def merge_pacbporfs(
pacbporfD,
pacbporfA,
queryOrfSetObj,
sbjctOrfSetObj,
allow_query_projecting=True,
allow_sbjct_projecting=True,
allow_query_mapping=True,
allow_sbjct_mapping=True,
allow_projecting=True,
allow_mapping=True,
verbose=False,
):
"""
Merge 2 PacbPORF objects with an interface into a gene structure
@type pacbporfD: PacbPORF object
@param pacbporfD: PacbPORF object that has to deliver PSSM donor objects
@type pacbporfA: PacbPORF object
@param pacbporfA: PacbPORF object that has to deliver PSSM acceptor objects
@type verbose: Boolean
@param verbose: print status/debugging messages to STDOUT
@rtype: list
@return: list with ( intron, intron ), in query and sbjct
"""
# input validation
IsPacbPORF(pacbporfD)
IsPacbPORF(pacbporfA)
# edit/create **kwargs dictionary for some forced attributes
kwargs = {}
_update_kwargs(kwargs, KWARGS_SPLICESITES)
# deal with allow_xxx attributes
if not allow_projecting:
allow_query_projecting = False
allow_sbjct_projecting = False
if not allow_mapping:
allow_query_mapping = False
allow_sbjct_mapping = False
# check if Orf objects of PacbPORFS are identical
queryOrfsIdentical = pacbporfD.orfQ.id == pacbporfA.orfQ.id
sbjctOrfsIdentical = pacbporfD.orfS.id == pacbporfA.orfS.id
# return data structure of introns
introns = {"query": [], "sbjct": []}
# Scan Orfs for splice sites.
# This has probably been performed before, but when not done,
# cached donor & acceptor sites lists seems to be empty -> no introns
pacbporfD.orfQ.scan_orf_for_pssm_splice_sites(
splicetype="donor",
min_pssm_score=kwargs["min_donor_pssm_score"],
allow_non_canonical=kwargs["allow_non_canonical_donor"],
non_canonical_min_pssm_score=kwargs["non_canonical_min_donor_pssm_score"],
)
pacbporfD.orfS.scan_orf_for_pssm_splice_sites(
splicetype="donor",
min_pssm_score=kwargs["min_donor_pssm_score"],
allow_non_canonical=kwargs["allow_non_canonical_donor"],
non_canonical_min_pssm_score=kwargs["non_canonical_min_donor_pssm_score"],
)
pacbporfA.orfQ.scan_orf_for_pssm_splice_sites(
splicetype="acceptor",
min_pssm_score=kwargs["min_acceptor_pssm_score"],
allow_non_canonical=kwargs["allow_non_canonical_acceptor"],
non_canonical_min_pssm_score=kwargs["non_canonical_min_acceptor_pssm_score"],
)
pacbporfA.orfS.scan_orf_for_pssm_splice_sites(
splicetype="acceptor",
min_pssm_score=kwargs["min_acceptor_pssm_score"],
allow_non_canonical=kwargs["allow_non_canonical_acceptor"],
non_canonical_min_pssm_score=kwargs["non_canonical_min_acceptor_pssm_score"],
)
if not queryOrfsIdentical and not sbjctOrfsIdentical:
introns1 = merge_pacbporfs_with_introns(pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns1 = _filter_aligned_introns_on_pssm_entropy_combination(introns1)
if (
pacbporfD.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD
and pacbporfA.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD
):
introns2 = merge_pacbporfs_with_closeby_independant_introns(pacbporfD, pacbporfA)
introns3 = merge_pacbporfs_with_phase_shift_introns(pacbporfD, pacbporfA)
introns4 = merge_pacbporfs_by_tinyexons(pacbporfD, pacbporfA, queryOrfSetObj, sbjctOrfSetObj)
introns5 = merge_pacbporfs_by_query_tinyexon_and_sbjct_intron(pacbporfD, pacbporfA, queryOrfSetObj)
introns6 = merge_pacbporfs_by_sbjct_tinyexon_and_query_intron(pacbporfD, pacbporfA, sbjctOrfSetObj)
introns7 = merge_pacbporfs_by_sbjct_equal_length_exon_and_query_intron(pacbporfD, pacbporfA, sbjctOrfSetObj)
introns8 = merge_pacbporfs_by_query_equal_length_exon_and_sbjct_intron(pacbporfD, pacbporfA, queryOrfSetObj)
else:
# do not allow more complex intron merging
introns2 = {}
introns3 = {}
introns4 = {}
introns5 = {}
introns6 = {}
introns7 = {}
introns8 = {}
introns9 = merge_pacbporfs_with_conserved_acceptor_introns(pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns9 = _filter_aligned_introns_on_pssm_entropy_combination(introns9)
introns10 = merge_pacbporfs_with_conserved_donor_introns(pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns10 = _filter_aligned_introns_on_pssm_entropy_combination(introns10)
# store introns obtained by most simplest case projecting/mapping
introns["query"].extend(Set([intrQ for (intrQ, intrS) in introns1]))
introns["sbjct"].extend(Set([intrS for (intrQ, intrS) in introns1]))
# only store introns from intron2 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["query"]]
keysS = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["sbjct"]]
for (intrQ, intrS, cigpacbp) in introns2:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
if k1 not in keysQ and k2 not in keysS:
introns["query"].append(intrQ)
introns["sbjct"].append(intrS)
# only store introns from intron3 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["query"]]
keysS = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["sbjct"]]
for (intrQ, intrS) in introns3:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
if k1 not in keysQ and k2 not in keysS:
introns["query"].append(intrQ)
introns["sbjct"].append(intrS)
# only store introns from intron4 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["query"]]
keysS = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["sbjct"]]
for (intrQ, intrS, pacbporf, intrQ2, intrS2) in introns4:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
k3 = (intrQ2.donor.pos, intrQ2.acceptor.pos)
k4 = (intrS2.donor.pos, intrS2.acceptor.pos)
if k1 not in keysQ and k2 not in keysS and k3 not in keysQ and k4 not in keysS:
introns["query"].append(intrQ)
introns["sbjct"].append(intrS)
introns["query"].append(intrQ2)
introns["sbjct"].append(intrS2)
# only store introns from intron5 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["query"]]
keysS = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["sbjct"]]
for (intrQ, intrS, pacbporf, intrQ2, intrS2) in introns4:
if intrQ:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
else:
k1 = None
if intrS:
k2 = (intrS.donor.pos, intrS.acceptor.pos)
else:
k2 = None
if intrQ2:
k3 = (intrQ2.donor.pos, intrQ2.acceptor.pos)
else:
k3 = None
if intrS2:
k4 = (intrS2.donor.pos, intrS2.acceptor.pos)
else:
k4 = None
if k1 not in keysQ and k2 not in keysS and k3 not in keysQ and k4 not in keysS:
introns["query"].append(intrQ)
introns["sbjct"].append(intrS)
introns["query"].append(intrQ2)
introns["sbjct"].append(intrS2)
# only store introns from intron6 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["query"]]
keysS = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["sbjct"]]
for (intrQ, intrS, pacbporf, intrQ2, intrS2) in introns6:
if intrQ:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
else:
k1 = None
if intrS:
k2 = (intrS.donor.pos, intrS.acceptor.pos)
else:
k2 = None
if intrQ2:
k3 = (intrQ2.donor.pos, intrQ2.acceptor.pos)
else:
k3 = None
if intrS2:
k4 = (intrS2.donor.pos, intrS2.acceptor.pos)
else:
k4 = None
if k1 not in keysQ and k2 not in keysS and k3 not in keysQ and k4 not in keysS:
introns["query"].append(intrQ)
introns["sbjct"].append(intrS)
introns["query"].append(intrQ2)
introns["sbjct"].append(intrS2)
# remove the 'None' in introns['sbjct'] due to latest addition
while None in introns["query"]:
introns["query"].remove(None)
while None in introns["sbjct"]:
introns["sbjct"].remove(None)
# only store introns from intron7 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["query"]]
keysS = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["sbjct"]]
for (intrS, pacbporf1, intrQ, pacbporf2, intrS2) in introns7:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
k3 = (intrS2.donor.pos, intrS2.acceptor.pos)
if k1 not in keysQ and k2 not in keysS and k3 not in keysS:
introns["query"].append(intrQ)
introns["sbjct"].append(intrS)
introns["sbjct"].append(intrS2)
# only store introns from intron8 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["query"]]
keysS = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["sbjct"]]
for (intrQ, pacbporf1, intrS, pacbporf2, intrQ2) in introns8:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
k3 = (intrQ2.donor.pos, intrQ2.acceptor.pos)
if k1 not in keysQ and k2 not in keysS and k3 not in keysQ:
introns["query"].append(intrQ)
introns["query"].append(intrQ2)
introns["sbjct"].append(intrS)
# only store introns from introns9 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["query"]]
keysS = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["sbjct"]]
for (intrQ, intrS) in introns9:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
if k1 == (2163, 2283):
print "STRACC", k1, intrQ, k1 not in keysQ
print "STRACC", k1, intrS, k2 not in keysS
# do NOT check if any of the introns is present yet;
# allow addition of each of these
if k1 not in keysQ:
introns["query"].append(intrQ)
if k2 not in keysS:
introns["sbjct"].append(intrS)
# only store introns from introns10 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["query"]]
keysS = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["sbjct"]]
for (intrQ, intrS) in introns10:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
if k1 == (1642, 1858):
print "STRDON", k1, intrQ, k1 not in keysQ
print "STRDON", k1, intrS, k2 not in keysS
# do NOT check if any of the introns is present yet;
# allow addition of each of these
if k1 not in keysQ:
introns["query"].append(intrQ)
if k2 not in keysS:
introns["sbjct"].append(intrS)
# finally, do the bridging thingy
introns0 = merge_pacbporfs_with_query_intron_bridgeing(pacbporfD, pacbporfA)
# only store introns from introns0 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["query"]]
for intrQ in introns0:
if intrQ.coords() not in keysQ:
introns["query"].append(intrQ)
# introns['query'].extend([ intrQ for (intrQ,intrS) in introns1 ] )
# introns['query'].extend([ intrQ for (intrQ,intrS,cigpacbp) in introns2 ] )
# introns['query'].extend([ intrQ for (intrQ,intrS) in introns3 ] )
# introns['query'].extend([ intrQ for (intrQ,a,b,c,d) in introns4 ] )
# introns['query'].extend([ intrQ for (a,b,c,intrQ,d) in introns4 ] )
# introns['query'].extend([ intrQ for (intrQ,a,b,c,d) in introns5 ] )
# introns['query'].extend([ intrQ for (a,b,c,intrQ,d) in introns5 ] )
# introns['sbjct'].extend([ intrS for (intrQ,intrS) in introns1 ] )
# introns['sbjct'].extend([ intrS for (intrQ,intrS,cigpacbp) in introns2 ] )
# introns['sbjct'].extend([ intrS for (intrQ,intrS) in introns3 ] )
# introns['sbjct'].extend([ intrS for (a,intrS,b,c,d) in introns4 ] )
# introns['sbjct'].extend([ intrS for (a,b,c,d,intrS) in introns4 ] )
# introns['sbjct'].extend([ intrS for (a,intrS,b,c,d) in introns5 ] )
# introns['sbjct'].extend([ intrS for (a,b,c,d,intrS) in introns5 ] )
# remove the 'None' in introns['sbjct'] due to latest addition
while None in introns["query"]:
introns["query"].remove(None)
while None in introns["sbjct"]:
introns["sbjct"].remove(None)
elif not queryOrfsIdentical:
seqerror = merge_pacbporf_with_sequenceerror_in_query(pacbporfD, pacbporfA)
introns1 = merge_pacbporfs_by_intron_in_query(pacbporfD, pacbporfA)
if (
pacbporfD.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD
and pacbporfA.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD
):
introns2 = merge_pacbporfs_by_intron_tinyexon_intron_in_query(pacbporfD, pacbporfA, queryOrfSetObj)
introns3 = merge_pacbporfs_by_two_tinyexons_in_query(pacbporfD, pacbporfA, queryOrfSetObj)
else:
# do not allow more complex intron merging
introns2 = {}
introns3 = {}
# store sequencerror if it exists
if seqerror:
introns["query"].append(seqerror)
# store introns obtained by most simplest case projecting/mapping
introns["query"].extend([prj.projected_introns[0] for prj in introns1])
# only store introns from intron2 that are NOT encountered already in introns1
keys = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["query"]]
for (intr1, intr2, exon) in introns2:
k1 = (intr1.donor.pos, intr1.acceptor.pos)
k2 = (intr2.donor.pos, intr2.acceptor.pos)
if k1 not in keys and k2 not in keys:
introns["query"].append(intr1)
introns["query"].append(intr2)
# only store introns from intron2 that are NOT encountered already in introns1
keys = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["query"]]
for (intr1, intr2, intr3, exon1, exon2) in introns3:
k1 = (intr1.donor.pos, intr1.acceptor.pos)
k2 = (intr2.donor.pos, intr2.acceptor.pos)
k3 = (intr3.donor.pos, intr3.acceptor.pos)
if k1 not in keys and k2 not in keys and k3 not in keys:
introns["query"].append(intr1)
introns["query"].append(intr2)
introns["query"].append(intr3)
if not introns["query"] and allow_sbjct_mapping and allow_query_mapping:
# just bridge Orfs by **best** intron(s).
introns0 = merge_pacbporfs_with_query_intron_bridgeing(pacbporfD, pacbporfA)
# potential stopless 3n intron in SBJCT
introns1 = merge_pacbporfs_with_introns(pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns1 = _filter_aligned_introns_on_pssm_entropy_combination(introns1)
# apply stopless3n intron filtering
introns1 = _filter_aligned_stopless_3n_introns(introns1)
introns2 = merge_pacbporfs_with_closeby_independant_introns(pacbporfD, pacbporfA)
if (
pacbporfD.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD
and pacbporfA.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD
):
introns3 = merge_pacbporfs_with_phase_shift_introns(pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns3 = _filter_aligned_introns_on_pssm_entropy_combination(introns3)
# apply stopless3n intron filtering
introns3 = _filter_aligned_stopless_3n_introns(introns3)
else:
# do not allow more complex intron merging
introns3 = {}
# only store introns from that are NOT encountered already
keys = [intron.coords() for intron in introns["query"]]
for intrQ, intrS in introns1:
if intrQ.coords() not in keys:
introns["query"].append(intrQ)
keys = [intron.coords() for intron in introns["query"]]
for (intrQ, intrS, cigpacbp) in introns2:
if intrQ.coords() not in keys:
introns["query"].append(intrQ)
keys = [intron.coords() for intron in introns["query"]]
for intrQ, intrS in introns3:
if intrQ.coords() not in keys:
introns["query"].append(intrQ)
keys = [intron.coords() for intron in introns["query"]]
for intron in introns0:
if intron.coords() not in keys:
introns["query"].append(intron)
keys = [intron.coords() for intron in introns["query"]]
keys = [intron.coords() for intron in introns["sbjct"]]
for intrQ, intrS in introns1:
if intrS.coords() not in keys:
introns["query"].append(intrS)
keys = [intron.coords() for intron in introns["sbjct"]]
for (intrQ, intrS, cigpacbp) in introns2:
if intrS.coords() not in keys:
introns["query"].append(intrS)
keys = [intron.coords() for intron in introns["sbjct"]]
for intrQ, intrS in introns3:
if intrS.coords() not in keys:
introns["query"].append(intrS)
keys = [intron.coords() for intron in introns["sbjct"]]
elif not introns["query"]:
# just bridge Orfs by **best** intron(s).
introns0 = merge_pacbporfs_with_query_intron_bridgeing(pacbporfD, pacbporfA)
# only store introns from that are NOT encountered already
keys = [intron.coords() for intron in introns["query"]]
for intron in introns0:
if intron.coords() not in keys:
introns["query"].append(intron)
else:
# projecting introns yielded results; do not try mapping
pass
elif not sbjctOrfsIdentical:
introns1 = merge_pacbporfs_by_intron_in_sbjct(pacbporfD, pacbporfA)
if (
pacbporfD.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD
and pacbporfA.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD
):
introns2 = merge_pacbporfs_by_intron_tinyexon_intron_in_sbjct(pacbporfD, pacbporfA, sbjctOrfSetObj)
introns3 = merge_pacbporfs_by_two_tinyexons_in_sbjct(pacbporfD, pacbporfA, sbjctOrfSetObj)
else:
# do not allow more complex intron merging
introns2 = {}
introns3 = {}
# store introns obtained by most simplest case projecting/mapping
introns["sbjct"].extend([prj.projected_introns[0] for prj in introns1])
# only store introns from intron2 that are NOT encountered already in introns1
keys = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["sbjct"]]
for (intr1, intr2, exon) in introns2:
k1 = (intr1.donor.pos, intr1.acceptor.pos)
k2 = (intr2.donor.pos, intr2.acceptor.pos)
if k1 not in keys and k2 not in keys:
introns["sbjct"].append(intr1)
introns["sbjct"].append(intr2)
# only store introns from intron2 that are NOT encountered already in introns1
keys = [(intron.donor.pos, intron.acceptor.pos) for intron in introns["sbjct"]]
for (intr1, intr2, intr3, exon1, exon2) in introns3:
k1 = (intr1.donor.pos, intr1.acceptor.pos)
k2 = (intr2.donor.pos, intr2.acceptor.pos)
k3 = (intr3.donor.pos, intr3.acceptor.pos)
if k1 not in keys and k2 not in keys and k3 not in keys:
introns["sbjct"].append(intr1)
introns["sbjct"].append(intr2)
introns["sbjct"].append(intr3)
if not introns["sbjct"] and allow_sbjct_mapping and allow_query_mapping:
# potential stopless 3n intron in QUERY
introns1 = merge_pacbporfs_with_introns(pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns1 = _filter_aligned_introns_on_pssm_entropy_combination(introns1)
# apply stopless3n intron filtering
introns1 = _filter_aligned_stopless_3n_introns(introns1)
introns2 = merge_pacbporfs_with_closeby_independant_introns(pacbporfD, pacbporfA)
if (
pacbporfD.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD
and pacbporfA.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD
):
introns3 = merge_pacbporfs_with_phase_shift_introns(pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns3 = _filter_aligned_introns_on_pssm_entropy_combination(introns3)
# apply stopless3n intron filtering
introns3 = _filter_aligned_stopless_3n_introns(introns3)
else:
# do not allow more complex intron merging
introns3 = {}
# store introns
introns["query"].extend(Set([intrQ for (intrQ, intrS) in introns1]))
introns["sbjct"].extend(Set([intrS for (intrQ, intrS) in introns1]))
introns["query"].extend([intrQ for (intrQ, intrS, cigpacbp) in introns2])
introns["query"].extend([intrQ for (intrQ, intrS) in introns3])
introns["sbjct"].extend([intrS for (intrQ, intrS, cigpacbp) in introns2])
introns["sbjct"].extend([intrS for (intrQ, intrS) in introns3])
else:
# projecting introns yielded results; do not try mapping
pass
elif queryOrfsIdentical and sbjctOrfsIdentical:
if allow_query_mapping:
introns1 = merge_pacbporfs_by_inframe_intron_in_query(pacbporfD, pacbporfA)
else:
# no mapping (unigene or continious alignment provided)
introns1 = []
if allow_sbjct_mapping:
introns2 = merge_pacbporfs_by_inframe_intron_in_sbjct(pacbporfD, pacbporfA)
else:
# no mapping (unigene or continious alignment provided)
introns2 = []
if allow_sbjct_mapping and allow_query_mapping:
introns3 = merge_pacbporfs_with_introns(pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns3 = _filter_aligned_introns_on_pssm_entropy_combination(introns3)
# apply stopless3n intron filtering
introns3 = _filter_aligned_stopless_3n_introns(introns3)
else:
# no mapping (unigene or continious alignment provided)
introns3 = []
# introns4 = merge_pacbporfs_with_closeby_independant_introns(
# pacbporfD,pacbporfA)
# introns5 = merge_pacbporfs_with_phase_shift_introns(
# pacbporfD,pacbporfA)
introns["query"].extend([prj.projected_introns[0] for prj in introns1])
introns["sbjct"].extend([prj.projected_introns[0] for prj in introns2])
introns["query"].extend([intrQ for (intrQ, intrS) in introns3])
introns["sbjct"].extend([intrS for (intrQ, intrS) in introns3])
else:
# none of these cases; allow_projecting or allow_mapping == False!
pass
# Filter for stopless3n introns
introns["query"] = _filter_stopless_3n_introns(introns["query"])
introns["sbjct"] = _filter_stopless_3n_introns(introns["sbjct"])
# return list of introns
return introns
def _find_qq_tinyexons_as_pacbporfs(target,tinyexondata,PCG,min_discovery_count=2):
""" """
target_tinyexon_pacbporf_data = {}
for informant in tinyexondata.keys():
if informant == target: continue
thepacbporfs = order_pacbporf_list(
PCG.get_pacbps_by_organisms(target,informant))
for exonQ in tinyexondata[target]:
if exonQ.orf.id in [ pf.orfQ.id for pf in thepacbporfs ]: continue
for (prevpos,nextpos) in [ (pos-1,pos) for pos in range(1,len(thepacbporfs)) ]:
prevPF = thepacbporfs[prevpos]
nextPF = thepacbporfs[nextpos]
if prevPF.orfS.id == nextPF.orfS.id:
# check if PacbPORFs are positioned more or less okay
if prevPF.distance_towards(nextPF) > 20: continue
# check if exonQ is positioned ~between these PacbPORFs
if exonQ.orf.dnapos2aapos(exonQ.end) < max(prevPF.alignment_protein_range_query())-12:
continue
if exonQ.orf.dnapos2aapos(exonQ.start) > min(nextPF.alignment_protein_range_query())+12:
continue
# check if gap can be projected already by a perfect intron
introns = merge_pacbporfs_by_intron_in_query(
prevPF,nextPF,max_aa_offset=1)
# if introns found => continue
if introns: continue
# orfObj is the orfS of prevPF or nextPF (just take any)
orfObj = prevPF.orfS
# assign elegiable range of tinyexon match on SBJCT
aapos_sbjct_range = range(
max(prevPF.alignment_protein_range_sbjct())-12,
min(nextPF.alignment_protein_range_sbjct())+12
)
tinyexonmatches = _find_match_on_orfobj(exonQ,orfObj)
for (aaseq,aapos) in tinyexonmatches:
# check if the match is obtained in the expected
# sbjct AA range; if not, ignore the match
if aapos not in aapos_sbjct_range: continue
# make pacbporf object
pacbpobj = PacbP(input=(
exonQ.proteinsequence(), aaseq,
exonQ.orf.dnapos2aapos(exonQ.start), aapos ) )
pacbporfobj = pacbp2pacbporf(pacbpobj,exonQ.orf,orfObj)
pacbporfobj.extend_pacbporf_after_stops()
# remove included pacbporfs
is_suborsuperset = False
for accepted_pacbporf in thepacbporfs:
if pacbporfobj.issubsetorsuperset(accepted_pacbporf):
is_suborsuperset = True
break
if is_suborsuperset:
continue
# check if 2 (perfect) introns can be projected
introns5p = merge_pacbporfs_by_intron_in_query(
prevPF,pacbporfobj,
max_aa_offset=1,
max_intron_nt_length=None)
#max_intron_nt_length=140)
introns3p = merge_pacbporfs_by_intron_in_query(
pacbporfobj,nextPF,
max_aa_offset=1,
max_intron_nt_length=None)
#max_intron_nt_length=140)
# continue if not is_confirmed_by_intron_projection
if not introns5p or not introns3p: continue
# check if placeable in PCG/pacbporflist
distPrev = prevPF.distance_towards(pacbporfobj)
distNext = pacbporfobj.distance_towards(nextPF)
ovrlPrev = pacbporfobj.overlap(prevPF)
ovrlNext = pacbporfobj.overlap(nextPF)
if distPrev and distNext:
rejected = False
elif not distPrev and ovrlPrev:
rejected = False
elif not distNext and ovrlNext:
rejected = False
elif ovrlPrev and ovrlNext:
rejected = False
else:
rejected = True
print "OKAY", exonQ.proteinsequence(), aaseq, rejected, informant, (distPrev,distNext,ovrlPrev,ovrlNext)
# label pacbporf as found by tinyexon QQ
pacbporfobj._tinyexon_label = "QQ"
# store to target_tinyexon_pacbporf_data
key = (exonQ.proteinsequence(),exonQ.start)
_update_tinyexon_pacbporf_dict(
target_tinyexon_pacbporf_data,
key,pacbporfobj,rejected,informant)
# cleanup tinyexon protein matches that have been observed to litte
_remove_dict_elements_with_short_value_list(
target_tinyexon_pacbporf_data,
min_value_list_size=min_discovery_count)
# return target_tinyexon_pacbporf_data
return target_tinyexon_pacbporf_data
def _find_qp_and_pq_tinyexons_as_pacbporfs(target,tinyexondata,PCG,min_discovery_count=2):
""" """
target_tinyexon_pacbporf_data = {}
for informant in tinyexondata.keys():
if informant == target: continue
thepacbporfs = order_pacbporf_list(
PCG.get_pacbps_by_organisms(target,informant))
for exonQ in tinyexondata[target]:
if exonQ.orf.id in [ pf.orfQ.id for pf in thepacbporfs ]: continue
for orfObj in PCG.get_orfs_of_graph(organism=informant):
tinyexonmatches = _find_qp_or_pq_match_on_orfobj(exonQ,orfObj)
for (aaseq,aapos) in tinyexonmatches:
# make pacbporf object
pacbpobj = PacbP(input=(
exonQ.proteinsequence(), aaseq,
exonQ.orf.dnapos2aapos(exonQ.start), aapos ) )
pacbporfobj = pacbp2pacbporf(pacbpobj,exonQ.orf,orfObj)
pacbporfobj.extend_pacbporf_after_stops()
# remove included pacbporfs
is_suborsuperset = False
for accepted_pacbporf in thepacbporfs:
if pacbporfobj.issubsetorsuperset(accepted_pacbporf):
is_suborsuperset = True
break
if is_suborsuperset:
continue
# check if a (perfect) intron can be projected
is_confirmed_by_intron_projection = False
for accepted_pacbporf in thepacbporfs:
if accepted_pacbporf.orfS.id == pacbporfobj.orfS.id:
if min(accepted_pacbporf.alignment_dna_range_query()) > min(pacbporfobj.alignment_dna_range_query()):
try:
introns = merge_pacbporfs_by_intron_in_query(
pacbporfobj,accepted_pacbporf,
max_aa_offset=0,
max_intron_nt_length=None)
#max_intron_nt_length=140)
except IndexError:
# unexpected event: TODO: solve in merge_pacbporfs_by_intron_in_query
introns = []
else:
try:
introns = merge_pacbporfs_by_intron_in_query(
accepted_pacbporf,pacbporfobj,
max_aa_offset=0,
max_intron_nt_length=None)
#max_intron_nt_length=140)
except IndexError:
# unexpected event: TODO: solve in merge_pacbporfs_by_intron_in_query
introns = []
if len(introns) >= 1:
is_confirmed_by_intron_projection = True
break
# continue if not is_confirmed_by_intron_projection
if not is_confirmed_by_intron_projection: continue
# check if placeable in PCG/pacbporflist
rejected = [ pf.is_postioned_compatibly(pacbporfobj) for pf in thepacbporfs ].count(False) > 0
# label pacbporf as found by tinyexon QP
pacbporfobj._tinyexon_label = "QP"
# store to target_tinyexon_pacbporf_data
key = (exonQ.proteinsequence(),exonQ.start)
_update_tinyexon_pacbporf_dict(
target_tinyexon_pacbporf_data,
key,pacbporfobj,rejected,informant)
# cleanup tinyexon protein matches that have been observed to litte
_remove_dict_elements_with_short_value_list(
target_tinyexon_pacbporf_data,
min_value_list_size=min_discovery_count)
# return target_tinyexon_pacbporf_data
return target_tinyexon_pacbporf_data
def _find_qq_tinyexons_as_pacbporfs(target,
tinyexondata,
PCG,
min_discovery_count=2):
""" """
target_tinyexon_pacbporf_data = {}
for informant in tinyexondata.keys():
if informant == target: continue
thepacbporfs = order_pacbporf_list(
PCG.get_pacbps_by_organisms(target, informant))
for exonQ in tinyexondata[target]:
if exonQ.orf.id in [pf.orfQ.id for pf in thepacbporfs]: continue
for (prevpos, nextpos) in [(pos - 1, pos)
for pos in range(1, len(thepacbporfs))]:
prevPF = thepacbporfs[prevpos]
nextPF = thepacbporfs[nextpos]
if prevPF.orfS.id == nextPF.orfS.id:
# check if PacbPORFs are positioned more or less okay
if prevPF.distance_towards(nextPF) > 20: continue
# check if exonQ is positioned ~between these PacbPORFs
if exonQ.orf.dnapos2aapos(exonQ.end) < max(
prevPF.alignment_protein_range_query()) - 12:
continue
if exonQ.orf.dnapos2aapos(exonQ.start) > min(
nextPF.alignment_protein_range_query()) + 12:
continue
# check if gap can be projected already by a perfect intron
introns = merge_pacbporfs_by_intron_in_query(
prevPF, nextPF, max_aa_offset=1)
# if introns found => continue
if introns: continue
# orfObj is the orfS of prevPF or nextPF (just take any)
orfObj = prevPF.orfS
# assign elegiable range of tinyexon match on SBJCT
aapos_sbjct_range = range(
max(prevPF.alignment_protein_range_sbjct()) - 12,
min(nextPF.alignment_protein_range_sbjct()) + 12)
tinyexonmatches = _find_match_on_orfobj(exonQ, orfObj)
for (aaseq, aapos) in tinyexonmatches:
# check if the match is obtained in the expected
# sbjct AA range; if not, ignore the match
if aapos not in aapos_sbjct_range: continue
# make pacbporf object
pacbpobj = PacbP(
input=(exonQ.proteinsequence(), aaseq,
exonQ.orf.dnapos2aapos(exonQ.start), aapos))
pacbporfobj = pacbp2pacbporf(pacbpobj, exonQ.orf,
orfObj)
pacbporfobj.extend_pacbporf_after_stops()
# remove included pacbporfs
is_suborsuperset = False
for accepted_pacbporf in thepacbporfs:
if pacbporfobj.issubsetorsuperset(
accepted_pacbporf):
is_suborsuperset = True
break
if is_suborsuperset:
continue
# check if 2 (perfect) introns can be projected
introns5p = merge_pacbporfs_by_intron_in_query(
prevPF,
pacbporfobj,
max_aa_offset=1,
max_intron_nt_length=None)
#max_intron_nt_length=140)
introns3p = merge_pacbporfs_by_intron_in_query(
pacbporfobj,
nextPF,
max_aa_offset=1,
max_intron_nt_length=None)
#max_intron_nt_length=140)
# continue if not is_confirmed_by_intron_projection
if not introns5p or not introns3p: continue
# check if placeable in PCG/pacbporflist
distPrev = prevPF.distance_towards(pacbporfobj)
distNext = pacbporfobj.distance_towards(nextPF)
ovrlPrev = pacbporfobj.overlap(prevPF)
ovrlNext = pacbporfobj.overlap(nextPF)
if distPrev and distNext:
rejected = False
elif not distPrev and ovrlPrev:
rejected = False
elif not distNext and ovrlNext:
rejected = False
elif ovrlPrev and ovrlNext:
rejected = False
else:
rejected = True
print "OKAY", exonQ.proteinsequence(
), aaseq, rejected, informant, (distPrev, distNext,
ovrlPrev, ovrlNext)
# label pacbporf as found by tinyexon QQ
pacbporfobj._tinyexon_label = "QQ"
# store to target_tinyexon_pacbporf_data
key = (exonQ.proteinsequence(), exonQ.start)
_update_tinyexon_pacbporf_dict(
target_tinyexon_pacbporf_data, key, pacbporfobj,
rejected, informant)
# cleanup tinyexon protein matches that have been observed to litte
_remove_dict_elements_with_short_value_list(
target_tinyexon_pacbporf_data, min_value_list_size=min_discovery_count)
# return target_tinyexon_pacbporf_data
return target_tinyexon_pacbporf_data
def _find_qp_and_pq_tinyexons_as_pacbporfs(target,
tinyexondata,
PCG,
min_discovery_count=2):
""" """
target_tinyexon_pacbporf_data = {}
for informant in tinyexondata.keys():
if informant == target: continue
thepacbporfs = order_pacbporf_list(
PCG.get_pacbps_by_organisms(target, informant))
for exonQ in tinyexondata[target]:
if exonQ.orf.id in [pf.orfQ.id for pf in thepacbporfs]: continue
for orfObj in PCG.get_orfs_of_graph(organism=informant):
tinyexonmatches = _find_qp_or_pq_match_on_orfobj(exonQ, orfObj)
for (aaseq, aapos) in tinyexonmatches:
# make pacbporf object
pacbpobj = PacbP(
input=(exonQ.proteinsequence(), aaseq,
exonQ.orf.dnapos2aapos(exonQ.start), aapos))
pacbporfobj = pacbp2pacbporf(pacbpobj, exonQ.orf, orfObj)
pacbporfobj.extend_pacbporf_after_stops()
# remove included pacbporfs
is_suborsuperset = False
for accepted_pacbporf in thepacbporfs:
if pacbporfobj.issubsetorsuperset(accepted_pacbporf):
is_suborsuperset = True
break
if is_suborsuperset:
continue
# check if a (perfect) intron can be projected
is_confirmed_by_intron_projection = False
for accepted_pacbporf in thepacbporfs:
if accepted_pacbporf.orfS.id == pacbporfobj.orfS.id:
if min(accepted_pacbporf.alignment_dna_range_query(
)) > min(pacbporfobj.alignment_dna_range_query()):
try:
introns = merge_pacbporfs_by_intron_in_query(
pacbporfobj,
accepted_pacbporf,
max_aa_offset=0,
max_intron_nt_length=None)
#max_intron_nt_length=140)
except IndexError:
# unexpected event: TODO: solve in merge_pacbporfs_by_intron_in_query
introns = []
else:
try:
introns = merge_pacbporfs_by_intron_in_query(
accepted_pacbporf,
pacbporfobj,
max_aa_offset=0,
max_intron_nt_length=None)
#max_intron_nt_length=140)
except IndexError:
# unexpected event: TODO: solve in merge_pacbporfs_by_intron_in_query
introns = []
if len(introns) >= 1:
is_confirmed_by_intron_projection = True
break
# continue if not is_confirmed_by_intron_projection
if not is_confirmed_by_intron_projection: continue
# check if placeable in PCG/pacbporflist
rejected = [
pf.is_postioned_compatibly(pacbporfobj)
for pf in thepacbporfs
].count(False) > 0
# label pacbporf as found by tinyexon QP
pacbporfobj._tinyexon_label = "QP"
# store to target_tinyexon_pacbporf_data
key = (exonQ.proteinsequence(), exonQ.start)
_update_tinyexon_pacbporf_dict(
target_tinyexon_pacbporf_data, key, pacbporfobj,
rejected, informant)
# cleanup tinyexon protein matches that have been observed to litte
_remove_dict_elements_with_short_value_list(
target_tinyexon_pacbporf_data, min_value_list_size=min_discovery_count)
# return target_tinyexon_pacbporf_data
return target_tinyexon_pacbporf_data
def merge_pacbporfs(pacbporfD,
pacbporfA,
queryOrfSetObj,
sbjctOrfSetObj,
allow_query_projecting=True,
allow_sbjct_projecting=True,
allow_query_mapping=True,
allow_sbjct_mapping=True,
allow_projecting=True,
allow_mapping=True,
verbose=False):
"""
Merge 2 PacbPORF objects with an interface into a gene structure
@type pacbporfD: PacbPORF object
@param pacbporfD: PacbPORF object that has to deliver PSSM donor objects
@type pacbporfA: PacbPORF object
@param pacbporfA: PacbPORF object that has to deliver PSSM acceptor objects
@type verbose: Boolean
@param verbose: print status/debugging messages to STDOUT
@rtype: list
@return: list with ( intron, intron ), in query and sbjct
"""
# input validation
IsPacbPORF(pacbporfD)
IsPacbPORF(pacbporfA)
# edit/create **kwargs dictionary for some forced attributes
kwargs = {}
_update_kwargs(kwargs, KWARGS_SPLICESITES)
# deal with allow_xxx attributes
if not allow_projecting:
allow_query_projecting = False
allow_sbjct_projecting = False
if not allow_mapping:
allow_query_mapping = False
allow_sbjct_mapping = False
# check if Orf objects of PacbPORFS are identical
queryOrfsIdentical = pacbporfD.orfQ.id == pacbporfA.orfQ.id
sbjctOrfsIdentical = pacbporfD.orfS.id == pacbporfA.orfS.id
# return data structure of introns
introns = {'query': [], 'sbjct': []}
# Scan Orfs for splice sites.
# This has probably been performed before, but when not done,
# cached donor & acceptor sites lists seems to be empty -> no introns
pacbporfD.orfQ.scan_orf_for_pssm_splice_sites(
splicetype="donor",
min_pssm_score=kwargs['min_donor_pssm_score'],
allow_non_canonical=kwargs['allow_non_canonical_donor'],
non_canonical_min_pssm_score=kwargs[
'non_canonical_min_donor_pssm_score'])
pacbporfD.orfS.scan_orf_for_pssm_splice_sites(
splicetype="donor",
min_pssm_score=kwargs['min_donor_pssm_score'],
allow_non_canonical=kwargs['allow_non_canonical_donor'],
non_canonical_min_pssm_score=kwargs[
'non_canonical_min_donor_pssm_score'])
pacbporfA.orfQ.scan_orf_for_pssm_splice_sites(
splicetype="acceptor",
min_pssm_score=kwargs['min_acceptor_pssm_score'],
allow_non_canonical=kwargs['allow_non_canonical_acceptor'],
non_canonical_min_pssm_score=kwargs[
'non_canonical_min_acceptor_pssm_score'])
pacbporfA.orfS.scan_orf_for_pssm_splice_sites(
splicetype="acceptor",
min_pssm_score=kwargs['min_acceptor_pssm_score'],
allow_non_canonical=kwargs['allow_non_canonical_acceptor'],
non_canonical_min_pssm_score=kwargs[
'non_canonical_min_acceptor_pssm_score'])
if not queryOrfsIdentical and not sbjctOrfsIdentical:
introns1 = merge_pacbporfs_with_introns(pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns1 = _filter_aligned_introns_on_pssm_entropy_combination(
introns1)
if pacbporfD.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD and\
pacbporfA.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD:
introns2 = merge_pacbporfs_with_closeby_independant_introns(
pacbporfD, pacbporfA)
introns3 = merge_pacbporfs_with_phase_shift_introns(
pacbporfD, pacbporfA)
introns4 = merge_pacbporfs_by_tinyexons(pacbporfD, pacbporfA,
queryOrfSetObj,
sbjctOrfSetObj)
introns5 = merge_pacbporfs_by_query_tinyexon_and_sbjct_intron(
pacbporfD, pacbporfA, queryOrfSetObj)
introns6 = merge_pacbporfs_by_sbjct_tinyexon_and_query_intron(
pacbporfD, pacbporfA, sbjctOrfSetObj)
introns7 = merge_pacbporfs_by_sbjct_equal_length_exon_and_query_intron(
pacbporfD, pacbporfA, sbjctOrfSetObj)
introns8 = merge_pacbporfs_by_query_equal_length_exon_and_sbjct_intron(
pacbporfD, pacbporfA, queryOrfSetObj)
else:
# do not allow more complex intron merging
introns2 = {}
introns3 = {}
introns4 = {}
introns5 = {}
introns6 = {}
introns7 = {}
introns8 = {}
introns9 = merge_pacbporfs_with_conserved_acceptor_introns(
pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns9 = _filter_aligned_introns_on_pssm_entropy_combination(
introns9)
introns10 = merge_pacbporfs_with_conserved_donor_introns(
pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns10 = _filter_aligned_introns_on_pssm_entropy_combination(
introns10)
# store introns obtained by most simplest case projecting/mapping
introns['query'].extend(Set([intrQ for (intrQ, intrS) in introns1]))
introns['sbjct'].extend(Set([intrS for (intrQ, intrS) in introns1]))
# only store introns from intron2 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['query']]
keysS = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['sbjct']]
for (intrQ, intrS, cigpacbp) in introns2:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
if k1 not in keysQ and k2 not in keysS:
introns['query'].append(intrQ)
introns['sbjct'].append(intrS)
# only store introns from intron3 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['query']]
keysS = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['sbjct']]
for (intrQ, intrS) in introns3:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
if k1 not in keysQ and k2 not in keysS:
introns['query'].append(intrQ)
introns['sbjct'].append(intrS)
# only store introns from intron4 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['query']]
keysS = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['sbjct']]
for (intrQ, intrS, pacbporf, intrQ2, intrS2) in introns4:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
k3 = (intrQ2.donor.pos, intrQ2.acceptor.pos)
k4 = (intrS2.donor.pos, intrS2.acceptor.pos)
if k1 not in keysQ and k2 not in keysS and k3 not in keysQ and k4 not in keysS:
introns['query'].append(intrQ)
introns['sbjct'].append(intrS)
introns['query'].append(intrQ2)
introns['sbjct'].append(intrS2)
# only store introns from intron5 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['query']]
keysS = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['sbjct']]
for (intrQ, intrS, pacbporf, intrQ2, intrS2) in introns4:
if intrQ: k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
else: k1 = None
if intrS: k2 = (intrS.donor.pos, intrS.acceptor.pos)
else: k2 = None
if intrQ2: k3 = (intrQ2.donor.pos, intrQ2.acceptor.pos)
else: k3 = None
if intrS2: k4 = (intrS2.donor.pos, intrS2.acceptor.pos)
else: k4 = None
if k1 not in keysQ and k2 not in keysS and k3 not in keysQ and k4 not in keysS:
introns['query'].append(intrQ)
introns['sbjct'].append(intrS)
introns['query'].append(intrQ2)
introns['sbjct'].append(intrS2)
# only store introns from intron6 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['query']]
keysS = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['sbjct']]
for (intrQ, intrS, pacbporf, intrQ2, intrS2) in introns6:
if intrQ: k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
else: k1 = None
if intrS: k2 = (intrS.donor.pos, intrS.acceptor.pos)
else: k2 = None
if intrQ2: k3 = (intrQ2.donor.pos, intrQ2.acceptor.pos)
else: k3 = None
if intrS2: k4 = (intrS2.donor.pos, intrS2.acceptor.pos)
else: k4 = None
if k1 not in keysQ and k2 not in keysS and k3 not in keysQ and k4 not in keysS:
introns['query'].append(intrQ)
introns['sbjct'].append(intrS)
introns['query'].append(intrQ2)
introns['sbjct'].append(intrS2)
# remove the 'None' in introns['sbjct'] due to latest addition
while None in introns['query']:
introns['query'].remove(None)
while None in introns['sbjct']:
introns['sbjct'].remove(None)
# only store introns from intron7 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['query']]
keysS = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['sbjct']]
for (intrS, pacbporf1, intrQ, pacbporf2, intrS2) in introns7:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
k3 = (intrS2.donor.pos, intrS2.acceptor.pos)
if k1 not in keysQ and k2 not in keysS and k3 not in keysS:
introns['query'].append(intrQ)
introns['sbjct'].append(intrS)
introns['sbjct'].append(intrS2)
# only store introns from intron8 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['query']]
keysS = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['sbjct']]
for (intrQ, pacbporf1, intrS, pacbporf2, intrQ2) in introns8:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
k3 = (intrQ2.donor.pos, intrQ2.acceptor.pos)
if k1 not in keysQ and k2 not in keysS and k3 not in keysQ:
introns['query'].append(intrQ)
introns['query'].append(intrQ2)
introns['sbjct'].append(intrS)
# only store introns from introns9 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['query']]
keysS = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['sbjct']]
for (intrQ, intrS) in introns9:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
if k1 == (2163, 2283):
print "STRACC", k1, intrQ, k1 not in keysQ
print "STRACC", k1, intrS, k2 not in keysS
# do NOT check if any of the introns is present yet;
# allow addition of each of these
if k1 not in keysQ:
introns['query'].append(intrQ)
if k2 not in keysS:
introns['sbjct'].append(intrS)
# only store introns from introns10 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['query']]
keysS = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['sbjct']]
for (intrQ, intrS) in introns10:
k1 = (intrQ.donor.pos, intrQ.acceptor.pos)
k2 = (intrS.donor.pos, intrS.acceptor.pos)
if k1 == (1642, 1858):
print "STRDON", k1, intrQ, k1 not in keysQ
print "STRDON", k1, intrS, k2 not in keysS
# do NOT check if any of the introns is present yet;
# allow addition of each of these
if k1 not in keysQ:
introns['query'].append(intrQ)
if k2 not in keysS:
introns['sbjct'].append(intrS)
# finally, do the bridging thingy
introns0 = merge_pacbporfs_with_query_intron_bridgeing(
pacbporfD, pacbporfA)
# only store introns from introns0 that are NOT encountered already in introns1
keysQ = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['query']]
for intrQ in introns0:
if intrQ.coords() not in keysQ:
introns['query'].append(intrQ)
#introns['query'].extend([ intrQ for (intrQ,intrS) in introns1 ] )
#introns['query'].extend([ intrQ for (intrQ,intrS,cigpacbp) in introns2 ] )
#introns['query'].extend([ intrQ for (intrQ,intrS) in introns3 ] )
#introns['query'].extend([ intrQ for (intrQ,a,b,c,d) in introns4 ] )
#introns['query'].extend([ intrQ for (a,b,c,intrQ,d) in introns4 ] )
#introns['query'].extend([ intrQ for (intrQ,a,b,c,d) in introns5 ] )
#introns['query'].extend([ intrQ for (a,b,c,intrQ,d) in introns5 ] )
#introns['sbjct'].extend([ intrS for (intrQ,intrS) in introns1 ] )
#introns['sbjct'].extend([ intrS for (intrQ,intrS,cigpacbp) in introns2 ] )
#introns['sbjct'].extend([ intrS for (intrQ,intrS) in introns3 ] )
#introns['sbjct'].extend([ intrS for (a,intrS,b,c,d) in introns4 ] )
#introns['sbjct'].extend([ intrS for (a,b,c,d,intrS) in introns4 ] )
#introns['sbjct'].extend([ intrS for (a,intrS,b,c,d) in introns5 ] )
#introns['sbjct'].extend([ intrS for (a,b,c,d,intrS) in introns5 ] )
# remove the 'None' in introns['sbjct'] due to latest addition
while None in introns['query']:
introns['query'].remove(None)
while None in introns['sbjct']:
introns['sbjct'].remove(None)
elif not queryOrfsIdentical:
seqerror = merge_pacbporf_with_sequenceerror_in_query(
pacbporfD, pacbporfA)
introns1 = merge_pacbporfs_by_intron_in_query(pacbporfD, pacbporfA)
if pacbporfD.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD and\
pacbporfA.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD:
introns2 = merge_pacbporfs_by_intron_tinyexon_intron_in_query(
pacbporfD, pacbporfA, queryOrfSetObj)
introns3 = merge_pacbporfs_by_two_tinyexons_in_query(
pacbporfD, pacbporfA, queryOrfSetObj)
else:
# do not allow more complex intron merging
introns2 = {}
introns3 = {}
# store sequencerror if it exists
if seqerror: introns['query'].append(seqerror)
# store introns obtained by most simplest case projecting/mapping
introns['query'].extend([prj.projected_introns[0] for prj in introns1])
# only store introns from intron2 that are NOT encountered already in introns1
keys = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['query']]
for (intr1, intr2, exon) in introns2:
k1 = (intr1.donor.pos, intr1.acceptor.pos)
k2 = (intr2.donor.pos, intr2.acceptor.pos)
if k1 not in keys and k2 not in keys:
introns['query'].append(intr1)
introns['query'].append(intr2)
# only store introns from intron2 that are NOT encountered already in introns1
keys = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['query']]
for (intr1, intr2, intr3, exon1, exon2) in introns3:
k1 = (intr1.donor.pos, intr1.acceptor.pos)
k2 = (intr2.donor.pos, intr2.acceptor.pos)
k3 = (intr3.donor.pos, intr3.acceptor.pos)
if k1 not in keys and k2 not in keys and k3 not in keys:
introns['query'].append(intr1)
introns['query'].append(intr2)
introns['query'].append(intr3)
if not introns['query'] and allow_sbjct_mapping and allow_query_mapping:
# just bridge Orfs by **best** intron(s).
introns0 = merge_pacbporfs_with_query_intron_bridgeing(
pacbporfD, pacbporfA)
# potential stopless 3n intron in SBJCT
introns1 = merge_pacbporfs_with_introns(pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns1 = _filter_aligned_introns_on_pssm_entropy_combination(
introns1)
# apply stopless3n intron filtering
introns1 = _filter_aligned_stopless_3n_introns(introns1)
introns2 = merge_pacbporfs_with_closeby_independant_introns(
pacbporfD, pacbporfA)
if pacbporfD.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD and\
pacbporfA.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD:
introns3 = merge_pacbporfs_with_phase_shift_introns(
pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns3 = _filter_aligned_introns_on_pssm_entropy_combination(
introns3)
# apply stopless3n intron filtering
introns3 = _filter_aligned_stopless_3n_introns(introns3)
else:
# do not allow more complex intron merging
introns3 = {}
# only store introns from that are NOT encountered already
keys = [intron.coords() for intron in introns['query']]
for intrQ, intrS in introns1:
if intrQ.coords() not in keys:
introns['query'].append(intrQ)
keys = [intron.coords() for intron in introns['query']]
for (intrQ, intrS, cigpacbp) in introns2:
if intrQ.coords() not in keys:
introns['query'].append(intrQ)
keys = [intron.coords() for intron in introns['query']]
for intrQ, intrS in introns3:
if intrQ.coords() not in keys:
introns['query'].append(intrQ)
keys = [intron.coords() for intron in introns['query']]
for intron in introns0:
if intron.coords() not in keys:
introns['query'].append(intron)
keys = [intron.coords() for intron in introns['query']]
keys = [intron.coords() for intron in introns['sbjct']]
for intrQ, intrS in introns1:
if intrS.coords() not in keys:
introns['query'].append(intrS)
keys = [intron.coords() for intron in introns['sbjct']]
for (intrQ, intrS, cigpacbp) in introns2:
if intrS.coords() not in keys:
introns['query'].append(intrS)
keys = [intron.coords() for intron in introns['sbjct']]
for intrQ, intrS in introns3:
if intrS.coords() not in keys:
introns['query'].append(intrS)
keys = [intron.coords() for intron in introns['sbjct']]
elif not introns['query']:
# just bridge Orfs by **best** intron(s).
introns0 = merge_pacbporfs_with_query_intron_bridgeing(
pacbporfD, pacbporfA)
# only store introns from that are NOT encountered already
keys = [intron.coords() for intron in introns['query']]
for intron in introns0:
if intron.coords() not in keys:
introns['query'].append(intron)
else:
# projecting introns yielded results; do not try mapping
pass
elif not sbjctOrfsIdentical:
introns1 = merge_pacbporfs_by_intron_in_sbjct(pacbporfD, pacbporfA)
if pacbporfD.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD and\
pacbporfA.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD:
introns2 = merge_pacbporfs_by_intron_tinyexon_intron_in_sbjct(
pacbporfD, pacbporfA, sbjctOrfSetObj)
introns3 = merge_pacbporfs_by_two_tinyexons_in_sbjct(
pacbporfD, pacbporfA, sbjctOrfSetObj)
else:
# do not allow more complex intron merging
introns2 = {}
introns3 = {}
# store introns obtained by most simplest case projecting/mapping
introns['sbjct'].extend([prj.projected_introns[0] for prj in introns1])
# only store introns from intron2 that are NOT encountered already in introns1
keys = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['sbjct']]
for (intr1, intr2, exon) in introns2:
k1 = (intr1.donor.pos, intr1.acceptor.pos)
k2 = (intr2.donor.pos, intr2.acceptor.pos)
if k1 not in keys and k2 not in keys:
introns['sbjct'].append(intr1)
introns['sbjct'].append(intr2)
# only store introns from intron2 that are NOT encountered already in introns1
keys = [(intron.donor.pos, intron.acceptor.pos)
for intron in introns['sbjct']]
for (intr1, intr2, intr3, exon1, exon2) in introns3:
k1 = (intr1.donor.pos, intr1.acceptor.pos)
k2 = (intr2.donor.pos, intr2.acceptor.pos)
k3 = (intr3.donor.pos, intr3.acceptor.pos)
if k1 not in keys and k2 not in keys and k3 not in keys:
introns['sbjct'].append(intr1)
introns['sbjct'].append(intr2)
introns['sbjct'].append(intr3)
if not introns['sbjct'] and allow_sbjct_mapping and allow_query_mapping:
# potential stopless 3n intron in QUERY
introns1 = merge_pacbporfs_with_introns(pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns1 = _filter_aligned_introns_on_pssm_entropy_combination(
introns1)
# apply stopless3n intron filtering
introns1 = _filter_aligned_stopless_3n_introns(introns1)
introns2 = merge_pacbporfs_with_closeby_independant_introns(
pacbporfD, pacbporfA)
if pacbporfD.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD and\
pacbporfA.gap_ratio_score() < PACBPORF_HIGH_GAP_RATIO_THRESHOLD:
introns3 = merge_pacbporfs_with_phase_shift_introns(
pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns3 = _filter_aligned_introns_on_pssm_entropy_combination(
introns3)
# apply stopless3n intron filtering
introns3 = _filter_aligned_stopless_3n_introns(introns3)
else:
# do not allow more complex intron merging
introns3 = {}
# store introns
introns['query'].extend(Set([intrQ
for (intrQ, intrS) in introns1]))
introns['sbjct'].extend(Set([intrS
for (intrQ, intrS) in introns1]))
introns['query'].extend(
[intrQ for (intrQ, intrS, cigpacbp) in introns2])
introns['query'].extend([intrQ for (intrQ, intrS) in introns3])
introns['sbjct'].extend(
[intrS for (intrQ, intrS, cigpacbp) in introns2])
introns['sbjct'].extend([intrS for (intrQ, intrS) in introns3])
else:
# projecting introns yielded results; do not try mapping
pass
elif queryOrfsIdentical and sbjctOrfsIdentical:
if allow_query_mapping:
introns1 = merge_pacbporfs_by_inframe_intron_in_query(
pacbporfD, pacbporfA)
else:
# no mapping (unigene or continious alignment provided)
introns1 = []
if allow_sbjct_mapping:
introns2 = merge_pacbporfs_by_inframe_intron_in_sbjct(
pacbporfD, pacbporfA)
else:
# no mapping (unigene or continious alignment provided)
introns2 = []
if allow_sbjct_mapping and allow_query_mapping:
introns3 = merge_pacbporfs_with_introns(pacbporfD, pacbporfA)
# filter for **best** candidates based on PSSM/entropy combination
introns3 = _filter_aligned_introns_on_pssm_entropy_combination(
introns3)
# apply stopless3n intron filtering
introns3 = _filter_aligned_stopless_3n_introns(introns3)
else:
# no mapping (unigene or continious alignment provided)
introns3 = []
#introns4 = merge_pacbporfs_with_closeby_independant_introns(
# pacbporfD,pacbporfA)
#introns5 = merge_pacbporfs_with_phase_shift_introns(
# pacbporfD,pacbporfA)
introns['query'].extend([prj.projected_introns[0] for prj in introns1])
introns['sbjct'].extend([prj.projected_introns[0] for prj in introns2])
introns['query'].extend([intrQ for (intrQ, intrS) in introns3])
introns['sbjct'].extend([intrS for (intrQ, intrS) in introns3])
else:
# none of these cases; allow_projecting or allow_mapping == False!
pass
# Filter for stopless3n introns
introns['query'] = _filter_stopless_3n_introns(introns['query'])
introns['sbjct'] = _filter_stopless_3n_introns(introns['sbjct'])
# return list of introns
return introns
