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):
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 which_one(region_loc, table_loc, chromosome, index_dict, zero_list):
if region_loc is not None:
## determine_table_titles(table_loc)
## region_list = create_region_list(region_loc, region_col_dict)
region_list = pc_toolbox.create_bp_region_list(region_loc)
## mb_region_list = pc_toolbox.create_region_list(region_loc)
## region_list = list()
## for mb_region in mb_region_list:
## region = RegInfo(chro = mb_region.chro, start = int(float(mb_region.start) * 1e6),
## end = int(float(mb_region.end) *1e6),
## band=mb_region.band, sym=mb_region.sym,
## ID=mb_region.ID,title=mb_region.title)
## region_list.append(region)
print region_list
else:
range_list = macro_ranges(table_loc, chromosome, index_dict)
## print(range_list)
region_list = macro_regions(chromosome, range_list)
## base, ext = os.path.splitext(table_loc)
## noZ_loc = base + '_noZs'+ext
fix_list, zr_list = identify_zerops(region_list, zero_list)
print (
"""
************************************************************************************
Here are the regions which will be drawn:
"""
)
for fix in fix_list:
print fix
print (
"""
The following regions contain zero p-values, and will be adapted:"""
)
for z in zr_list:
print z
print (
"""
************************************************************************************"""
)
sys.stdout.flush()
return fix_list, zr_list
def main(argv):
global altref, altannot
altref = False
altannot = False
yank_loc = "/home/jkb4y/cphgdesk_share/Projects/IMCHIP/Intersect_SNP_list/eurmeta_10172012/RegionYank/eurmeta_yank.tbl"
#region_loc = '/home/jkb4y/work/data/Region_Lists/hg19/T1D_regions_hg19_09202012.txt'
#region_loc = '/home/jkb4y/work/data/Region_Lists/hg19/T1D_regions_hg19_09202012_chr19_20_21_22_23.txt'
region_loc = '/home/jkb4y/work/data/Region_Lists/hg19/achilleas_all_09202012.txt'
#region_loc = '/home/jkb4y/work/data/Region_Lists/hg19/achilleas_chr21_22_23_09202012.txt'
#region_loc = '/home/jkb4y/work/data/Region_Lists/hg19/MHC_zoom.txt'
#assoc_loc = '/home/jkb4y/ubs/work/results/July2012/ModelComparison/AA_cov_12_nosex.assoc.logistic'
assoc_loc = '/home/jkb4y/ubs/work/results/July2012/ModelComparison/AA_cov_12_nosex_SIlz.assoc.logistic'
#outfolder = '/home/jkb4y/ubs/work/results/July2012/RegionGraphs/RefTopUK'
#outfolder = '/home/jkb4y/cphgdesk_share/Projects/IMCHIP/July2012/RegionGraphs/MHC'
#outfolder = '/home/jkb4y/ubs/work/results/July2012/RegionGraphs/RefTopUK_expand_0.2'
#outfolder = '/home/jkb4y/ubs/work/results/July2012/RegionGraphs/SI_Annot_expansion_0.1'
outfolder = '/home/jkb4y/ubs/work/results/July2012/RegionGraphs/Achilleas_regions'
outfolder = '/home/jkb4y/cphgdesk_share/Projects/IMCHIP/July2012/RegionGraphs/Achilleas_regions_expansion_0.1'
#assoc_loc = fix_it.locate_fixed_table(assoc_loc, build="hg19",table_type = "assoc")
regions = pc_toolbox.create_bp_region_list(region_loc)
expansion = int(.1e6)
ref_dict = make_ref_dict(yank_loc)
print ref_dict
for region in regions:
prefix = region.ID + '_AA'
cache_folder = os.path.join(outfolder, 'ld_caches')
if not os.path.exists(cache_folder):
os.makedirs(cache_folder)
ld_cache = os.path.join(cache_folder, 'chr{0}_ld_cache.db'.format(region.chro))
lz_args = ["locuszoom", "--metal", assoc_loc,
'--chr',region.chro, '--start',str(region.start - expansion),
'--end',str(region.end + expansion),'--pvalcol','P','--markercol','EXTREME_LZ',
"--pop","AFR",'--build','hg19','--source','1000G_Nov2010',
'--prefix', prefix,
#'annotCol=annotation','annotPch=24,25,22,23,21',
#'annotOrder=splice,nonsyn,coding,utr,no-annotation',
'--plotonly','--verbose','--no-date','--delim','whitespace','ymax=5',
'--cache',ld_cache]
if altannot:
lz_args.extend([#'prelude=./altannot_prelude.R',
'postlude=/home/jkb4y/h4t1/programs/plink_python/aa_postlude.R',
'refsnpTextColor=transparent',
'annotCol=SI_annotation',
'annotPch=8,21','annotOrder=SI,none'])
else:
lz_args.extend(['annotCol=annotation','annotPch=24,25,22,23,21',
'annotOrder=splice,nonsyn,coding,utr,no-annotation'])
## if refsnp in ['rs75793288'] and not altref:
## lz_args.extend(['--no-ld'])
#if region.title in ['20p13'] and not altref:
# lz_args.extend(['--no-ld'])
if region.ID in ['1p21.2_y','1q23.3_b_y','12p13.33_y'] and not altref:
lz_args.extend(['--no-ld'])
if int(region.chro) > 22:
lz_args.extend(['--no-ld'])
if region.title not in ['6p21.32'] and altref:
refsnp = ref_dict[region.ID][0]
if refsnp in ['rs75793288','rs3216815','rs12416116']:
lz_args.extend(['--no-ld'])
title = "{0}: AA population, refsnp {1}".format(region.ID, refsnp)
lz_args.extend(["--refsnp",refsnp,'title={0}'.format(title)])
else:
lz_args.extend(['title={0}'.format(region.ID)])
if region.ID in ['20p13']:
lz_args.extend(['--no-ld'])
if region.ID in ['6p21.32']:
lz_args.extend(['rfrows=7'])
locuszoom(lz_args, outfolder)
