def main(argv):
global map_loc, flip_loc, repair_loc
cl_arguments(sys.argv[1:])
## map_loc = ''
## try:
## opts, args = getopt.getopt(argv, "hm:",
## ["help","map="])
## except getopt.GetoptError:
## usage()
## sys.exit(2)
## for opt, arg in opts:
## if opt in ("-h","--help"):
## usage()
## sys.exit()
## elif opt in ("-m","--map"):
## map_loc = arg
## elif opt in ("--flip"):
## flip_loc = arg
repair_dict = pc_toolbox.read_dict(repair_loc)
sort_fo = list_info(map_loc)
base, ext = os.path.splitext(map_loc)
extract_loc = base+'_extractList.txt'
exclude_bfile = base + "_excludeDup"
extract_bfile = base + "_extractDup"
find_dups(sort_fo, extract_loc, repair_dict)
#write and use the script to extract the non-rs duplicates
extract_script = base + '_extractScript.txt'
plink_extract(base, extract_loc, extract_bfile,extract_script,flip_loc)
plink(extract_script)
#write and use the script to exclude the non-rs duplicates
exclude_script = base + '_excludeScript.txt'
plink_exclude(base, extract_loc, exclude_bfile,exclude_script)
plink(exclude_script)
#convert the map files from both results to use only chr:position form
uniform_map(extract_bfile+'.bim')
uniform_map(exclude_bfile+'.bim')
#run concordance check
merge_script = base + '_mergeScript.txt'
merge_out = base + '_DupMerge'
plink_merge(exclude_bfile, extract_bfile,merge_out, merge_script)
plink(merge_script)
#summarize the results of the diff file
summarize_diff(merge_out)
def fix_map(map_loc, repair_loc):
'''
Replaces all SNP names that do not begin with 'rs' with a name using
chr<chromosome#>:<basepair position> format.
Args:
map_loc -- filepath of bim or map file
'''
(basepath, ext) = os.path.splitext(map_loc)
orig_rename = basepath + '~'
new_loc = str(rename_as_necessary(orig_rename, ext)) + ext
shutil.copy(map_loc, new_loc)
repair_dict = pc_toolbox.read_dict(repair_loc)
with open(new_loc, mode='r') as original_map:
with open (map_loc, mode='w') as new_map:
for orig_line in original_map:
orig_list = orig_line.split()
## if orig_list[1] in dup_list:
## if orig_list[1] in repair_dict:
## new_snp = repair_dict[orig_list[1]]
## orig_list[1] = new_snp
## else:
## new_snp = 'chr'+ orig_list[0]+':'+ orig_list[3]
## orig_list[1] = new_snp
if orig_list[1].startswith('rs'):
new_snp = orig_list[1]
elif orig_list[1] in repair_dict:
new_snp = repair_dict[orig_list[1]]
else:
new_snp = 'chr'+ orig_list[0]+':'+ orig_list[3]
## if orig_list[1] in repair_dict:
## new_snp = repair_dict[orig_list[1]]
## else:
## new_snp = 'chr'+ orig_list[0]+':'+ orig_list[3]
orig_list[1] = new_snp
new_map.write('\t'.join(orig_list)+'\n')