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achilleas_gene_lz.py
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achilleas_gene_lz.py
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'''
@author Jessica Bonnie
Created Aug 30, 2012
'''
import os
import sys
import pc_toolbox
import subprocess
def locate_prelude(outfolder, gene, cell_type, region_ID):
prelude_gene_name = cell_type + '_' + region_ID + '_'+gene +'_'+ "prelude.R"
prelude_gene_loc = os.path.join(outfolder, prelude_gene_name)
return prelude_gene_loc
def write_prelude(base_prelude_loc, gene, gene_prelude_loc):
prelude = open(gene_prelude_loc, mode = "w")
prelude.write("gene = '"+gene+"'\n")
base = open(base_prelude_loc, mode = "r")
for line in base:
prelude.write(line)
def create_prefix(cell_type, region_ID, gene=None, perm=True, cis=True):
prefix = region_ID + '_' + cell_type
if perm:
prefix = prefix + '_perm'
if gene is not None:
prefix = prefix + '_' + gene
if cis:
prefix = prefix + '_cis'
return prefix
def create_title(cell_type, region, gene=None, perm=True):
title = "{0} Cells: {1}".format(cell_type, region)
## if perm:
## title = title + ' (perm)'
if gene is not None:
title = title + ', {0}'.format(gene)
return title
def read_list(list_loc):
listy = list()
try:
with open(list_loc, mode="r") as filey:
for line in filey:
lstrip = line.strip()
if len(lstrip) > 0:
listy.append(lstrip)
except IOError:
pass
return listy
def locate_postlude(cell_type, postlude_folder):
postlude_loc = os.path.join(postlude_folder,'eqtl_postlude_{0}.R'.format(cell_type))
return postlude_loc
def locuszoom(table_loc, region, graph_title, index_dict, outfolder, refsnp=None, prefix=None, prelude=None, postlude=None):
global population
global out_flag, build, table_type
print('''
NOW ENTERING LOCUSZOOM
''')
print(refsnp)
b_arg = list()
if build == 'hg19':
b_arg.extend(['--build','hg19','--source','1000G_Nov2010','--pop',population])
if build == 'hg18':
b_arg.extend(['--build','hg18','--pop',population])
if region.chro not in ['23','24','25','26']:
b_arg.extend(['--source','1000G_June2010'])
#else:
#b_arg.extend(['--build','hg18','--source','1000G_June2010','--pop',population])#, 'showRecomb=False'])
sys.stdout.flush()
print(index_dict)
markertitle = str(index_dict['snp'])
pvaltitle = str(index_dict['p'])
path_dir = os.path.abspath(os.path.join(os.path.dirname(outfolder),".."))
#path_dir = os.path.dirname(outfolder)
cache_folder = os.path.join(path_dir, '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_cl_args = ['locuszoom','--metal', table_loc,
'--chr',region.chro, '--start',str(region.start),
'--end',str(region.end),'--pvalcol',index_dict['pvalcol'],
'--markercol','EXTREME_LZ',#index_dict['markercol'],
'--delim','whitespace', '--cache',ld_cache,
'--prefix', prefix,
'--plotonly',
'--verbose','--no-date',
'geneFontSize=.6',
'--snpset','None','ymax=4',
'title={0}'.format(graph_title)]
lz_cl_args.extend(b_arg)
if refsnp in ['chr2:204576923','chr2:204732714','chr1:206898330',
'chr12:58218799','chr6:32549808','chr6:32904980',
'chr6:31322486','chr6:32974400']:
lz_cl_args.extend(['--no-ld'])
#refsnp = None
## if refsnp == 'chr21:43823910':
## refsnp = None
if refsnp is not None:
lz_cl_args.extend(['--refsnp',refsnp])
if postlude is not None:
lz_cl_args.extend(['refsnpTextColor=transparent',
'postlude='+postlude])
if prelude is not None:
lz_cl_args.extend(['prelude='+prelude])
##options used in hg19 graphs of ANY type:
if build == 'hg19':
lz_cl_args.extend(['annotCol=annotation','annotPch=24,25,22,23,21',
'annotOrder=splice,nonsyn,coding,utr,no-annotation'])
## if region.ID in no_ld_list:
## lz_cl_args.extend(['--no-ld'])
print lz_cl_args
## lz_cl_args.extend(b_arg)
sys.stdout.flush()
p = subprocess.Popen(lz_cl_args, bufsize = 0, executable=None,stdin=None,
stdout=None,stderr=None, preexec_fn=None,close_fds=False,
shell=False,cwd=None,env=None, universal_newlines=False,
startupinfo=None, creationflags=0)
sys.stdout.flush()
p.wait()
sys.stdout.flush()
def read_single(file_loc):
line1 = True
with open(file_loc)as filey:
for line in filey:
if line1:
return line.strip()
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
if __name__=='__main__':
main(sys.argv[1:])