[assoc_indices['p']] == 'NA':

if reg_chr == int(line_list[assoc_indices['chr']]) and pc_toolbox.in_interval(snp_pos,

reg_start, reg_end):

cur_p = float(line_list[assoc_indices['p']])

cur_snp , lz_snp = pc_toolbox.correct_snp(assoc_indices,line_list)

## cur_snp = line_list[assoc_indices['snp']]

## lz_snp = '--'

## if not cur_snp.startswith('rs'):

## lz_snp = 'chr'+str(reg_chr)+':'+ str(snp_pos)

## else:

## lz_snp = cur_snp

cur_out = [str(reg_chr), str(reg_start), str(reg_end),gene_name,

cur_snp,lz_snp, str(cur_p), str(snp_pos),'--']

if cur_p == old_p:

multi_counter = multi_counter + 1

cur_tup = (cur_snp, lz_snp,str(cur_p))

old_tup = (old_out[4], old_out[5],str(old_p))

sig_list.append(cur_tup)

if old_tup not in sig_list:

sig_list.append(old_tup)

print('NOTE: Both {0} and {1} have p-values of {2}.'.format(old_out[4],cur_snp, cur_p))

print('There are no Z-scores with which to decide between them, so I arbitrarily retain {0}.'.format(old_out[4]))

old_out[8]='{0}SNPs(p={1})'.format(multi_counter, old_p)

print(old_out[8])

elif cur_p < old_p:

multi_counter = 1

old_p = cur_p

old_out = cur_out

sig_list = []

assoc_counter = assoc_counter + 1

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

Keyword arguments:

argv -- commandline arguments (?)

'''

global position_form, assoc_loc, region_loc, out_file, freq_loc

position_form = POSITION_FORM

assoc_loc = ASSOC_LOC

region_loc = REGION_LOC

out_file = OUT_FILE

freq_loc = FREQ_LOC

map_loc = MAP_LOC

try:

opts, args = getopt.getopt(argv, "ha:r:o:m:",

["help","assoc=","region-list=",

"out=","map=","bp-form="])

except getopt.GetoptError:

usage()

sys.exit(2)

for opt, arg in opts:

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

usage()

sys.exit()

elif opt in ("--bp-form"):

position_form = arg

elif opt in ("-a","--assoc"):

assoc_loc = arg

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

freq_loc = arg

elif opt in ("-m","--map"):

map_loc = arg

elif opt in ("-r","--region-list"):

region_loc = arg

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

global out_file

title_list = ['chr','region_start(Mb)',

'region_end(Mb)','gene_symbol',

'snp_name','locuszoom_snp','p-value','snp_position','notes']

sig_title_list = ['snp_name','locuszoom_snp','p-value','MAF','MAF_A1','MAF_A2']

title_line = '\t'.join(title_list)

sig_line = '\t'.join(sig_title_list)

with open(out_file, mode="w") as out_text:

out_text.write(title_line +'\n')

with open(out_file, mode="a") as out_text:

for gene in gene_list:

gene_info, sig_list = read_assoc(assoc_loc, gene,gene_region_dict)

if not sig_list == []:

sig_start, ext = os.path.splitext(out_file)

sig_path = sig_start+'_'+'Chr'+gene_info[0] + '_'+ gene_info[3]+'.txt'

sigs = open(sig_path,mode='w')

sigs.write(sig_line +'\n')

for sig in sig_list:

sigs.write('\t'.join(sig)+'\n')

sigs.close()

gene_info[1]=str(float(gene_info[1])*1e-6)

gene_info[2]=str(float(gene_info[2])*1e-6)

gene_line = '\t'.join(gene_info[:9])

print(gene_info[:9])

out_text.write(gene_line + '\n')

global out_file

if gene_info[8]== '--':

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

subfolder_path = os.path.join(head, 'assoc_condition_lists')

if not os.path.exists(subfolder_path):

os.makedirs(subfolder_path)

snp_name = gene_info[4]

chr_num = gene_info[0]

position = gene_info[7]

gene_sym = gene_info[3]

mb_range = gene_info[1] + '-'+gene_info[2]

filestart = os.path.join(subfolder_path,'Chr'+chr_num + '_')

filename = filestart + gene_sym + '.txt'

clist = open(filename, mode='w')

clist.write(gene_info[5])

global out_file, region_loc, position_form, assoc_loc

cl_arguments(sys.argv[1:])

gene_region_dict = create_region_dict(region_loc,position_form)

key_list = gene_region_dict.keys()

gene_list = sorted(key_list,key=lambda gene:gene_region_dict[gene][0])