def __init__(self,
start,
phase=None,
strand='+',
pattern=None,
pattern_offset=(0, 0),
pssm_score=None,
gff={}):
"""
Initialization function of Basal SpliceSite logic
Recommended is to use only one of the inheriting classes
@type start: number
@param start: start coord of site (e.g GT) or pattern (e.g. tgtGTcgat)
@type phase: number
@param phase: [0,1,2] or None
@type phase: number
@param phase: [0,1,2] or None, default None
@type strand: string
@param strand: ['+','-'] or None, default '+'
@type pattern: string
@param pattern: splice site pattern sequence (e.g. tgtGTcgat)
@type pattern_offset: tuple
@param pattern_offset: tuple with 2 integers, specifying 5p and 3p
offset towards actual splice site.
e.g. (3,4) for tgtGTcgat
@type pssm_score: float
@param pssm_score: PSSM score of splice site pattern
@type gff: dictionary
@param gff: dictionary with gff data. Possible keys are:
'fref', 'fmethod', 'fstrand', 'fsource', 'gclass', 'gname'
"""
BasicGFF.__init__(self)
self.start = start
self.strand = strand
self.phase = phase
self.end = None # to be filled in inheriting classes
self.pos = None # to be filled in inheriting classes
self.canonical_donor = "GT"
self.canonical_acceptor = "AG"
# pattern, pattern_offset and pssm_score are only truely
# functional in inheriting classes SpliceDonor and SpliceAcceptor
self.pattern = pattern
self.pssm_score = pssm_score
self._offset_5p = pattern_offset[0]
self._offset_3p = pattern_offset[1]
# and some GFF data thingies
self._gff['fscore'] = self.pssm_score
self._gff.update(gff)
# and error-check the data
self.check()
def __init__(self,start,end,pattern="",gff={}):
""" """
BasicGFF.__init__(self)
self._gff.update(gff)
self.start = start
self.end = end
self.pos = self.start
self.pattern = pattern
def __init__(self,pos,gff={}):
""" """
BasicGFF.__init__(self)
self._gff.update(gff)
self.pos = pos
self.start = self.pos
self.end = self.start+3
self.pssm_score = 1.0 # default, dummy value
self.phase = 0
def __init__(self, pos, gff={}):
""" """
BasicGFF.__init__(self)
self._gff.update(gff)
self.pos = pos
self.start = self.pos
self.end = self.start + 3
self.pssm_score = 1.0 # default, dummy value
self.phase = 0
def __init__(self, acceptor, donor, gff={}):
BasicGFF.__init__(self)
self.donor = donor
self.acceptor = acceptor
# init by splice site objects
self._init_by_splicesites()
# update gff attributes
self._gff.update(gff)
def __init__(self,acceptor,donor,gff={}):
BasicGFF.__init__(self)
self.donor = donor
self.acceptor = acceptor
# init by splice site objects
self._init_by_splicesites()
# update gff attributes
self._gff.update(gff)
def __init__(self, pos, gff={}):
""" """
BasicGFF.__init__(self)
self._gff.update(gff)
self.pos = pos
self.start = self.pos - 2
self.end = self.pos
self.pssm_score = 1.0 # default, dummy value
self.phase = None # no phase for this feature!
def __init__(self,start,phase='.',strand='+',pattern=None,
pattern_offset=(0,0),pssm_score=None,gff={}):
"""
Initialization function of Basal TranslationalStartSiteBase logic
Recommended is to use only one of the inheriting classes
@type start: number
@param start: start coord of site (ATG) or pattern (e.g. nncancATGgcnnn)
@type phase: number
@param phase: [0,1,2] or None; only relevant when sequence ISA orf
@type strand: string
@param strand: ['+','-'] or None, default '+'
@type pattern: string
@param pattern: splice site pattern sequence (e.g. nncancATGgcnnn)
@type pattern_offset: tuple
@param pattern_offset: tuple with 2 integers, specifying 5p and 3p
offset towards actual splice site.
e.g. (0,0) for the base class (no PSSM)
e.g. (6,5) for nncancATGgcnnn
e.g. (9,7) for another implementation
@type pssm_score: float
@param pssm_score: PSSM score of splice site pattern
@type gff: dictionary
@param gff: dictionary with gff data. Possible keys are:
'fref', 'fmethod', 'fstrand', 'fsource', 'gclass', 'gname'
"""
# initialize basal BasicGff
BasicGFF.__init__(self)
self.start = start
self.strand = strand
self.phase = phase
self.end = None # to be filled in inheriting classes
self.pos = None # to be filled in inheriting classes
self.tss = None # to be filled in inheriting classes
self.canonical_tss = "ATG"
# pattern, pattern_offset and pssm_score are only truely
# functional in inheriting class TranslationalStartSite,
# not in TranslationalStartSiteATG
self.pattern = pattern
self.pssm_score = pssm_score
self._offset_5p = pattern_offset[0]
self._offset_3p = pattern_offset[1]
# update gff dict
self._gff.update(gff)
# and error-check the data
IsProperPhase(self.phase)
self.check()
def __init__(self, start, end, pattern="", gff={}):
""" """
BasicGFF.__init__(self)
self._gff.update(gff)
self.start = start
self.end = end
self.pos = self.start
self.pattern = pattern
self.length = self.end - self.start
if not self._gff.has_key('fscore'):
self._gff['fscore'] = self.length
def __init__(self,start,end,pattern="",gff={}):
""" """
BasicGFF.__init__(self)
self._gff.update(gff)
self.start = start
self.end = end
self.pos = self.start
self.pattern = pattern
self.length = self.end - self.start
if not self._gff.has_key('fscore'):
self._gff['fscore'] = self.length
def __init__(self,start,phase=None,strand='+',pattern=None,
pattern_offset=(0,0),pssm_score=None,gff={}):
"""
Initialization function of Basal SpliceSite logic
Recommended is to use only one of the inheriting classes
@type start: number
@param start: start coord of site (e.g GT) or pattern (e.g. tgtGTcgat)
@type phase: number
@param phase: [0,1,2] or None
@type phase: number
@param phase: [0,1,2] or None, default None
@type strand: string
@param strand: ['+','-'] or None, default '+'
@type pattern: string
@param pattern: splice site pattern sequence (e.g. tgtGTcgat)
@type pattern_offset: tuple
@param pattern_offset: tuple with 2 integers, specifying 5p and 3p
offset towards actual splice site.
e.g. (3,4) for tgtGTcgat
@type pssm_score: float
@param pssm_score: PSSM score of splice site pattern
@type gff: dictionary
@param gff: dictionary with gff data. Possible keys are:
'fref', 'fmethod', 'fstrand', 'fsource', 'gclass', 'gname'
"""
BasicGFF.__init__(self)
self.start = start
self.strand = strand
self.phase = phase
self.end = None # to be filled in inheriting classes
self.pos = None # to be filled in inheriting classes
self.canonical_donor = "GT"
self.canonical_acceptor = "AG"
# pattern, pattern_offset and pssm_score are only truely
# functional in inheriting classes SpliceDonor and SpliceAcceptor
self.pattern = pattern
self.pssm_score = pssm_score
self._offset_5p = pattern_offset[0]
self._offset_3p = pattern_offset[1]
# and some GFF data thingies
self._gff['fscore'] = self.pssm_score
self._gff.update(gff)
# and error-check the data
self.check()
def __init__(self,start,end,score,tss=None,intron=None,gff={}):
"""
@attention: when spliced by intron:
a) provide Intron object
b) provide end coordinate as if UNSPLICED (length*3nt)
"""
BasicGFF.__init__(self)
self.start = start
self.pos = self.start
self.end = end
self.length = self.end - self.start
self.pssm_score = score
self.tss = tss
self.intron = intron
self._gff.update(gff)
if not self._gff.has_key('fmethod'):
self._gff['fmethod'] = 'predSignalPeptide'
def __init__(self, start, end, score, tss=None, intron=None, gff={}):
"""
@attention: when spliced by intron:
a) provide Intron object
b) provide end coordinate as if UNSPLICED (length*3nt)
"""
BasicGFF.__init__(self)
self.start = start
self.pos = self.start
self.end = end
self.length = self.end - self.start
self.pssm_score = score
self.tss = tss
self.intron = intron
self._gff.update(gff)
if not self._gff.has_key('fmethod'):
self._gff['fmethod'] = 'predSignalPeptide'
def __init__(self,donor,acceptor,shared_nts,gff={}):
# input validation
IsDonor(donor)
IsAcceptor(acceptor)
# initialization
BasicGFF.__init__(self)
self._gff.update(gff)
self.donor = donor
self.acceptor = acceptor
# init by splice site objects
self._init_by_splicesites()
# forward compatibility with IntronConnectingOrfs
self.nt_from_stop_donor = None
self.nt_from_stop_acceptor = None
# set shared nt/aa data
self.shared_nts = shared_nts
self.shared_aa = ""
if self.shared_nts:
self.shared_aa = dna2prot.dna2protein(self.shared_nts)
def togff(self, gff={}):
""" Overwrites BasicGFF.togff() functionality """
if not self._gff.has_key('gname'):
self._gff['gname'] = "%s_%s" % (self.start, self.end)
if not self._gff.has_key('gclass'):
self._gff['gclass'] = self.__class__.__name__
# call basal BasicGFF.togff() function
gfflines = [BasicGFF.togff(self)]
# gff default for TSS/ATG
tss_gff = {
'fref': self._gff['fref'],
'gname': self._gff['gname'],
'gclass': self._gff['gclass'],
}
# if SignalPeptide is spliced -> make 2 tracks!
if self.intron:
# calculate lengths
signalp_length = self.end - self.start
signalp_5p_length = self.intron.donor.pos - self.start
signalp_3p_length = signalp_length - signalp_5p_length
# create SignalP 5p and 3p tracks
exon5p = list(gfflines[0])
exon3p = list(gfflines[0])
exon5p[4] = self.intron.donor.pos
exon3p[3] = self.intron.acceptor.pos + 1
exon3p[4] = self.intron.acceptor.pos + signalp_3p_length
if self.tss: exon5p[3] += 3
gfflines = [tuple(exon5p), tuple(exon3p)]
if self.tss: gfflines.insert(0, self.tss.togff(gff=tss_gff))
elif self.tss:
# correct SignalPeptide start coord to 1nt after the ATG codon
track = list(gfflines[0])
track[3] += 3
gfflines = [tuple(track)]
gfflines.insert(0, self.tss.togff(gff=tss_gff))
else:
pass
# return list with gff tuples
return gfflines
def togff(self,gff={}):
""" Overwrites BasicGFF.togff() functionality """
if not self._gff.has_key('gname'):
self._gff['gname'] = "%s_%s" % (self.start,self.end)
if not self._gff.has_key('gclass'):
self._gff['gclass'] = self.__class__.__name__
# call basal BasicGFF.togff() function
gfflines = [ BasicGFF.togff(self) ]
# gff default for TSS/ATG
tss_gff = { 'fref' : self._gff['fref'],
'gname' : self._gff['gname'],
'gclass': self._gff['gclass'], }
# if SignalPeptide is spliced -> make 2 tracks!
if self.intron:
# calculate lengths
signalp_length = self.end-self.start
signalp_5p_length = self.intron.donor.pos - self.start
signalp_3p_length = signalp_length - signalp_5p_length
# create SignalP 5p and 3p tracks
exon5p = list(gfflines[0])
exon3p = list(gfflines[0])
exon5p[4] = self.intron.donor.pos
exon3p[3] = self.intron.acceptor.pos + 1
exon3p[4] = self.intron.acceptor.pos + signalp_3p_length
if self.tss: exon5p[3]+=3
gfflines = [ tuple(exon5p), tuple(exon3p) ]
if self.tss: gfflines.insert(0, self.tss.togff(gff=tss_gff) )
elif self.tss:
# correct SignalPeptide start coord to 1nt after the ATG codon
track = list(gfflines[0])
track[3]+=3
gfflines = [ tuple(track) ]
gfflines.insert(0, self.tss.togff(gff=tss_gff) )
else:
pass
# return list with gff tuples
return gfflines
def togff(self,gff={}):
""" Overwrites BasicGFF.togff() """
if not gff.has_key('gname') and not self._gff.has_key('gname'):
gff['gname'] = "%s-%s" % (self.start, self.end)
return BasicGFF.togff(self,gff=gff)
def togff(self, gff={}):
""" Overwrites BasicGFF.togff() """
if not gff.has_key('gname'): gff['gname'] = str(self.pos)
return BasicGFF.togff(self, gff=gff)
def togff(self,gff={}):
""" Overwrites BasicGFF.togff() """
if not gff.has_key('gname'): gff['gname'] = str(self.pos)
return BasicGFF.togff(self,gff=gff)
