def loadChains(path):
"name says it."
try:
EPO = epo.Chain._parse_file(path, True)
except:
sys.stderr.write(
"ERROR: {} does not appear to be a valid chain file. Exiting!\n".
format(path))
exit(1)
## convert coordinates w.r.t the forward strand (into slices)
## compute cummulative intervals
for i in range(len(EPO)):
ch, S, T, Q = EPO[i]
if ch.tStrand == '-':
ch = ch._replace(tEnd=ch.tSize - ch.tStart,
tStart=ch.tSize - ch.tEnd)
if ch.qStrand == '-':
ch = ch._replace(qEnd=ch.qSize - ch.qStart,
qStart=ch.qSize - ch.qEnd)
EPO[i] = (ch, epo.cummulative_intervals(S, T),
epo.cummulative_intervals(S, Q))
##now each element of epo is (chain_header, target_intervals, query_intervals)
assert all(t[0].tStrand == '+'
for t in EPO), "all target strands should be +"
return EPO
def loadChains(path):
"name says it."
EPO = epo.Chain._parse_file(path, True)
## convert coordinates w.r.t the forward strand (into slices)
## compute cummulative intervals
for i in range(len(EPO)):
ch, S, T, Q = EPO[i]
if ch.tStrand == '-':
ch = ch._replace(tEnd=ch.tSize - ch.tStart,
tStart=ch.tSize - ch.tEnd)
if ch.qStrand == '-':
ch = ch._replace(qEnd=ch.qSize - ch.qStart,
qStart=ch.qSize - ch.qEnd)
EPO[i] = (ch, epo.cummulative_intervals(S, T),
epo.cummulative_intervals(S, Q))
##now each element of epo is (chain_header, target_intervals, query_intervals)
assert all(map(lambda t: t[0].tStrand == '+',
EPO)), "all target strands should be +"
return EPO
def loadChains(path):
"name says it."
EPO = epo.Chain._parse_file(path, True)
## convert coordinates w.r.t the forward strand (into slices)
## compute cummulative intervals
for i in range( len(EPO) ):
ch, S, T, Q = EPO[i]
if ch.tStrand == '-':
ch = ch._replace(tEnd = ch.tSize - ch.tStart,
tStart = ch.tSize - ch.tEnd)
if ch.qStrand == '-':
ch = ch._replace(qEnd = ch.qSize - ch.qStart,
qStart = ch.qSize - ch.qEnd)
EPO[i] = (ch,
epo.cummulative_intervals(S, T),
epo.cummulative_intervals(S, Q)
)
##now each element of epo is (chain_header, target_intervals, query_intervals)
assert all( map(lambda t: t[0].tStrand == '+', EPO) ), "all target strands should be +"
return EPO