def parse_folder(folder, db, gencode_file):
contents = os.listdir(folder)
logging.info("Processing gencode file")
class GencodeCallback(object):
def __init__(self, contents):
self.contents = {gene:True for gene in contents}
self.genes = {}
def __call__(self, gencode):
if gencode.name in self.contents:
self.genes[gencode.name] = gencode.ensemble_version
callback = GencodeCallback(contents)
GencodeFile.parse_gencode_file(gencode_file, callback)
gene_names = callback.genes
logging.info("processing folder")
genes = {}
for content in contents:
if not content in gene_names:
logging.log(9, "Gene %s not in gencode", content)
continue
sub_path = TWASFormat.build_subpaths(folder, content)
map_path = sub_path + ".wgt.map"
snps = TWASFormat.load_map(map_path)
weights = TWASFormat.build_weights(sub_path)
rows = []
gene_id = gene_names[content]
for i, snp in enumerate(snps):
w = weights[i]
row = (snp[TWASFormat.MTF.snp], gene_id, content, w, snp[TWASFormat.MTF.a1], snp[TWASFormat.MTF.a2] )
rows.append(row)
genes[content] = rows
Utilities.insert_entries(db, genes)
def build_twas_gene_folder(weight_folder, working_folder, gwas_results, content):
print "yo"
sub_path = TWASFormat.build_subpaths(weight_folder, content)
map_path = sub_path + ".wgt.map"
snps = TWASFormat.load_map(map_path)
cor_path = sub_path + ".wgt.cor"
cors = TWASFormat.load_cor(cor_path)
ld_path = sub_path + ".wgt.ld"
zscores = []
for i,snp in enumerate(snps):
zscore = 0
rsid = snp[TWASFormat.MTF.snp]
a1 = snp[TWASFormat.MTF.a1]
a2 = snp[TWASFormat.MTF.a2]
if rsid in gwas_results:
result = gwas_results[rsid]
if result[GTF.a1] == a1 and result[GTF.a2] == a2:
zscore = result[GTF.z]
elif result[GTF.a1] == a2 and result[GTF.a2] == a1:
zscore = -1.0*result[GTF.z]
else:
cors[i] = 0
else:
cors[i] = 0
if zscore == 0:
continue
zscore = str(zscore)
pos = snp[TWASFormat.MTF.pos]
zscore_row = (rsid, pos, a1, a2, zscore)
zscores.append(zscore_row)
working_path = os.path.join(working_folder, content)
os.makedirs(working_path)
sub_working_path = os.path.join(working_path, content)
working_cor = sub_working_path +".wgt.cor"
with open(working_cor, "w") as file:
for cor in cors:
line = str(cor)+"\n"
file.write(line)
working_ld_path = sub_working_path + ".wgt.ld"
shutil.copy(ld_path, working_ld_path)
working_map_path = sub_working_path + ".wgt.map"
shutil.copy(map_path, working_map_path)
zscore_path = sub_working_path + ".zscore"
with open(zscore_path, "w") as file:
file.write("SNP_ID SNP_Pos Ref_Allele Alt_Allele Z-score\n")
for z in zscores:
line = " ".join(z) + "\n"
file.write(line)
return working_path
