def setUp(self):
self.cns_filename = "data/rice_v6_sorghum_v1/rice_v6_sorghum_v1.cns.txt"
self.pairsfile = "data/rice_v6_sorghum_v1/rice_v6_sorghum_v1.pairs.txt"
self.qbed = Bed("data/rice_v6_sorghum_v1/rice_v6.bed") ;self.qbed.fill_dict()
self.sbed = Bed("data/rice_v6_sorghum_v1/sorghum_v1.bed") ;self.sbed.fill_dict()
self.cns_dict, self.evalue_dict = get_cns_dict(self.cns_filename)
self.qpair_map, self.spair_map = make_pair_maps(self.pairsfile, "pair", self.qbed, self.sbed)
def setUp(self):
self.cns_filename = "data/rice_v6_sorghum_v1/rice_v6_sorghum_v1.cns.txt"
self.pairsfile = "data/rice_v6_sorghum_v1/rice_v6_sorghum_v1.pairs.txt"
self.qbed = Bed("data/rice_v6_sorghum_v1/rice_v6.bed")
self.qbed.fill_dict()
self.sbed = Bed("data/rice_v6_sorghum_v1/sorghum_v1.bed")
self.sbed.fill_dict()
self.cns_dict, self.evalue_dict = get_cns_dict(self.cns_filename)
self.qpair_map, self.spair_map = make_pair_maps(
self.pairsfile, "pair", self.qbed, self.sbed)
def main(cnsfile, qbed_file, sbed_file, qorg, sorg, padding):
qbed = Bed(qbed_file); qbed.fill_dict()
sbed = Bed(sbed_file); sbed.fill_dict()
cnsdict = get_cns_dict(cnsfile)
out = sys.stdout
fmt = "%(qaccn)s,%(qchr)s,%(qstart)i,%(qstop)i,%(qstrand)s," + \
"%(saccn)s,%(schr)s,%(sstart)i,%(sstop)i,%(sstrand)s,%(link)s"
print >>out, "#" + fmt.replace("%(","").replace(")s","").replace(")i","")
for cns, qfeat, sfeat in assign(cnsdict, qbed, sbed):
d = cns_fmt_dict(cns, qfeat, sfeat)
d['link'] = assign_url(cns.sstart, cns.schr, cns.qstart, cns.qchr, sorg, qorg, padding)
print >>out, fmt % d