Exemple #1
0
 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)
Exemple #2
0
 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)
Exemple #3
0
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