def read_tfgenes(tgfile):
"""Read tf-gene pairs"""
logger.info('Reading TF-gene pairs in %s ...', tgfile)
reader = TsvReader(tgfile, cnames=False)
ret = {} # gene => tf
for row in reader:
ret.setdefault(row[1], set()).add(row[0])
reader.close()
return ret
# get gene, snp pairs
"""
chr1 12463073 12463074 AADACL4 0 + chr1 12463073 12463074 chr1_12463073_rs7547740_A_G 0 +
chr1 12480504 12480505 AADACL4 0 + chr1 12480504 12480505 chr1_12480504_rs6660365_T_C 0 +
chr1 12496021 12496022 AADACL4 0 + chr1 12496021 12496022 chr1_12496021_rs6541023_T_C 0 +
"""
mutgenes = defaultdict(lambda: [])
intereader = TsvReader(interfile)
genes = set()
for r in intereader:
if not r[3] in genetfs:
continue
mutgenes[r[9]].append(r[3])
genes.add(r[3])
intereader.close()
# shrink the sets
genetfs = {g: genetfs[g] for g in genes}
tfs = list({tf for gtfs in genetfs.values() for tf in gtfs})
# nothing, write empty files
if not mutgenes or not genes:
open(outdata, 'w').close()
open(outgroup, 'w').close()
open(outcase, 'w').close()
exit(0)
# save the data file
# expfile
"""
infile = {{i.infile | quote}}
snpfile = {{o.snpfile | quote}}
genefile = {{o.genefile | quote}}
snppergene = {{args.snppergene | repr}}
nchr = {{args.nchr | repr}}
seed = {{args.seed | repr}}
# distances between genes
dist = {{args.dist | repr}}
random.seed(seed)
reader = TsvReader(infile, cnames=False)
allsnps = set(reader.dump(0))
reader.rewind()
allgenes = set(reader.dump(1))
reader.close()
# assign a probability to each snp
nsnps = len(allsnps)
ngenes = len(allgenes)
snp_probs = dict(zip(allsnps, random.choices(range(ngenes * snppergene),
k=nsnps)))
genebed = TsvWriter(genefile)
snpbed = TsvWriter(snpfile)
geneperchr = math.ceil(float(ngenes) / float(nchr))
for i, gene in enumerate(allgenes):
chrname = 'chr' + str(int(i % nchr) + 1)
start = (int(i / nchr) + 1) * dist
end = start + 1