def testNumberDef(self):
NumDef = Enumeration("NumDef",
(("neg", None, None, -2),
("zero", None, None, 0),
("pos", None, None, 2),
("big", None, None, 3)))
values = [(str(v), int(v)) for v in NumDef.values]
self.failUnlessEqual(values, [('neg', -2), ('zero', 0), ('pos', 2), ('big', 3)])
self.failUnlessEqual(NumDef.getByNumValue(2), NumDef.pos)
def testBitSetValues(self):
Stat = Enumeration("Stat",
["okay",
("notConserved","notConserved", ("no_alignment",)),
"bad_3_splice", "bad_5_splice"],
bitSetValues=True)
self.failUnlessEqual(Stat.okay, 1)
self.failUnlessEqual(Stat.notConserved, 2)
self.failUnlessEqual(Stat.bad_5_splice, 8)
self.failUnlessEqual(int(Stat.bad_5_splice), 8)
self.failUnlessEqual(Stat.maxNumValue, 8)
vals = Stat.getValues(9)
self.failUnlessEqual(len(vals), 2)
self.failUnless(vals[0] is Stat.okay)
self.failUnless(vals[1] is Stat.bad_5_splice)
def testAliases(self):
Name = Enumeration("Name", ["Fred", ("Rick", "Richard", ("Dick", "HeyYou")), ("Bill", "Willian")])
self.failUnlessEqual(Name.lookup("Richard"), Name.Rick)
self.failUnless(Name.lookup("Richard") is Name.Rick)
self.failUnlessEqual(Name.lookup("Dick"), Name.Rick)
self.failUnless(Name.lookup("Dick") is Name.Rick)
self.failUnless(Name.lookup("Rick") == Name.Rick)
self.failUnless(Name.lookup("HeyYou") == Name.Rick)
self.failUnless(Name.lookup("Fred") == Name.Fred)
self.failUnless(Name.lookup("Fred") is Name.Fred)
self.failUnless(str(Name.Rick) == "Richard")
def testAliasesBug1(self):
"forgot comma in one-element tuple"
try:
Stat = Enumeration("Stat",
["okay",
("notConserved","notConserved", ("no_alignment")),
"bad_3_splice", "bad_5_splice"])
if __debug__:
self.fail("should have raised exception")
except TypeError:
pass
# Copyright 2006-2012 Mark Diekhans
import copy
from pycbio.sys import fileOps, dbOps
from pycbio.hgdata.AutoSql import intArraySplit, intArrayJoin
from pycbio.sys.Enumeration import Enumeration
CdsStat = Enumeration(
"CdsStat",
[
("none", "none"), # No CDS (non-coding)
("unknown", "unk"), # CDS is unknown (coding, but not known)
("incomplete", "incmpl"), # CDS is not complete at this end
("complete", "cmpl")
]) # CDS is complete at this end
genePredColumns = ("name", "chrom", "strand", "txStart", "txEnd", "cdsStart",
"cdsEnd", "exonCount", "exonStarts", "exonEnds", "score",
"name2", "cdsStartStat", "cdsEndStat", "exonFrames")
genePredExtColumns = ("name", "chrom", "strand", "txStart", "txEnd",
"cdsStart", "cdsEnd", "exonCount", "exonStarts",
"exonEnds")
class Range(object):
"start and end coordinates"
__slots__ = ("start", "end")
def __init__(self, start, end):
self.start = start
self.end = end
def __getColors(self):
return Enumeration("Colors", ["red", "green", "blue"])
class CycleException(ExRunException):
"Exception indicating a cycle has occured"
def __init__(self, cycle):
desc = []
for n in cycle:
desc.append(" " + str(n) + " ->")
ExRunException.__init__(self, "cycle detected:\n" + "\n".join(desc))
# state of a Production and valid transitions
# - bad - doesn't exist and no rule to create
# - failed - rule to create failed
# - blocked - blocked because some requirement can't be built
ProdState = Enumeration(
"ProdState",
("unknown", "outdated", "current", "failed", "blocked", "bad"))
_prodStateTbl = {}
_prodStateTbl[ProdState.unknown] = frozenset(
[ProdState.outdated, ProdState.current, ProdState.blocked, ProdState.bad])
_prodStateTbl[ProdState.outdated] = frozenset(
[ProdState.current, ProdState.blocked, ProdState.failed, ProdState.bad])
_prodStateTbl[ProdState.current] = _emptySet
_prodStateTbl[ProdState.failed] = _emptySet
_prodStateTbl[ProdState.blocked] = _emptySet
_prodStateTbl[ProdState.bad] = _emptySet
# state of a Rule and valid transitions
# - failed - rule failed
# - blocked - blocked because some requirement can't be built
RuleState = Enumeration(
else:
raise ValueError("invalid nmd column value: \"" + val + "\"")
def nmdFmt(val):
"format value of the NMD column (ok or nmd)"
if val:
return "ok"
else:
return "nmd"
nmdType = (nmdParse, nmdFmt)
# frame status
Frame = Enumeration("FrameStat",
["ok", "bad", "mismatch", "discontig", "noCDS"])
#acc chr chrStart chrEnd strand stat frame start stop orfStop cdsGap cdsMult3Gap utrGap cdsUnknownSplice utrUnknownSplice cdsNonCanonSplice utrNonCanonSplice numExons numCds numUtr5 numUtr3 numCdsIntrons numUtrIntrons nmd causes
typeMap = {
"acc": intern,
"chrStart": int,
"chrEnd": int,
"strand": intern,
"stat": statType,
"frame": Frame,
"start": startStopType,
"stop": startStopType,
"orfStop": int,
"cdsGap": int,
"cdsMult3Gap": int,
"utrGap": int,
