def write_multi_table(table_loc, multi_loc, key_dict, annot_dict):
new = open(multi_loc, mode="w")
base, ext = os.path.splitext(table_loc)
kicked_loc = base + '_kick'+ext
kicked = open(kicked_loc, mode="w")
snp_index = 2
chr_index = 3
bp_index = 4
line1 = True
with open(table_loc, mode="r") as old:
for line in old:
lsplit = line.strip().split()
if line1:
snp_index = lsplit.index('SNP')
chr_index = lsplit.index('CHR')
bp_index = lsplit.index('BP')
lsplit[snp_index]=AP_SNP_TITLE
lsplit.append(IM_SNP_TITLE)
kicked.write('\t'.join(lsplit)+'\n')
lsplit.extend([JB_SNP_TITLE,LZ_TITLE,ANNOT_TITLE,EXTREME_LZ])
new.write('\t'.join(lsplit)+'\n')
line1 = False
else:
snp = lsplit[snp_index]
im = key_dict[snp]
lsplit.append(im)
## chrom = lsplit[chr_index]
## pos = lsplit[bp_index]
## elz = "chr{0}:{1}".format(chrom,bp)
## lsplit.append(elz)
try:
annot = fix_it.get_lz_annot(annot_dict,im)
lz = annot_dict[im].lz
chrom = annot_dict[im].hg19_chr
pos = annot_dict[im].hg19_pos
elz = "chr{0}:{1}".format(chrom,pos)
lsplit.extend([lz,lz,annot,elz])
## lsplit.append(annot)
## lsplit.append(elz)
except KeyError:
kicked.write('\t'.join(lsplit)+'\n')
lz_jb = 'NA'
lz = snp
chrom = lsplit[chr_index]
pos = lsplit[bp_index]
elz = "chr{0}:{1}".format(chrom,pos)
annot = 'no-annotation'
lsplit.extend([lz_jb,lz,annot,elz])
new.write('\t'.join(lsplit)+'\n')
kicked.close()
new.close()
def give_table_annotation(table_loc,new_table_loc,index_dict, annot_dict):
new = open(new_table_loc, mode = "w")
line1 = True
with open(table_loc, mode="r") as table:
for line in table:
line_list = line.strip().split()
if line1:
line_list.append('annotation')
line1 = False
else:
snp = line_list[index_dict['snp']]
annot = fix_it.get_lz_annot(annot_dict,snp)
line_list.append(annot)
new.write('\t'.join(line_list)+'\n')
