def bridge_two_pacbporfs_by_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):
"""
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 dictionary with exon coordinates (keys) and exons/introns
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 = "TODO"
preceding_intron = IntronConnectingOrfs(
donor,tinyexon.acceptor,
shared_nts_A,preceding_orf,tinyexon.orf )
# make subsequent intron
shared_nts_B = "TODO"
subsequent_intron = IntronConnectingOrfs(
tinyexon.donor, acceptor,
shared_nts_B,tinyexon.orf,subsequent_orf )
# and append to exons
key = ( tinyexon.acceptor.pos, tinyexon.donor.pos )
#returnexons.append( ( preceding_intron, tinyexon, subsequent_intron ) )
if key not in returnexons.keys():
returnexons[key] = tinyexon
# and return the list of intron/exon/intron
return _order_intron_list( returnexons.values() )
def scan_orf_for_tiny_exon(orfX,order_by='total_pssm',
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,
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,
min_intron_nt_length=None,
max_intron_nt_length=None,
donor_phase=None,
acceptor_phase=None,
preceeding_donor_site=None,
subsequent_acceptor_site=None,
min_acceptor_pos=None,
max_donor_pos=None):
"""
Find tiny exons on an orf by length range
@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 max_donor_pos: integer or None
@param max_donor_pos: maximal elegiable donor position
@type min_acceptor_pos: integer or None
@param min_acceptor_pos: minimal elegiable acceptor position
@type order_by: TODO
@param order_by: TODO
"""
# 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=TINYEXON_ALLOW_NON_CANONICAL_DONOR,
non_canonical_min_pssm_score=TINYEXON_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=TINYEXON_ALLOW_NON_CANONICAL_ACCEPTOR,
non_canonical_min_pssm_score=TINYEXON_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:
if acceptor_phase in [0,1,2] and acceptor.phase != acceptor_phase:
continue
if acceptor.pssm_score < min_acceptor_pssm_score:
continue
if min_acceptor_pos and acceptor.pos < min_acceptor_pos:
continue
if preceeding_donor_site:
if preceeding_donor_site.phase != acceptor.phase:
continue
if min_intron_nt_length and acceptor.pos - preceeding_donor_site.pos < min_intron_nt_length:
continue
if max_intron_nt_length and acceptor.pos - preceeding_donor_site.pos > max_intron_nt_length:
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:
if donor_phase in [0,1,2] and donor.phase != donor_phase:
continue
if donor.pssm_score < min_donor_pssm_score:
continue
if max_donor_pos and donor.pos > max_donor_pos:
continue
if subsequent_acceptor_site:
if subsequent_acceptor_site.phase != donor.phase:
continue
if min_intron_nt_length and subsequent_acceptor_site.pos - donor.pos < min_intron_nt_length:
continue
if max_intron_nt_length and subsequent_acceptor_site.pos - donor.pos > max_intron_nt_length:
continue
# if we reach this point, compatible site!
compatible_donor_sites.append( donor )
###print "lib_tinyexon, comp d & a:", len(compatible_donor_sites), len(compatible_acceptor_sites), "orf:", orfX.id, min_donor_pssm_score, min_acceptor_pssm_score
# 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 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,
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 order_by: TODO
@param order_by: TODO
@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
"""
# scan for splice sites on this (tiny) orf
orfX.scan_orf_for_pssm_splice_sites(
splicetype="donor",
min_pssm_score=TINYEXON_MIN_DONOR_PSSM_SCORE,
allow_non_canonical=TINYEXON_ALLOW_NON_CANONICAL_DONOR,
non_canonical_min_pssm_score=TINYEXON_NON_CANONICAL_MIN_DONOR_PSSM_SCORE)
orfX.scan_orf_for_pssm_splice_sites(
splicetype="acceptor",
min_pssm_score=TINYEXON_MIN_ACCEPTOR_PSSM_SCORE,
allow_non_canonical=TINYEXON_ALLOW_NON_CANONICAL_ACCEPTOR,
non_canonical_min_pssm_score=TINYEXON_NON_CANONICAL_MIN_ACCEPTOR_PSSM_SCORE)
# return list with exons
exons = []
# 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
except:
message = "a variable is NOT a positive integer as expected"
raise InproperlyAppliedArgument, message
# 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)
