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 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 merge_orfs_with_tinyexon(preceding_orf,subsequent_orf,
preceding_donor_sites=[],
subsequent_acceptor_sites=[],
orflist=[],
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,
**kwargs):
"""
Bridge two `neighbouring` Orfs by a 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
@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
@rtype: list
@return: list of tuples ( preceding_intron, tinyexon, subsequent_intron )
@attention: Global vars that have to be set upon usage:
MIN_DONOR_PSSM_SCORE
MIN_ACCEPTOR_PSSM_SCORE
# and all TINYEXON variable named
TINYEXON_MAX_NT_LENGTH
TINYEXON_MIN_NT_LENGTH
TINYEXON_MAX_INTRON_NT_LENGTH
TINYEXON_MIN_INTRON_NT_LENGTH
TINYEXON_MIN_PSSM_SCORE
TINYEXON_MIN_DONOR_PSSM_SCORE
TINYEXON_MIN_ACCEPTOR_PSSM_SCORE
TINYEXON_ALLOW_NON_CANONICAL_DONOR
TINYEXON_ALLOW_NON_CANONICAL_ACCEPTOR
TINYEXON_NON_CANONICAL_MIN_PSSM_SCORE
TINYEXON_NON_CANONICAL_MIN_DONOR_PSSM_SCORE
TINYEXON_NON_CANONICAL_MIN_ACCEPTOR_PSSM_SCORE
"""
if not preceding_donor_sites:
return []
if not subsequent_acceptor_sites:
return []
if not orflist:
return []
# return list with (intron,tinyexon,intron) tuples
returnexons = []
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
if orfX.endPY <= min_preceding_donor_sites_pos: continue
if orfX.startPY >= max_subsequent_acceptor_sites_pos: continue
# if here, we can try to make a bridge by a tinyexon
for donor in preceding_donor_sites:
# orf not correctly positions towards the donor site
if orfX.endPY <= donor.pos: continue
# check pssm_score of donor site
# TODO: this is in fact the donor on the normal, large orf
# TODO: do we want to check this pssm score?
if donor.pssm_score < min_donor_pssm_score: continue
for acceptor in subsequent_acceptor_sites:
if orfX.startPY >= acceptor.pos: continue
# check pssm_score of acceptor site
# TODO: this is in fact the acceptor on the normal, large orf
# TODO: do we want to check this pssm score?
if acceptor.pssm_score < min_acceptor_pssm_score: continue
# okay, now try to bridge it!
exons = find_tiny_exon_on_orf(orfX,order_by='total_pssm',
max_tinyexon_nt_length=max_tinyexon_nt_length,
min_tinyexon_nt_length=min_tinyexon_nt_length,
max_tinyexon_intron_nt_length=max_tinyexon_intron_nt_length,
min_tinyexon_intron_nt_length=min_tinyexon_intron_nt_length,
min_donor_pssm_score=min_donor_pssm_score,
min_acceptor_pssm_score=min_acceptor_pssm_score,
min_total_pssm_score=min_total_pssm_score,
preceding_donor=donor,
subsequent_acceptor=acceptor
)
# and append to returnexons
for tinyexon in exons:
# make preceding intron
shared_nts_A = get_shared_nucleotides_at_splicesite(
tinyexon.orf,preceding_orf,
tinyexon.acceptor,donor
)
preceding_intron = IntronConnectingOrfs(
donor,tinyexon.acceptor,
shared_nts_A,preceding_orf,tinyexon.orf )
# make subsequent intron
shared_nts_B = get_shared_nucleotides_at_splicesite(
subsequent_orf,tinyexon.orf,
acceptor,tinyexon.donor
)
subsequent_intron = IntronConnectingOrfs(
tinyexon.donor, acceptor,
shared_nts_B,tinyexon.orf,subsequent_orf )
# and append to exons
returnexons.append( ( preceding_intron, tinyexon, subsequent_intron ) )
# and return the list of intron/exon/intron
return returnexons
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 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 merge_orfs_with_tinyexon(
preceding_orf,
subsequent_orf,
preceding_donor_sites=[],
subsequent_acceptor_sites=[],
orflist=[],
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,
**kwargs):
"""
Bridge two `neighbouring` Orfs by a 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
@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
@rtype: list
@return: list of tuples ( preceding_intron, tinyexon, subsequent_intron )
@attention: Global vars that have to be set upon usage:
MIN_DONOR_PSSM_SCORE
MIN_ACCEPTOR_PSSM_SCORE
# and all TINYEXON variable named
TINYEXON_MAX_NT_LENGTH
TINYEXON_MIN_NT_LENGTH
TINYEXON_MAX_INTRON_NT_LENGTH
TINYEXON_MIN_INTRON_NT_LENGTH
TINYEXON_MIN_PSSM_SCORE
TINYEXON_MIN_DONOR_PSSM_SCORE
TINYEXON_MIN_ACCEPTOR_PSSM_SCORE
TINYEXON_ALLOW_NON_CANONICAL_DONOR
TINYEXON_ALLOW_NON_CANONICAL_ACCEPTOR
TINYEXON_NON_CANONICAL_MIN_PSSM_SCORE
TINYEXON_NON_CANONICAL_MIN_DONOR_PSSM_SCORE
TINYEXON_NON_CANONICAL_MIN_ACCEPTOR_PSSM_SCORE
"""
if not preceding_donor_sites:
return []
if not subsequent_acceptor_sites:
return []
if not orflist:
return []
# return list with (intron,tinyexon,intron) tuples
returnexons = []
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
if orfX.endPY <= min_preceding_donor_sites_pos: continue
if orfX.startPY >= max_subsequent_acceptor_sites_pos: continue
# if here, we can try to make a bridge by a tinyexon
for donor in preceding_donor_sites:
# orf not correctly positions towards the donor site
if orfX.endPY <= donor.pos: continue
# check pssm_score of donor site
# TODO: this is in fact the donor on the normal, large orf
# TODO: do we want to check this pssm score?
if donor.pssm_score < min_donor_pssm_score: continue
for acceptor in subsequent_acceptor_sites:
if orfX.startPY >= acceptor.pos: continue
# check pssm_score of acceptor site
# TODO: this is in fact the acceptor on the normal, large orf
# TODO: do we want to check this pssm score?
if acceptor.pssm_score < min_acceptor_pssm_score: continue
# okay, now try to bridge it!
exons = find_tiny_exon_on_orf(
orfX,
order_by='total_pssm',
max_tinyexon_nt_length=max_tinyexon_nt_length,
min_tinyexon_nt_length=min_tinyexon_nt_length,
max_tinyexon_intron_nt_length=max_tinyexon_intron_nt_length,
min_tinyexon_intron_nt_length=min_tinyexon_intron_nt_length,
min_donor_pssm_score=min_donor_pssm_score,
min_acceptor_pssm_score=min_acceptor_pssm_score,
min_total_pssm_score=min_total_pssm_score,
preceding_donor=donor,
subsequent_acceptor=acceptor)
# and append to returnexons
for tinyexon in exons:
# make preceding intron
shared_nts_A = get_shared_nucleotides_at_splicesite(
tinyexon.orf, preceding_orf, tinyexon.acceptor, donor)
preceding_intron = IntronConnectingOrfs(
donor, tinyexon.acceptor, shared_nts_A, preceding_orf,
tinyexon.orf)
# make subsequent intron
shared_nts_B = get_shared_nucleotides_at_splicesite(
subsequent_orf, tinyexon.orf, acceptor, tinyexon.donor)
subsequent_intron = IntronConnectingOrfs(
tinyexon.donor, acceptor, shared_nts_B, tinyexon.orf,
subsequent_orf)
# and append to exons
returnexons.append(
(preceding_intron, tinyexon, subsequent_intron))
# and return the list of intron/exon/intron
return returnexons
