class Gene(object):
def __init__(self, FeatureObject):
""" initializes chromosome, strand, and Ids from FeatureObject so we don't have to call these every time"""
self.features=[]
self.exons = RangeFinder()
self.chr = FeatureObject.chr
self.strand = FeatureObject.strand
self.tId = FeatureObject.tId
self.gId = FeatureObject.gId
self.features.append(FeatureObject)
def add(self, FeatureObject):
"""adds FeatureObject to Gene object"""
self.features.append(FeatureObject)
def makeExons(self):
""" take features list and create a list of exonstarts and stops. This means merging utr and exon features"""
self.exonStarts = []
self.exonEnds= []
keepStart =''
keepStop = 0
for f in self.features:
if (f.start - 1 > keepStop): # if it is a new exon
if(keepStop > 0):
self.exonStarts.append(keepStart)
self.exonEnds.append(keepStop)
keepStart = f.start
keepStop = f.stop
# now add the last
self.exonStarts.append(keepStart)
self.exonEnds.append(keepStop)
def addExons(self): # addExons can not be part of add, since the exons must first be created in makeExons under the Gene class
""" add exons to Gene object """
for i in xrange(len(self.exonStarts)):
self.exons.add(self.chr, self.exonStarts[i], self.exonEnds[i], self, self.strand)
def isIdentical(self, otherGene):
""" this should only be used after getTranscripts, because it assumes chromosome and strand are identical """
if not (len(self.features) == len (otherGene.features)):
return False
for f in xrange(len(self.features)):
if not (self.features[f].descriptor == otherGene.features[f].descriptor and self.features[f].start == otherGene.features[f].start and self.features[f].stop == otherGene.features[f].stop):
return False
return True # if the number of exons is the same and the features are all the same
def justCDS(self):
""" tests if the gene has UTR features. Returns False if it does"""
for f in self.features:
if (f.descriptor == "5UTR" or f.descriptor == "3UTR"):
return False
return True
def cdsIdentical(self, otherGene):
selfFeatures = []
otherFeatures = []
for f in self.features:
if f.descriptor == "CDS":
selfFeatures.append(f)
for f in otherGene.features:
if f.descriptor == "CDS":
otherFeatures.append(f)
# now compare
if not (len(selfFeatures) == len (otherFeatures)):
return False
for f in xrange(len(selfFeatures)):
if not (selfFeatures[f].descriptor == otherFeatures[f].descriptor and selfFeatures[f].start == otherFeatures[f].start and selfFeatures[f].stop == otherFeatures[f].stop):
return False
return True # if the number of exons is the same and the features are all the same
class Gene(object):
def __init__(self, FeatureObject):
""" initializes chromosome, strand, and Ids from FeatureObject so we don't have to call these every time"""
self.features = []
self.exons = RangeFinder()
self.chr = FeatureObject.chr
self.strand = FeatureObject.strand
self.tId = FeatureObject.tId
self.gId = FeatureObject.gId
self.features.append(FeatureObject)
def add(self, FeatureObject):
"""adds FeatureObject to Gene object"""
self.features.append(FeatureObject)
def makeExons(self):
""" take features list and create a list of exonstarts and stops. This means merging utr and exon features"""
self.exonStarts = []
self.exonEnds = []
keepStart = ''
keepStop = 0
for f in self.features:
if (f.start - 1 > keepStop): # if it is a new exon
if (keepStop > 0):
self.exonStarts.append(keepStart)
self.exonEnds.append(keepStop)
keepStart = f.start
keepStop = f.stop
# now add the last
self.exonStarts.append(keepStart)
self.exonEnds.append(keepStop)
def addExons(
self
): # addExons can not be part of add, since the exons must first be created in makeExons under the Gene class
""" add exons to Gene object """
for i in xrange(len(self.exonStarts)):
self.exons.add(self.chr, self.exonStarts[i], self.exonEnds[i],
self, self.strand)
def isIdentical(self, otherGene):
""" this should only be used after getTranscripts, because it assumes chromosome and strand are identical """
if not (len(self.features) == len(otherGene.features)):
return False
for f in xrange(len(self.features)):
if not (self.features[f].descriptor
== otherGene.features[f].descriptor
and self.features[f].start == otherGene.features[f].start
and self.features[f].stop == otherGene.features[f].stop):
return False
return True # if the number of exons is the same and the features are all the same
def justCDS(self):
""" tests if the gene has UTR features. Returns False if it does"""
for f in self.features:
if (f.descriptor == "5UTR" or f.descriptor == "3UTR"):
return False
return True
def cdsIdentical(self, otherGene):
selfFeatures = []
otherFeatures = []
for f in self.features:
if f.descriptor == "CDS":
selfFeatures.append(f)
for f in otherGene.features:
if f.descriptor == "CDS":
otherFeatures.append(f)
# now compare
if not (len(selfFeatures) == len(otherFeatures)):
return False
for f in xrange(len(selfFeatures)):
if not (selfFeatures[f].descriptor == otherFeatures[f].descriptor
and selfFeatures[f].start == otherFeatures[f].start
and selfFeatures[f].stop == otherFeatures[f].stop):
return False
return True # if the number of exons is the same and the features are all the same
