Commit c568ba6d by Eric Coissac

Add gap length estimation

parent c89e0cdf
/orgasm.test/
/build/
/ORG.asm-0.00.alpha/
/MANIFEST
/dist/
/__pycache__/
......@@ -88,7 +88,8 @@ def run(config):
fa = path2fasta(asm,cg,path,
identifier="Seq_%d" % c,
back=back,
minlink=config['orgasm']['minlink'])
minlink=config['orgasm']['minlink'],
logger=logger)
print(fa,file=fastaout)
print(" ".join([str(x) for x in path]),file=pathout)
......
......@@ -111,7 +111,8 @@ def run(config):
fa = path2fasta(asm,cg,path,
identifier="Seq_%d" % c,
back=back,
minlink=config['orgasm']['minlink'])
minlink=config['orgasm']['minlink'],
logger=logger)
print(fa,file=fastaout)
print(" ".join([str(x) for x in path]),file=pathout)
......
......@@ -101,7 +101,8 @@ def run(config):
fa = path2fasta(asm,cg,path,
identifier="Seq_%d" % c,
back=back,
minlink=5)
minlink=config['orgasm']['minlink'],
logger=logger)
print(fa, file=fastaout)
print(" ".join([str(x) for x in path]),file=pathout)
......
......@@ -218,22 +218,41 @@ cdef class Index:
trueoverlap = len(probe)
lext = self.getExtensions(probe)
if restrict is not None:
ks = lext.keys()
ks = list(lext.keys())
for k in ks:
rs=lext[k][1]
rk=[]
for r in rs:
rn = self.getPairedRead(r)
if rn:
rn = self.getIds(rn)[0]
if rn in restrict:
rk.append(r)
if r in restrict:
rk.append(r)
else:
rn = self.getPairedRead(r)
if rn:
rn = self.getIds(rn)[0]
if rn in restrict:
rk.append(r)
if rk:
lext[k][1]=rk
else:
del lext[k]
# if restrict is not None:
# ks = lext.keys()
# for k in ks:
# rs=lext[k][1]
# rk=[]
# for r in rs:
# rn = self.getPairedRead(r)
# if rn:
# rn = self.getIds(rn)[0]
# if rn in restrict:
# rk.append(r)
# if rk:
# lext[k][1]=rk
# else:
# del lext[k]
if lext:
for e in lext.itervalues():
......
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