def merge(b1, b2):
geneIds = set(typeOps.mkiter(b1.geneIds)) | set(typeOps.mkiter(b2.geneIds))
b = GeneBoundsBed.create(b1.chrom,
min(b1.start, b2.start),
max(b1.end, b2.end),
b1.name,
strand=b1.strand,
geneSym=b1.geneSym,
hgncId=b1.hgncId,
geneIds=list(geneIds),
geneType=b1.geneType)
return b
def linkRequires(self, requires):
"""link in productions required by this node. Can be single nodes, or
lists or sets of nodes, reverse links are created"""
for r in typeOps.mkiter(requires):
if not isinstance(r, Production):
raise ExRunException("Rule " + str(self) + " requires can only be linked to a Production, attempt to link to: " + str(r))
r.linkRequiredBy(self)
def linkProduces(self, produces):
"""link in productions produced by this node. Can be single nodes, or
lists or sets of nodes, reverse links are created"""
for p in typeOps.mkiter(produces):
if not isinstance(p, Production):
raise ExRunException("Rule " + str(self) + " produces can only be linked to a Production, attempt to link to: " + str(p))
p.linkProducedBy(self)
def __specsToStateTbl(self, notOkSpecs):
"convert spec lists no tables"
notOkStates = {}
for spec in notOkSpecs:
for n in typeOps.mkiter(spec[0]):
notOkStates[n] = spec[1]
return notOkStates
def linkRequires(self, requires):
"""link in productions or targets required by this node. Can be single nodes,
or lists or sets of nodes"""
for r in typeOps.mkiter(requires):
if not (isinstance(r, Production) or isinstance(r, Target)):
raise ExRunException("Target " + str(self) + " requires can only be linked to a Production or a Target, attempt to link to: " + str(r))
self.requires.add(r)
def __addCmdStdio(self, fspecs, specSet, exclude=None):
"add None, a single or a list of file specs as requires or produces links"
for fspec in typeOps.mkiter(fspecs):
if (isinstance(fspec, FileIn) or isinstance(fspec, FileOut)):
fspec = fspec.file # get File object for reference
if (isinstance(fspec, File) and ((exclude == None) or (fspec not in exclude))):
specSet.add(fspec)
def __specsToStateTbl(self, notOkSpecs):
"convert spec lists no tables"
notOkStates = {}
for spec in notOkSpecs:
for n in typeOps.mkiter(spec[0]):
notOkStates[n] = spec[1]
return notOkStates
def __addCmdStdio(self, fspecs, specSet, exclude=None):
"add None, a single or a list of file specs as requires or produces links"
for fspec in typeOps.mkiter(fspecs):
if (isinstance(fspec, FileIn) or isinstance(fspec, FileOut)):
fspec = fspec.file # get File object for reference
if (isinstance(fspec, File)
and ((exclude == None) or (fspec not in exclude))):
specSet.add(fspec)
def linkRequiredBy(self, requiredBy):
"""link to rules that require production, can be single rule, lists or
sets of rules, reverse links are created"""
for r in typeOps.mkiter(requiredBy):
if not isinstance(r, Rule):
raise ExRunException("Production " + str(self) + " requiredBy can only be linked to a Rule, attempt to link to: " + str(r))
self.requiredBy.add(r)
r.requires.add(self);
def getFiles(self, paths):
"""like getFile(), only path can be a single path, or a list of paths,
or a File object, or list of File objects. Returns a list of File
objects"""
files = []
for p in typeOps.mkiter(paths):
files.append(self.getFile(p))
return files
def getFiles(self, paths):
"""like getFile(), only path can be a single path, or a list of paths,
or a File object, or list of File objects. Returns a list of File
objects"""
files = []
for p in typeOps.mkiter(paths):
files.append(self.getFile(p))
return files
def linkRequires(self, requires):
"""link in productions or targets required by this node. Can be single nodes,
or lists or sets of nodes"""
for r in typeOps.mkiter(requires):
if not (isinstance(r, Production) or isinstance(r, Target)):
raise ExRunException(
"Target " + str(self) +
" requires can only be linked to a Production or a Target, attempt to link to: "
+ str(r))
self.requires.add(r)
def linkRequires(self, requires):
"""link in productions required by this node. Can be single nodes, or
lists or sets of nodes, reverse links are created"""
for r in typeOps.mkiter(requires):
if not isinstance(r, Production):
raise ExRunException(
"Rule " + str(self) +
" requires can only be linked to a Production, attempt to link to: "
+ str(r))
r.linkRequiredBy(self)
def linkProduces(self, produces):
"""link in productions produced by this node. Can be single nodes, or
lists or sets of nodes, reverse links are created"""
for p in typeOps.mkiter(produces):
if not isinstance(p, Production):
raise ExRunException(
"Rule " + str(self) +
" produces can only be linked to a Production, attempt to link to: "
+ str(p))
p.linkProducedBy(self)
def __getRunTargets(self, targets=None):
"get list of targets to run, return the default if none specified"
ts = []
for t in typeOps.mkiter(targets):
if isinstance(t, Target):
ts.append(t)
else:
ts.append(self.getTarget(t))
if len(ts) == 0:
ts.append(self.getTarget(self.defaultTargetName))
return ts
def linkRequiredBy(self, requiredBy):
"""link to rules that require production, can be single rule, lists or
sets of rules, reverse links are created"""
for r in typeOps.mkiter(requiredBy):
if not isinstance(r, Rule):
raise ExRunException(
"Production " + str(self) +
" requiredBy can only be linked to a Rule, attempt to link to: "
+ str(r))
self.requiredBy.add(r)
r.requires.add(self)
def __getRunTargets(self, targets=None):
"get list of targets to run, return the default if none specified"
ts = []
for t in typeOps.mkiter(targets):
if isinstance(t, Target):
ts.append(t)
else:
ts.append(self.getTarget(t))
if len(ts) == 0:
ts.append(self.getTarget(self.defaultTargetName))
return ts
def geneBoundsBigBedRead(bigBedFh, chrom, start, end):
if start >= end:
return iter(())
for entry in typeOps.mkiter(bigBedFh.entries(chrom, start, end)):
data = entry[2].split('\t')
yield GeneBoundsBed.create(chrom,
entry[0],
entry[1],
data[0],
score=data[1],
strand=data[2],
thickStart=data[3],
thickEnd=data[4],
itemRgb=data[5],
geneSym=data[6],
hgncId=data[7],
geneIds=data[8],
geneType=data[9])
