def find_stopless3n_introns_on_orf(orfObj,
has_branchpoint=False,
has_polypyrimidine=False,
order_by='length',
**kwargs):
"""
Find potential stopless3n introns on this orf
@attention: **kwargs can contain other (here) unnecessarily arguments
@attention: **kwargs are required in the merge_orfs_with_intron() function
@type orfObj: Orf object
@param orfObj: Orf object which is scanned for stopless3n introns
@rtype: list
@return: list with introns
"""
# input validation
IsOrf(orfObj)
# edit **kwargs dictionary for some forced attributes
_update_kwargs(kwargs, KWARGS_STOPLESS_3N_INTRONS)
# find stopless3nintrons
stopless3nintrons = merge_orfs_with_intron(orfObj, orfObj, **kwargs)
# filter for presence of branchpoint / polypyrimidine tracks
if has_branchpoint or has_polypyrimidine:
filtered = []
for intron in stopless3nintrons:
intron.assign_bp_and_ppts()
if has_branchpoint and not intron.branchpoint:
continue
intron_bp_dist = intron.get_branchpoint_nt_distance()
if has_branchpoint and intron_bp_dist == None:
continue
intron_bp_optimality = min([
abs(offset - intron_bp_dist)
for offset in OPTIMAL_BRACNHPOINT_TO_ACCEPTOR_DISTANCE
])
if has_branchpoint and intron_bp_optimality > MAXIMAL_OPTIMAL_BRACNHPOINT_TO_ACCEPTOR_DISTANCE:
continue
if has_polypyrimidine and not (intron.ppt5p or intron.ppt3p):
continue
# if here, accepted!
filtered.append(intron)
else:
filtered = stopless3nintrons
# return ordered intron list
return _order_intron_list(filtered, order_by=order_by)
def find_stopless3n_introns_on_orf(orfObj,
has_branchpoint = False,
has_polypyrimidine = False,
order_by = 'length',**kwargs):
"""
Find potential stopless3n introns on this orf
@attention: **kwargs can contain other (here) unnecessarily arguments
@attention: **kwargs are required in the merge_orfs_with_intron() function
@type orfObj: Orf object
@param orfObj: Orf object which is scanned for stopless3n introns
@rtype: list
@return: list with introns
"""
# input validation
IsOrf(orfObj)
# edit **kwargs dictionary for some forced attributes
_update_kwargs(kwargs,KWARGS_STOPLESS_3N_INTRONS)
# find stopless3nintrons
stopless3nintrons = merge_orfs_with_intron(orfObj,orfObj,**kwargs)
# filter for presence of branchpoint / polypyrimidine tracks
if has_branchpoint or has_polypyrimidine:
filtered = []
for intron in stopless3nintrons:
intron.assign_bp_and_ppts()
if has_branchpoint and not intron.branchpoint:
continue
intron_bp_dist = intron.get_branchpoint_nt_distance()
if has_branchpoint and intron_bp_dist == None:
continue
intron_bp_optimality = min([ abs(offset-intron_bp_dist) for offset in OPTIMAL_BRACNHPOINT_TO_ACCEPTOR_DISTANCE ])
if has_branchpoint and intron_bp_optimality > MAXIMAL_OPTIMAL_BRACNHPOINT_TO_ACCEPTOR_DISTANCE:
continue
if has_polypyrimidine and not (intron.ppt5p or intron.ppt3p):
continue
# if here, accepted!
filtered.append( intron )
else:
filtered = stopless3nintrons
# return ordered intron list
return _order_intron_list(filtered,order_by=order_by)
def merge_orfs_with_two_tinyexons(preceding_orf,subsequent_orf,
preceding_donor_sites=[],
subsequent_acceptor_sites=[],
orflist=[],**kwargs):
"""
Bridge two `neighbouring` Orfs by TWO tinyexon by applying preceding donors and subsequent acceptors
@type preceding_orf: Orf object
@param preceding_orf: Orf object that contains preceding_donor_site(s)
@type subsequent_orf: Orf object
@param subsequent_orf: Orf object that contains subsequent_acceptor_site(s)
@type preceding_donor_sites: list
@param preceding_donor_sites: list with SpliceDonorGT and/or SpliceDonor objects
@type subsequent_acceptor_sites: list
@param subsequent_acceptor_sites: list with SpliceAcceptorAG and/or SpliceAcceptor objects
@type orflist: list
@param orflist: list with Orf objects
@attention: see get_potential_tiny_exons_on_orf for additional **kwargs
@rtype: list
@return: list of tuples ( preceding_intron, tinyexon1, central_intron, tinyexon2, subsequent_intron )
"""
if not preceding_donor_sites:
return []
if not subsequent_acceptor_sites:
return []
if not orflist:
return []
# edit **kwargs dictionary for some forced attributes
_update_kwargs(kwargs,KWARGS_PROJECTED_TINYEXON)
# return list with (intron,tinyexon,intron) tuples
returntinyexons = []
tinyexoncollection = []
tinyexoncombis = []
min_preceding_donor_sites_pos = min([ d.pos for d in preceding_donor_sites ])
max_subsequent_acceptor_sites_pos = max([ a.pos for a in subsequent_acceptor_sites ])
for orfX in orflist:
# check if orf is correctly positions towards the splice sites' extremes
min_pos = min_preceding_donor_sites_pos + kwargs['min_tinyexon_intron_nt_length']
max_pos = max_subsequent_acceptor_sites_pos - kwargs['min_tinyexon_intron_nt_length']
# if so, do not check this Orf
if orfX.endPY <= min_pos: continue
if orfX.startPY >= max_pos: continue
# extend the tinyexoncollection
tinyexoncollection.extend( get_potential_tiny_exons_on_orf(orfX,**kwargs) )
# make tinyexoncollection ordered on start pos
tinyexoncollection = _order_intron_list(tinyexoncollection,order_by='donor_pos')
# donor_pos makes REVERSE ordering; restore this by reversing
tinyexoncollection.reverse()
# make 2-elemented tuples of tinyexons which can co-occur together
for tinyexon1 in tinyexoncollection:
for pos in range(len(tinyexoncollection)-1,-1,-1):
tinyexon2 = tinyexoncollection[pos]
if tinyexon2.donor.pos < tinyexon1.donor.pos: break
intron_length = tinyexon2.acceptor.pos - tinyexon1.donor.pos
if intron_length < kwargs['min_tinyexon_intron_nt_length']: continue
if intron_length > kwargs['max_tinyexon_intron_nt_length']: continue
if tinyexon1.donor.phase != tinyexon2.acceptor.phase: continue
# if here, elegiable combi!
intron = IntronConnectingOrfs(
tinyexon1.donor,tinyexon2.acceptor,
get_shared_nucleotides_at_splicesite(
subsequent_orf,preceding_orf,
tinyexon2.acceptor,tinyexon1.donor
),
preceding_orf,subsequent_orf)
totlen = tinyexon1.length+tinyexon2.length
combi = ( totlen, tinyexon1, intron, tinyexon2 )
tinyexoncombis.append( combi )
# return an ordered list based on length
tinyexoncombis.sort()
return [ (exon1,intron,exon2) for l,exon1,intron,exon2 in tinyexoncombis ]
def get_potential_tiny_exons_on_orf(orfX,order_by='length',
max_tinyexon_nt_length =TINYEXON_MAX_NT_LENGTH,
min_tinyexon_nt_length =TINYEXON_MIN_NT_LENGTH,
min_donor_pssm_score =TINYEXON_MIN_DONOR_PSSM_SCORE,
min_acceptor_pssm_score =TINYEXON_MIN_ACCEPTOR_PSSM_SCORE,
allow_non_canonical_donor = TINYEXON_ALLOW_NON_CANONICAL_DONOR,
allow_non_canonical_acceptor= TINYEXON_ALLOW_NON_CANONICAL_ACCEPTOR,
non_canonical_min_donor_pssm_score = TINYEXON_NON_CANONICAL_MIN_DONOR_PSSM_SCORE,
non_canonical_min_acceptor_pssm_score = TINYEXON_NON_CANONICAL_MIN_ACCEPTOR_PSSM_SCORE,
min_total_pssm_score=TINYEXON_MIN_TOTAL_PSSM_SCORE,**kwargs):
"""
Predict all possible tiny exons on this Orf
@attention: **kwargs can contain other (here) unnecessarily arguments
@type orfX: Orf object
@param orfX: Orf object to scan for a tinyexon
@type max_tinyexon_nt_length: integer
@param max_tinyexon_nt_length: positive integer, largest length of tinyexon in nt
@type min_tinyexon_nt_length: integer
@param min_tinyexon_nt_length: positive integer, smallest length of tinyexon in nt
@type min_total_pssm_score: float or None
@param min_total_pssm_score: minimal sum of donor - acceptor pssm score pair of tinyexon
@type min_donor_pssm_score: float or None
@param min_donor_pssm_score: minimal donor pssm score of tinyexon
@type min_acceptor_pssm_score: float or None
@param min_acceptor_pssm_score: minimal acceptor pssm score of tinyexon
@type allow_non_canonical_donor: Boolean
@param allow_non_canonical_donor: search for non-canonical donor sites too
@type allow_non_canonical_acceptor: Boolean
@param allow_non_canonical_acceptor: search for non-canonical acceptor splice sites too
@type non_canonical_min_donor_pssm_score: float
@param non_canonical_min_donor_pssm_score: minimal pssm score of non-canonical donor
@type non_canonical_min_acceptor_pssm_score: float
@param non_canonical_min_acceptor_pssm_score: minimal pssm score of non-canonical acceptor
@type order_by: TODO
@param order_by: TODO
@rtype: list
@return: list with tinyexons
"""
# scan for splice sites on this (tiny) orf
forced = orfX._donor_sites == []
orfX.scan_orf_for_pssm_splice_sites(
splicetype="donor",forced=forced,
min_pssm_score=min_donor_pssm_score,
allow_non_canonical=allow_non_canonical_donor,
non_canonical_min_pssm_score=non_canonical_min_donor_pssm_score)
forced = orfX._acceptor_sites == []
orfX.scan_orf_for_pssm_splice_sites(
splicetype="acceptor",forced=forced,
min_pssm_score=min_acceptor_pssm_score,
allow_non_canonical=allow_non_canonical_acceptor,
non_canonical_min_pssm_score=non_canonical_min_acceptor_pssm_score)
# return list with exons
tinyexons = []
# most quickest scan possible: are there donors & acceptors?
if orfX._donor_sites == [] or orfX._acceptor_sites == []:
# no exons possible because splice sites are missing
return tinyexons
# and combine sites to exons!
for acceptor in orfX._acceptor_sites:
for donor in orfX._donor_sites:
# length of exon
exon_length = donor.pos - acceptor.pos
# continue if exon to short
if exon_length < min_tinyexon_nt_length: continue
# continue if exon to long
if exon_length > max_tinyexon_nt_length: continue
# check sum of donor and acceptor pssm score
if (min_total_pssm_score or min_total_pssm_score==0.0) and\
donor.pssm_score + acceptor.pssm_score < min_total_pssm_score:
continue
# (re) check individual PSSM scores; in case this Orf had
# already pre-assigned slice sites, potentially stricter
# parameters are not applied!
if donor.is_canonical() and\
(min_donor_pssm_score or min_donor_pssm_score == 0.0) and\
donor.pssm_score < min_donor_pssm_score:
continue
if not donor.is_canonical() and\
(non_canonical_min_donor_pssm_score or non_canonical_min_donor_pssm_score == 0.0) and\
donor.pssm_score < non_canonical_min_donor_pssm_score:
continue
if (min_acceptor_pssm_score or min_acceptor_pssm_score == 0.0) and\
acceptor.pssm_score < min_acceptor_pssm_score:
continue
# make a Exon object
exon = ExonOnOrf(acceptor,donor,orfX)
tinyexons.append(exon)
# return ordered exon list
return _order_intron_list(tinyexons,order_by=order_by)
def merge_orfs_with_intron(orfD,orfA,
max_intron_nt_length = MAX_INTRON_NT_LENGTH,
min_intron_nt_length = MIN_INTRON_NT_LENGTH,
min_donor_pssm_score = MIN_DONOR_PSSM_SCORE,
min_acceptor_pssm_score = MIN_ACCEPTOR_PSSM_SCORE,
allow_non_canonical_donor = ALLOW_NON_CANONICAL_DONOR,
allow_non_canonical_acceptor = ALLOW_NON_CANONICAL_ACCEPTOR,
non_canonical_min_donor_pssm_score = NON_CANONICAL_MIN_DONOR_PSSM_SCORE,
non_canonical_min_acceptor_pssm_score = NON_CANONICAL_MIN_ACCEPTOR_PSSM_SCORE,
min_donor_pos=None,
max_donor_pos=None,
min_acceptor_pos=None,
max_acceptor_pos=None,
order_by = 'length',**kwargs):
"""
Merge 2 Orf objects by introns
@attention: **kwargs can contain other (here) unnecessarily arguments
@type orfD: Orf object
@param orfD: Orf object that has to deliver a PSSM donor object
@type orfA: Orf object
@param orfA: Orf object that has to deliver a PSSM acceptor object
@type max_intron_nt_length: integer
@param max_intron_nt_length: maximal length (nt) of the intron
@type min_intron_nt_length: integer
@param min_intron_nt_length: minimal length (nt) of the intron
@type min_donor_pssm_score: float
@param min_donor_pssm_score: minimal pssm score of donor splice site
@type min_acceptor_pssm_score: float
@param min_acceptor_pssm_score: minimal pssm score of acceptor splice site
@type allow_non_canonical_donor: Boolean
@param allow_non_canonical_donor: search for non-canonical donor sites too
@type allow_non_canonical_acceptor: Boolean
@param allow_non_canonical_acceptor: search for non-canonical acceptor splice sites too
@type non_canonical_min_donor_pssm_score: float
@param non_canonical_min_donor_pssm_score: minimal pssm score of non-canonical donor
@type non_canonical_min_acceptor_pssm_score: float
@param non_canonical_min_acceptor_pssm_score: minimal pssm score of non-canonical acceptor
@rtype: list
@return: list with introns
"""
# input validation
IsOrf(orfD)
IsOrf(orfA)
# scan for splice sites (if not already done -> is checked in function)
orfD.scan_orf_for_pssm_splice_sites(
splicetype="donor",
min_pssm_score=min_donor_pssm_score,
allow_non_canonical=allow_non_canonical_donor,
non_canonical_min_pssm_score=non_canonical_min_donor_pssm_score)
orfA.scan_orf_for_pssm_splice_sites(
splicetype="acceptor",
min_pssm_score=min_acceptor_pssm_score,
allow_non_canonical=allow_non_canonical_acceptor,
non_canonical_min_pssm_score=non_canonical_min_acceptor_pssm_score)
# return list with introns
introns = []
# most quickest scan possible: are there donors & acceptors?
if orfD._donor_sites == [] or orfA._acceptor_sites == []:
# no introns possible because splice sites are missing
return introns
# very quick scan: are exons not to far from each other?
if max_intron_nt_length and\
(orfA._acceptor_sites[0].pos - orfD._donor_sites[0].pos) > max_intron_nt_length:
# no introns possible that can bridge this gap
return introns
for donor in orfD._donor_sites:
if not allow_non_canonical_donor and not donor.is_canonical():
continue
elif donor.is_canonical() and donor.pssm_score < min_donor_pssm_score:
continue
elif not donor.is_canonical() and donor.pssm_score < non_canonical_min_donor_pssm_score:
continue
elif (min_donor_pos or min_donor_pos==0) and donor.pos < min_donor_pos:
continue
elif (max_donor_pos or max_donor_pos==0) and donor.pos > max_donor_pos:
continue
else:
# donor site accepted
pass
for acceptor in orfA._acceptor_sites:
if not allow_non_canonical_acceptor and not acceptor.is_canonical():
continue
elif acceptor.is_canonical() and acceptor.pssm_score < min_acceptor_pssm_score:
continue
elif not acceptor.is_canonical() and acceptor.pssm_score < non_canonical_min_acceptor_pssm_score:
continue
elif (min_acceptor_pos or min_acceptor_pos==0) and acceptor.pos < min_acceptor_pos:
continue
elif (max_acceptor_pos or max_acceptor_pos==0) and acceptor.pos > max_acceptor_pos:
continue
else:
# acceptor site accepted
pass
# generate intron length and phase variable
intron_length = acceptor.pos - donor.pos
intron_phase = intron_length % 3
# check phase compatibilty (1) of splice sites
if donor.phase != acceptor.phase: continue
# check phase compatibilty (2) of splice sites
if ( intron_phase + orfD.frame ) % 3 != orfA.frame % 3: continue
# check if intron length is in between the boundaries
if max_intron_nt_length and intron_length > max_intron_nt_length: continue
if min_intron_nt_length and intron_length < min_intron_nt_length: continue
# okay, if we reach this point, we have a valid intron
shared_nts = get_shared_nucleotides_at_splicesite(
orfA,orfD,acceptor,donor
)
# make a IntronConnectingOrfs object
intron = IntronConnectingOrfs(donor,acceptor,shared_nts,orfD,orfA)
introns.append(intron)
# return ordered intron list
return _order_intron_list(introns,order_by=order_by)
def find_tiny_exon_on_orf(orfX,order_by='total_pssm',
max_tinyexon_nt_length =TINYEXON_MAX_NT_LENGTH,
min_tinyexon_nt_length =TINYEXON_MIN_NT_LENGTH,
max_tinyexon_intron_nt_length=TINYEXON_MAX_INTRON_NT_LENGTH,
min_tinyexon_intron_nt_length=TINYEXON_MIN_INTRON_NT_LENGTH,
min_donor_pssm_score =TINYEXON_MIN_DONOR_PSSM_SCORE,
min_acceptor_pssm_score =TINYEXON_MIN_ACCEPTOR_PSSM_SCORE,
min_total_pssm_score =TINYEXON_MIN_TOTAL_PSSM_SCORE,
allow_non_canonical_donor = TINYEXON_ALLOW_NON_CANONICAL_DONOR,
allow_non_canonical_acceptor = TINYEXON_ALLOW_NON_CANONICAL_ACCEPTOR,
non_canonical_min_donor_pssm_score = TINYEXON_NON_CANONICAL_MIN_DONOR_PSSM_SCORE,
non_canonical_min_acceptor_pssm_score = TINYEXON_NON_CANONICAL_MIN_ACCEPTOR_PSSM_SCORE,
preceding_donor=None,
subsequent_acceptor=None,
preceding_donor_pos=None,
subsequent_acceptor_pos=None):
"""
Find a tiny exon on an orf by a leading donor and a trailing acceptor site.
@type orfX: Orf object
@param orfX: Orf object to scan for a tinyexon
@type preceding_donor: object
@param preceding_donor: SpliceDonorGT or SpliceDonor object
@type subsequent_acceptor: object
@param subsequent_acceptor: SpliceAcceptorAG or SpliceAcceptor object
@type max_tinyexon_nt_length: integer
@param max_tinyexon_nt_length: positive integer, largest length of tinyexon in nt
@type min_tinyexon_nt_length: integer
@param min_tinyexon_nt_length: positive integer, smallest length of tinyexon in nt
@type max_tinyexon_intron_nt_length: integer
@param max_tinyexon_intron_nt_length: positive integer, largest length of intron around tinyexon in nt
@type min_tinyexon_intron_nt_length: integer
@param min_tinyexon_intron_nt_length: positive integer, smallest length of intron around tinyexon in nt
@type min_total_pssm_score: float or None
@param min_total_pssm_score: minimal sum of donor - acceptor pssm score pair of tinyexon
@type min_donor_pssm_score: float or None
@param min_donor_pssm_score: minimal donor pssm score of tinyexon
@type min_acceptor_pssm_score: float or None
@param min_acceptor_pssm_score: minimal acceptor pssm score of tinyexon
@type allow_non_canonical_donor: Boolean
@param allow_non_canonical_donor: search for non-canonical donor sites too
@type allow_non_canonical_acceptor: Boolean
@param allow_non_canonical_acceptor: search for non-canonical acceptor splice sites too
@type non_canonical_min_donor_pssm_score: float
@param non_canonical_min_donor_pssm_score: minimal pssm score of non-canonical donor
@type non_canonical_min_acceptor_pssm_score: float
@param non_canonical_min_acceptor_pssm_score: minimal pssm score of non-canonical acceptor
@type order_by: TODO
@param order_by: TODO
"""
# do some input data processing on preceding_donor
if preceding_donor == None:
# preceding donor MUST be set!
message = "preceding_donor is not a `SpliceDonorGT` or `SpliceDonor` object"
raise InproperlyAppliedArgument, message
elif preceding_donor.__class__.__name__ in ['SpliceDonorGT','SpliceDonor']:
pass
else:
message = "preceding_donor is not a `SpliceDonorGT` or `SpliceDonor` object, but a `%s`" % preceding_donor.__class__.__name__
raise InproperlyAppliedArgument, message
# do some input data processing on subsequent_acceptor
if subsequent_acceptor == None:
# subsequent acceptor MUST be set
message = "subsequent_acceptor is not a `SpliceAcceptorAG` or `SpliceAcceptor` object"
raise InproperlyAppliedArgument, message
elif subsequent_acceptor.__class__.__name__ in ['SpliceAcceptorAG','SpliceAcceptor']:
pass
else:
message = "subsequent_acceptor is not a `SpliceAcceptorAG` or `SpliceAcceptor` object, but a `%s`" % subsequent_acceptor.__class__.__name__
raise InproperlyAppliedArgument, message
# check phases of acceptor and donor
if subsequent_acceptor.phase not in [0,1,2]:
raise UnexpectedSpliceSitePhase
if preceding_donor.phase not in [0,1,2]:
raise UnexpectedSpliceSitePhase
# some further integrity check on integer arguments
for variable in ( max_tinyexon_nt_length, min_tinyexon_nt_length,
max_tinyexon_intron_nt_length, min_tinyexon_intron_nt_length):
try:
variable = int(variable)
if variable <= 0:
raise "WUF... WUF..."
except:
message = "a variable is NOT a positive integer as expected"
raise InproperlyAppliedArgument, message
# scan for splice sites on this (tiny) orf
orfX.scan_orf_for_pssm_splice_sites(
splicetype="donor",
min_pssm_score=min_donor_pssm_score,
allow_non_canonical=allow_non_canonical_donor,
non_canonical_min_pssm_score=non_canonical_min_donor_pssm_score)
orfX.scan_orf_for_pssm_splice_sites(
splicetype="acceptor",
min_pssm_score=min_acceptor_pssm_score,
allow_non_canonical=allow_non_canonical_acceptor,
non_canonical_min_pssm_score=non_canonical_min_acceptor_pssm_score)
# return list with exons
exons = []
# most quickest scan possible: are there donors & acceptors?
if orfX._donor_sites == [] or orfX._acceptor_sites == []:
# no exons possible because splice sites are missing
return exons
# make a list of compatible_acceptor_sites
compatible_acceptor_sites = []
for acceptor in orfX._acceptor_sites:
# TODO: check! do we need a combi of donor and acceptor or acceptor and acceptor?
if acceptor.phase != preceding_donor.phase:
continue
if acceptor.pssm_score < min_acceptor_pssm_score:
continue
if acceptor.pos - preceding_donor.pos < min_tinyexon_intron_nt_length:
# intron to short
continue
if acceptor.pos - preceding_donor.pos > max_tinyexon_intron_nt_length:
# intron to long
continue
# if we reach this point, compatible site!
compatible_acceptor_sites.append( acceptor )
# make a list of compatible_donor_sites
compatible_donor_sites = []
for donor in orfX._donor_sites:
# TODO: check! do we need a combi of donor and acceptor or donor and donor?
if donor.phase != subsequent_acceptor.phase:
continue
if donor.pssm_score < min_donor_pssm_score:
continue
if subsequent_acceptor.pos - donor.pos > max_tinyexon_intron_nt_length:
# intron to long
continue
if subsequent_acceptor.pos - donor.pos < min_tinyexon_intron_nt_length:
# intron to short
continue
# if we reach this point, compatible site!
compatible_donor_sites.append( donor )
# and combine sites to exons!
for acceptor in compatible_acceptor_sites:
for donor in compatible_donor_sites:
# length of exon
exon_length = donor.pos - acceptor.pos
# continue if exon to short
if exon_length < min_tinyexon_nt_length: continue
# continue if exon to long
if exon_length > max_tinyexon_nt_length: continue
# check sum of donor and acceptor pssm score
if (min_total_pssm_score or min_total_pssm_score==0.0) and\
donor.pssm_score + acceptor.pssm_score < min_total_pssm_score:
continue
# make a Exon object
exon = ExonOnOrf(acceptor,donor,orfX)
exons.append(exon)
# return ordered exon list
return _order_intron_list(exons,order_by=order_by)
def merge_orfs_with_two_tinyexons(preceding_orf,
subsequent_orf,
preceding_donor_sites=[],
subsequent_acceptor_sites=[],
orflist=[],
**kwargs):
"""
Bridge two `neighbouring` Orfs by TWO tinyexon by applying preceding donors and subsequent acceptors
@type preceding_orf: Orf object
@param preceding_orf: Orf object that contains preceding_donor_site(s)
@type subsequent_orf: Orf object
@param subsequent_orf: Orf object that contains subsequent_acceptor_site(s)
@type preceding_donor_sites: list
@param preceding_donor_sites: list with SpliceDonorGT and/or SpliceDonor objects
@type subsequent_acceptor_sites: list
@param subsequent_acceptor_sites: list with SpliceAcceptorAG and/or SpliceAcceptor objects
@type orflist: list
@param orflist: list with Orf objects
@attention: see get_potential_tiny_exons_on_orf for additional **kwargs
@rtype: list
@return: list of tuples ( preceding_intron, tinyexon1, central_intron, tinyexon2, subsequent_intron )
"""
if not preceding_donor_sites:
return []
if not subsequent_acceptor_sites:
return []
if not orflist:
return []
# edit **kwargs dictionary for some forced attributes
_update_kwargs(kwargs, KWARGS_PROJECTED_TINYEXON)
# return list with (intron,tinyexon,intron) tuples
returntinyexons = []
tinyexoncollection = []
tinyexoncombis = []
min_preceding_donor_sites_pos = min([d.pos for d in preceding_donor_sites])
max_subsequent_acceptor_sites_pos = max(
[a.pos for a in subsequent_acceptor_sites])
for orfX in orflist:
# check if orf is correctly positions towards the splice sites' extremes
min_pos = min_preceding_donor_sites_pos + kwargs[
'min_tinyexon_intron_nt_length']
max_pos = max_subsequent_acceptor_sites_pos - kwargs[
'min_tinyexon_intron_nt_length']
# if so, do not check this Orf
if orfX.endPY <= min_pos: continue
if orfX.startPY >= max_pos: continue
# extend the tinyexoncollection
tinyexoncollection.extend(
get_potential_tiny_exons_on_orf(orfX, **kwargs))
# make tinyexoncollection ordered on start pos
tinyexoncollection = _order_intron_list(tinyexoncollection,
order_by='donor_pos')
# donor_pos makes REVERSE ordering; restore this by reversing
tinyexoncollection.reverse()
# make 2-elemented tuples of tinyexons which can co-occur together
for tinyexon1 in tinyexoncollection:
for pos in range(len(tinyexoncollection) - 1, -1, -1):
tinyexon2 = tinyexoncollection[pos]
if tinyexon2.donor.pos < tinyexon1.donor.pos: break
intron_length = tinyexon2.acceptor.pos - tinyexon1.donor.pos
if intron_length < kwargs['min_tinyexon_intron_nt_length']:
continue
if intron_length > kwargs['max_tinyexon_intron_nt_length']:
continue
if tinyexon1.donor.phase != tinyexon2.acceptor.phase: continue
# if here, elegiable combi!
intron = IntronConnectingOrfs(
tinyexon1.donor, tinyexon2.acceptor,
get_shared_nucleotides_at_splicesite(subsequent_orf,
preceding_orf,
tinyexon2.acceptor,
tinyexon1.donor),
preceding_orf, subsequent_orf)
totlen = tinyexon1.length + tinyexon2.length
combi = (totlen, tinyexon1, intron, tinyexon2)
tinyexoncombis.append(combi)
# return an ordered list based on length
tinyexoncombis.sort()
return [(exon1, intron, exon2)
for l, exon1, intron, exon2 in tinyexoncombis]
def get_potential_tiny_exons_on_orf(
orfX,
order_by='length',
max_tinyexon_nt_length=TINYEXON_MAX_NT_LENGTH,
min_tinyexon_nt_length=TINYEXON_MIN_NT_LENGTH,
min_donor_pssm_score=TINYEXON_MIN_DONOR_PSSM_SCORE,
min_acceptor_pssm_score=TINYEXON_MIN_ACCEPTOR_PSSM_SCORE,
allow_non_canonical_donor=TINYEXON_ALLOW_NON_CANONICAL_DONOR,
allow_non_canonical_acceptor=TINYEXON_ALLOW_NON_CANONICAL_ACCEPTOR,
non_canonical_min_donor_pssm_score=TINYEXON_NON_CANONICAL_MIN_DONOR_PSSM_SCORE,
non_canonical_min_acceptor_pssm_score=TINYEXON_NON_CANONICAL_MIN_ACCEPTOR_PSSM_SCORE,
min_total_pssm_score=TINYEXON_MIN_TOTAL_PSSM_SCORE,
**kwargs):
"""
Predict all possible tiny exons on this Orf
@attention: **kwargs can contain other (here) unnecessarily arguments
@type orfX: Orf object
@param orfX: Orf object to scan for a tinyexon
@type max_tinyexon_nt_length: integer
@param max_tinyexon_nt_length: positive integer, largest length of tinyexon in nt
@type min_tinyexon_nt_length: integer
@param min_tinyexon_nt_length: positive integer, smallest length of tinyexon in nt
@type min_total_pssm_score: float or None
@param min_total_pssm_score: minimal sum of donor - acceptor pssm score pair of tinyexon
@type min_donor_pssm_score: float or None
@param min_donor_pssm_score: minimal donor pssm score of tinyexon
@type min_acceptor_pssm_score: float or None
@param min_acceptor_pssm_score: minimal acceptor pssm score of tinyexon
@type allow_non_canonical_donor: Boolean
@param allow_non_canonical_donor: search for non-canonical donor sites too
@type allow_non_canonical_acceptor: Boolean
@param allow_non_canonical_acceptor: search for non-canonical acceptor splice sites too
@type non_canonical_min_donor_pssm_score: float
@param non_canonical_min_donor_pssm_score: minimal pssm score of non-canonical donor
@type non_canonical_min_acceptor_pssm_score: float
@param non_canonical_min_acceptor_pssm_score: minimal pssm score of non-canonical acceptor
@type order_by: TODO
@param order_by: TODO
@rtype: list
@return: list with tinyexons
"""
# scan for splice sites on this (tiny) orf
forced = orfX._donor_sites == []
orfX.scan_orf_for_pssm_splice_sites(
splicetype="donor",
forced=forced,
min_pssm_score=min_donor_pssm_score,
allow_non_canonical=allow_non_canonical_donor,
non_canonical_min_pssm_score=non_canonical_min_donor_pssm_score)
forced = orfX._acceptor_sites == []
orfX.scan_orf_for_pssm_splice_sites(
splicetype="acceptor",
forced=forced,
min_pssm_score=min_acceptor_pssm_score,
allow_non_canonical=allow_non_canonical_acceptor,
non_canonical_min_pssm_score=non_canonical_min_acceptor_pssm_score)
# return list with exons
tinyexons = []
# most quickest scan possible: are there donors & acceptors?
if orfX._donor_sites == [] or orfX._acceptor_sites == []:
# no exons possible because splice sites are missing
return tinyexons
# and combine sites to exons!
for acceptor in orfX._acceptor_sites:
for donor in orfX._donor_sites:
# length of exon
exon_length = donor.pos - acceptor.pos
# continue if exon to short
if exon_length < min_tinyexon_nt_length: continue
# continue if exon to long
if exon_length > max_tinyexon_nt_length: continue
# check sum of donor and acceptor pssm score
if (min_total_pssm_score or min_total_pssm_score==0.0) and\
donor.pssm_score + acceptor.pssm_score < min_total_pssm_score:
continue
# (re) check individual PSSM scores; in case this Orf had
# already pre-assigned slice sites, potentially stricter
# parameters are not applied!
if donor.is_canonical() and\
(min_donor_pssm_score or min_donor_pssm_score == 0.0) and\
donor.pssm_score < min_donor_pssm_score:
continue
if not donor.is_canonical() and\
(non_canonical_min_donor_pssm_score or non_canonical_min_donor_pssm_score == 0.0) and\
donor.pssm_score < non_canonical_min_donor_pssm_score:
continue
if (min_acceptor_pssm_score or min_acceptor_pssm_score == 0.0) and\
acceptor.pssm_score < min_acceptor_pssm_score:
continue
# make a Exon object
exon = ExonOnOrf(acceptor, donor, orfX)
tinyexons.append(exon)
# return ordered exon list
return _order_intron_list(tinyexons, order_by=order_by)
def merge_orfs_with_intron(
orfD,
orfA,
max_intron_nt_length=MAX_INTRON_NT_LENGTH,
min_intron_nt_length=MIN_INTRON_NT_LENGTH,
min_donor_pssm_score=MIN_DONOR_PSSM_SCORE,
min_acceptor_pssm_score=MIN_ACCEPTOR_PSSM_SCORE,
allow_non_canonical_donor=ALLOW_NON_CANONICAL_DONOR,
allow_non_canonical_acceptor=ALLOW_NON_CANONICAL_ACCEPTOR,
non_canonical_min_donor_pssm_score=NON_CANONICAL_MIN_DONOR_PSSM_SCORE,
non_canonical_min_acceptor_pssm_score=NON_CANONICAL_MIN_ACCEPTOR_PSSM_SCORE,
min_donor_pos=None,
max_donor_pos=None,
min_acceptor_pos=None,
max_acceptor_pos=None,
order_by='length',
**kwargs):
"""
Merge 2 Orf objects by introns
@attention: **kwargs can contain other (here) unnecessarily arguments
@type orfD: Orf object
@param orfD: Orf object that has to deliver a PSSM donor object
@type orfA: Orf object
@param orfA: Orf object that has to deliver a PSSM acceptor object
@type max_intron_nt_length: integer
@param max_intron_nt_length: maximal length (nt) of the intron
@type min_intron_nt_length: integer
@param min_intron_nt_length: minimal length (nt) of the intron
@type min_donor_pssm_score: float
@param min_donor_pssm_score: minimal pssm score of donor splice site
@type min_acceptor_pssm_score: float
@param min_acceptor_pssm_score: minimal pssm score of acceptor splice site
@type allow_non_canonical_donor: Boolean
@param allow_non_canonical_donor: search for non-canonical donor sites too
@type allow_non_canonical_acceptor: Boolean
@param allow_non_canonical_acceptor: search for non-canonical acceptor splice sites too
@type non_canonical_min_donor_pssm_score: float
@param non_canonical_min_donor_pssm_score: minimal pssm score of non-canonical donor
@type non_canonical_min_acceptor_pssm_score: float
@param non_canonical_min_acceptor_pssm_score: minimal pssm score of non-canonical acceptor
@rtype: list
@return: list with introns
"""
# input validation
IsOrf(orfD)
IsOrf(orfA)
# scan for splice sites (if not already done -> is checked in function)
orfD.scan_orf_for_pssm_splice_sites(
splicetype="donor",
min_pssm_score=min_donor_pssm_score,
allow_non_canonical=allow_non_canonical_donor,
non_canonical_min_pssm_score=non_canonical_min_donor_pssm_score)
orfA.scan_orf_for_pssm_splice_sites(
splicetype="acceptor",
min_pssm_score=min_acceptor_pssm_score,
allow_non_canonical=allow_non_canonical_acceptor,
non_canonical_min_pssm_score=non_canonical_min_acceptor_pssm_score)
# return list with introns
introns = []
# most quickest scan possible: are there donors & acceptors?
if orfD._donor_sites == [] or orfA._acceptor_sites == []:
# no introns possible because splice sites are missing
return introns
# very quick scan: are exons not to far from each other?
if max_intron_nt_length and\
(orfA._acceptor_sites[0].pos - orfD._donor_sites[0].pos) > max_intron_nt_length:
# no introns possible that can bridge this gap
return introns
for donor in orfD._donor_sites:
if not allow_non_canonical_donor and not donor.is_canonical():
continue
elif donor.is_canonical() and donor.pssm_score < min_donor_pssm_score:
continue
elif not donor.is_canonical(
) and donor.pssm_score < non_canonical_min_donor_pssm_score:
continue
elif (min_donor_pos
or min_donor_pos == 0) and donor.pos < min_donor_pos:
continue
elif (max_donor_pos
or max_donor_pos == 0) and donor.pos > max_donor_pos:
continue
else:
# donor site accepted
pass
for acceptor in orfA._acceptor_sites:
if not allow_non_canonical_acceptor and not acceptor.is_canonical(
):
continue
elif acceptor.is_canonical(
) and acceptor.pssm_score < min_acceptor_pssm_score:
continue
elif not acceptor.is_canonical(
) and acceptor.pssm_score < non_canonical_min_acceptor_pssm_score:
continue
elif (min_acceptor_pos or min_acceptor_pos
== 0) and acceptor.pos < min_acceptor_pos:
continue
elif (max_acceptor_pos or max_acceptor_pos
== 0) and acceptor.pos > max_acceptor_pos:
continue
else:
# acceptor site accepted
pass
# generate intron length and phase variable
intron_length = acceptor.pos - donor.pos
intron_phase = intron_length % 3
# check phase compatibilty (1) of splice sites
if donor.phase != acceptor.phase: continue
# check phase compatibilty (2) of splice sites
if (intron_phase + orfD.frame) % 3 != orfA.frame % 3: continue
# check if intron length is in between the boundaries
if max_intron_nt_length and intron_length > max_intron_nt_length:
continue
if min_intron_nt_length and intron_length < min_intron_nt_length:
continue
# okay, if we reach this point, we have a valid intron
shared_nts = get_shared_nucleotides_at_splicesite(
orfA, orfD, acceptor, donor)
# make a IntronConnectingOrfs object
intron = IntronConnectingOrfs(donor, acceptor, shared_nts, orfD,
orfA)
introns.append(intron)
# return ordered intron list
return _order_intron_list(introns, order_by=order_by)
def find_tiny_exon_on_orf(
orfX,
order_by='total_pssm',
max_tinyexon_nt_length=TINYEXON_MAX_NT_LENGTH,
min_tinyexon_nt_length=TINYEXON_MIN_NT_LENGTH,
max_tinyexon_intron_nt_length=TINYEXON_MAX_INTRON_NT_LENGTH,
min_tinyexon_intron_nt_length=TINYEXON_MIN_INTRON_NT_LENGTH,
min_donor_pssm_score=TINYEXON_MIN_DONOR_PSSM_SCORE,
min_acceptor_pssm_score=TINYEXON_MIN_ACCEPTOR_PSSM_SCORE,
min_total_pssm_score=TINYEXON_MIN_TOTAL_PSSM_SCORE,
allow_non_canonical_donor=TINYEXON_ALLOW_NON_CANONICAL_DONOR,
allow_non_canonical_acceptor=TINYEXON_ALLOW_NON_CANONICAL_ACCEPTOR,
non_canonical_min_donor_pssm_score=TINYEXON_NON_CANONICAL_MIN_DONOR_PSSM_SCORE,
non_canonical_min_acceptor_pssm_score=TINYEXON_NON_CANONICAL_MIN_ACCEPTOR_PSSM_SCORE,
preceding_donor=None,
subsequent_acceptor=None,
preceding_donor_pos=None,
subsequent_acceptor_pos=None):
"""
Find a tiny exon on an orf by a leading donor and a trailing acceptor site.
@type orfX: Orf object
@param orfX: Orf object to scan for a tinyexon
@type preceding_donor: object
@param preceding_donor: SpliceDonorGT or SpliceDonor object
@type subsequent_acceptor: object
@param subsequent_acceptor: SpliceAcceptorAG or SpliceAcceptor object
@type max_tinyexon_nt_length: integer
@param max_tinyexon_nt_length: positive integer, largest length of tinyexon in nt
@type min_tinyexon_nt_length: integer
@param min_tinyexon_nt_length: positive integer, smallest length of tinyexon in nt
@type max_tinyexon_intron_nt_length: integer
@param max_tinyexon_intron_nt_length: positive integer, largest length of intron around tinyexon in nt
@type min_tinyexon_intron_nt_length: integer
@param min_tinyexon_intron_nt_length: positive integer, smallest length of intron around tinyexon in nt
@type min_total_pssm_score: float or None
@param min_total_pssm_score: minimal sum of donor - acceptor pssm score pair of tinyexon
@type min_donor_pssm_score: float or None
@param min_donor_pssm_score: minimal donor pssm score of tinyexon
@type min_acceptor_pssm_score: float or None
@param min_acceptor_pssm_score: minimal acceptor pssm score of tinyexon
@type allow_non_canonical_donor: Boolean
@param allow_non_canonical_donor: search for non-canonical donor sites too
@type allow_non_canonical_acceptor: Boolean
@param allow_non_canonical_acceptor: search for non-canonical acceptor splice sites too
@type non_canonical_min_donor_pssm_score: float
@param non_canonical_min_donor_pssm_score: minimal pssm score of non-canonical donor
@type non_canonical_min_acceptor_pssm_score: float
@param non_canonical_min_acceptor_pssm_score: minimal pssm score of non-canonical acceptor
@type order_by: TODO
@param order_by: TODO
"""
# do some input data processing on preceding_donor
if preceding_donor == None:
# preceding donor MUST be set!
message = "preceding_donor is not a `SpliceDonorGT` or `SpliceDonor` object"
raise InproperlyAppliedArgument, message
elif preceding_donor.__class__.__name__ in [
'SpliceDonorGT', 'SpliceDonor'
]:
pass
else:
message = "preceding_donor is not a `SpliceDonorGT` or `SpliceDonor` object, but a `%s`" % preceding_donor.__class__.__name__
raise InproperlyAppliedArgument, message
# do some input data processing on subsequent_acceptor
if subsequent_acceptor == None:
# subsequent acceptor MUST be set
message = "subsequent_acceptor is not a `SpliceAcceptorAG` or `SpliceAcceptor` object"
raise InproperlyAppliedArgument, message
elif subsequent_acceptor.__class__.__name__ in [
'SpliceAcceptorAG', 'SpliceAcceptor'
]:
pass
else:
message = "subsequent_acceptor is not a `SpliceAcceptorAG` or `SpliceAcceptor` object, but a `%s`" % subsequent_acceptor.__class__.__name__
raise InproperlyAppliedArgument, message
# check phases of acceptor and donor
if subsequent_acceptor.phase not in [0, 1, 2]:
raise UnexpectedSpliceSitePhase
if preceding_donor.phase not in [0, 1, 2]:
raise UnexpectedSpliceSitePhase
# some further integrity check on integer arguments
for variable in (max_tinyexon_nt_length, min_tinyexon_nt_length,
max_tinyexon_intron_nt_length,
min_tinyexon_intron_nt_length):
try:
variable = int(variable)
if variable <= 0:
raise "WUF... WUF..."
except:
message = "a variable is NOT a positive integer as expected"
raise InproperlyAppliedArgument, message
# scan for splice sites on this (tiny) orf
orfX.scan_orf_for_pssm_splice_sites(
splicetype="donor",
min_pssm_score=min_donor_pssm_score,
allow_non_canonical=allow_non_canonical_donor,
non_canonical_min_pssm_score=non_canonical_min_donor_pssm_score)
orfX.scan_orf_for_pssm_splice_sites(
splicetype="acceptor",
min_pssm_score=min_acceptor_pssm_score,
allow_non_canonical=allow_non_canonical_acceptor,
non_canonical_min_pssm_score=non_canonical_min_acceptor_pssm_score)
# return list with exons
exons = []
# most quickest scan possible: are there donors & acceptors?
if orfX._donor_sites == [] or orfX._acceptor_sites == []:
# no exons possible because splice sites are missing
return exons
# make a list of compatible_acceptor_sites
compatible_acceptor_sites = []
for acceptor in orfX._acceptor_sites:
# TODO: check! do we need a combi of donor and acceptor or acceptor and acceptor?
if acceptor.phase != preceding_donor.phase:
continue
if acceptor.pssm_score < min_acceptor_pssm_score:
continue
if acceptor.pos - preceding_donor.pos < min_tinyexon_intron_nt_length:
# intron to short
continue
if acceptor.pos - preceding_donor.pos > max_tinyexon_intron_nt_length:
# intron to long
continue
# if we reach this point, compatible site!
compatible_acceptor_sites.append(acceptor)
# make a list of compatible_donor_sites
compatible_donor_sites = []
for donor in orfX._donor_sites:
# TODO: check! do we need a combi of donor and acceptor or donor and donor?
if donor.phase != subsequent_acceptor.phase:
continue
if donor.pssm_score < min_donor_pssm_score:
continue
if subsequent_acceptor.pos - donor.pos > max_tinyexon_intron_nt_length:
# intron to long
continue
if subsequent_acceptor.pos - donor.pos < min_tinyexon_intron_nt_length:
# intron to short
continue
# if we reach this point, compatible site!
compatible_donor_sites.append(donor)
# and combine sites to exons!
for acceptor in compatible_acceptor_sites:
for donor in compatible_donor_sites:
# length of exon
exon_length = donor.pos - acceptor.pos
# continue if exon to short
if exon_length < min_tinyexon_nt_length: continue
# continue if exon to long
if exon_length > max_tinyexon_nt_length: continue
# check sum of donor and acceptor pssm score
if (min_total_pssm_score or min_total_pssm_score==0.0) and\
donor.pssm_score + acceptor.pssm_score < min_total_pssm_score:
continue
# make a Exon object
exon = ExonOnOrf(acceptor, donor, orfX)
exons.append(exon)
# return ordered exon list
return _order_intron_list(exons, order_by=order_by)
