def main(argv):
out_folder = '/home/jkb4y/cphgdesk_share/Yan/UBASH3A'
eurmeta_out = os.path.join(out_folder, 'eurmeta_UBASH3A_122112.txt')
eurmeta_in = '/home/jkb4y/work/data/2012Feb1/eurmeta_Oct2012/eurmeta_lz_hg19_intersect.tbl'
eurmeta_dict, thing = pc_toolbox.create_index_dict(eurmeta_in, 'meta')
family_out = os.path.join(out_folder, 'eurgdtscan_UBASH3A_122112.txt')
family_in = '/home/jkb4y/work/data/2012Feb1/Family_Nov2012/eurgdtscan_lz_hg19_intersect.txt'
family_dict, thing = pc_toolbox.create_index_dict(family_in, 'family')
region_loc ='/home/jkb4y/work/data/Region_Lists/hg19/T1D_regions_hg19_09202012.txt'
region_list = pc_toolbox.create_bp_region_list(region_loc)
for region in region_list:
if region.ID == '21q22.3_a':
print region
filter_by_region(region, eurmeta_in,eurmeta_out, eurmeta_dict)
filter_by_region(region, family_in, family_out, family_dict)
def main():
build = 'hg19'
table_loc = '/home/jkb4y/ubs/work/results/July2012/Logistic_pc8/AA_8.assoc.logistic'
annot_dict = pc_toolbox.create_annot_dict(build,'LOG')
base, ext = os.path.splitext(table_loc)
base2, ext2 = os.path.splitext(base)
new_loc = base2 + '_lz'+ext2+ext
index_dict, line = pc_toolbox.create_index_dict(table_loc,'assoc')
pc_toolbox.give_table_annotation(table_loc,new_loc,index_dict,annot_dict)
def main(argv):
global table_type, region_loc, cell_type, table_loc, perm, build, population
build = 'hg19'
cis = True
population = 'EUR'
region_loc = '/home/jkb4y/work/data/Region_Lists/hg19/T1D_regions_hg19_05242012_extra.5MB.txt'
prelude_base = '/home/jkb4y/h4t1/programs/achilleas_plots/gene_prelude.R'
cell_type = "CD8"
postlude_folder= '/home/jkb4y/h4t1/programs/achilleas_plots/postludes'
tablefold = '/home/jkb4y/ubs/work/data/Achilleas/cis-eQTL/'
table_loc = os.path.join(tablefold,'{0}_cis_eqtls_permwBP_JB_LZ.txt'.format(cell_type))
table_type = 'perm'
index_dict, thing = pc_toolbox.create_index_dict(table_loc, table_type)
perm = True
achilleas_cell_results = "/home/jkb4y/ubs/work/results/Achilleas/hg19/{0}".format(cell_type)
genefolder = os.path.join(achilleas_cell_results,'GeneLists')
base_outfolder = os.path.join(achilleas_cell_results, 'PerGene')
if not os.path.exists(base_outfolder):
os.makedirs(base_outfolder)
regions = pc_toolbox.create_bp_region_list(region_loc)
for region in regions:
ID = region.ID
band = region.band
outfolder = os.path.join(base_outfolder, ID)
if not os.path.exists(outfolder):
os.makedirs(outfolder)
os.chdir(outfolder)
region_genefolder = os.path.join(genefolder, ID)
genelist = os.path.join(region_genefolder, ID+'_genes.list')
genes = read_list(genelist)
for gene in genes:
## outfolder = os.path.join(base_outfolder, region.ID)
## if not os.path.exists(outfolder):
## os.makedirs(outfolder)
refsnp_loc = os.path.join(region_genefolder, gene + '_ref.txt')
refsnp = read_single(refsnp_loc)
gene_prelude = locate_prelude(outfolder, gene, cell_type, ID)
cell_postlude = None#locate_postlude(cell_type, postlude_folder)
write_prelude(prelude_base, gene, gene_prelude)
graph_title = create_title(cell_type, ID, gene)
prefix = create_prefix(cell_type, band, gene, perm, cis)
## os.chdir(outfolder)
locuszoom(table_loc, region,graph_title, index_dict, outfolder,
refsnp, prefix, gene_prelude, cell_postlude)
os.chdir(base_outfolder)
try:
os.rmdir(outfolder)
except OSError:
pass
def main(argv):
global out_base, freq_loc, table_loc, bfile, table_type
global covar_loc, annot, weight_min, build, region_loc, pop, aa_freq_loc
cl_arguments(argv)
zlist = list()
index_dict, input_title_line = pc_toolbox.create_index_dict(table_loc, table_type)
region_list = pc_toolbox.create_region_list(region_loc)
annot_dict = create_annot_dict(build, 'LOG')
out_file = out_base + '_yank.tbl'
output_title_line = create_output_title_line(table_type, input_title_line)
with open(out_file, mode="w") as out_text:
## title_line = '\t'.join(META_TITLE_LIST)
out_text.write(output_title_line +'\n')
for region in region_list:
print zlist
sig_line, zlist, multicounter = read_table(table_loc, index_dict, region, weight_min, table_type, annot_dict, zlist)
info = document_result(sig_line, region, index_dict, table_type,annot_dict, multicounter)
if table_type == 'assoc':
if pop == 'AA':
for item in AA_ASSOC_ORDER_LIST:
out_text.write(str(info[item]) + '\t')
if pop == 'UK':
for item in ASSOC_ORDER_LIST:
out_text.write(str(info[item]) + '\t')
## if table_type in ['perm']:
## out_list = sig_line.strip().split()
## out_list.append(info['note'])
## out_list.append(info['band'])
## out_list.append(info['ID'])
## out_text.write('\t'.join(out_list))
if table_type in ['meta','family']:
for item in META_ORDER_LIST:
out_text.write(str(info[item]) + '\t')
if table_type =='perm':
for item in PERM_ORDER_LIST:
out_text.write(str(info[item]) + '\t')
out_text.write('\n')
if table_type in ['meta','family']:
repair_meta_for_lz(zlist, table_loc, index_dict, weight_min)