def get_cnr_psl(rcomp_psl_file):
"""
return dictionary where
cnr_psl[graph][node]
is a list of read aligned to that node
c - comp
n - node
r - read
"""
cnr_psl = defaultdict(lambda : defaultdict(list))
for psl in read_psl(rcomp_psl_file):
comp, node = psl.tName.split(":")
cnr_psl[comp][node].append(psl)
return cnr_psl
def get_rcc_psl(rcont_psl_file):
"""
return a defaultdict(lambda : defaultdict(list))
where
rcc_psl[read][graph]
is a list of alignments to contigs in that graph
r - read
1st c - comp
2nd c - contig
"""
rcc_psl = defaultdict(lambda : defaultdict(list))
for psl in read_psl(rcont_psl_file):
rcc_psl[psl.qName][psl.tName.split("_")[0]].append(psl)
return rcc_psl