def _filter_introns_on_entropy(intronlist,pacbporfD,pacbporfA,
min_donor_site_entropy=0.0,min_acceptor_site_entropy=0.0,verbose=False):
""" """
remove_list_index_ids = []
# accelerator. Do no re-obtain entropy when already omitted on this position
remove_list_donor_positions = []
remove_list_accep_positions = []
for pos in range(0,len(intronlist)):
intron = intronlist[pos]
if intron.donor.pos in remove_list_donor_positions:
remove_list_index_ids.append(pos)
continue
if intron.acceptor.pos in remove_list_accep_positions:
remove_list_index_ids.append(pos)
continue
is_accepted = True
succes = set_apps_intron_query(intron,pacbporfD,pacbporfA)
if intron._apps_donor < min_donor_site_entropy:
is_accepted = False
remove_list_donor_positions.append( intron.donor.pos )
if intron._apps_accep < min_acceptor_site_entropy:
is_accepted = False
remove_list_accep_positions.append( intron.acceptor.pos )
if not is_accepted:
remove_list_index_ids.append(pos)
# remove aligned introns
remove_list_index_ids.reverse()
for pos in remove_list_index_ids: intronlist.pop(pos)
# return intronlist
return intronlist
def _filter_introns_on_entropy(intronlist,
pacbporfD,
pacbporfA,
min_donor_site_entropy=0.0,
min_acceptor_site_entropy=0.0,
verbose=False):
""" """
remove_list_index_ids = []
# accelerator. Do no re-obtain entropy when already omitted on this position
remove_list_donor_positions = []
remove_list_accep_positions = []
for pos in range(0, len(intronlist)):
intron = intronlist[pos]
if intron.donor.pos in remove_list_donor_positions:
remove_list_index_ids.append(pos)
continue
if intron.acceptor.pos in remove_list_accep_positions:
remove_list_index_ids.append(pos)
continue
is_accepted = True
succes = set_apps_intron_query(intron, pacbporfD, pacbporfA)
if intron._apps_donor < min_donor_site_entropy:
is_accepted = False
remove_list_donor_positions.append(intron.donor.pos)
if intron._apps_accep < min_acceptor_site_entropy:
is_accepted = False
remove_list_accep_positions.append(intron.acceptor.pos)
if not is_accepted:
remove_list_index_ids.append(pos)
# remove aligned introns
remove_list_index_ids.reverse()
for pos in remove_list_index_ids:
intronlist.pop(pos)
# return intronlist
return intronlist
def merge_pacbporfs_with_query_intron_bridgeing(pacbporfD,
pacbporfA,
verbose=False,
**kwargs):
"""
Merge query Orfs in PacbPORF by **best** intron
@attention: see orfs.merge_orfs_with_intron for **kwargs
@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 **kwargs dictionary for some forced attributes
_update_kwargs(kwargs, KWARGS_MAPPED_INTRON)
if not kwargs.has_key('aligned_site_max_triplet_distance'):
kwargs['aligned_site_max_triplet_distance'] = kwargs['max_aa_offset']
# calculate maximal/minimal donor/acceptor site position based on alignment
ELEGIABLE_SPLICE_SITE_AA_RANGE = 75
qdr = pacbporfD.alignment_dna_range_query()
qar = pacbporfA.alignment_dna_range_query()
min_donor_query_pos = max(
[min(qdr), max(qdr) - (ELEGIABLE_SPLICE_SITE_AA_RANGE * 3)])
max_accep_query_pos = min(
[max(qar), min(qar) + (ELEGIABLE_SPLICE_SITE_AA_RANGE * 3)])
# get list of introns
intronlist = merge_orfs_with_intron(pacbporfD.orfQ,
pacbporfA.orfQ,
min_donor_pos=min_donor_query_pos,
max_acceptor_pos=max_accep_query_pos,
**kwargs)
# filter on entropy
# settings for minimal alignment entropy score
if min([pacbporfD.identityscore, pacbporfA.identityscore]) > 0.55:
min_donor_site_entropy = 0.01
min_acceptor_site_entropy = 0.01
intronlist = _filter_introns_on_entropy(
intronlist,
pacbporfD,
pacbporfA,
min_donor_site_entropy=min_donor_site_entropy,
min_acceptor_site_entropy=min_acceptor_site_entropy)
else:
# do not filter, but do not forget to store apps data to intron(s)
for intron in intronlist:
succes = set_apps_intron_query(intron, pacbporfD, pacbporfA)
for intron in intronlist:
intron._distance = 0 # ??
# set GFF fsource attribute for recognition of intron sources
intron._gff['fsource'] = 'ABGPbridgeing'
# get unique list of donors & acceptors
donor = olba(list(Set([intron.donor for intron in intronlist])),
order_by='pos')
accep = olba(list(Set([intron.acceptor for intron in intronlist])),
order_by='pos')
############################################################################
if verbose:
print "dQ1", [d.pos for d in donor], "aQ1", [a.pos for a in accep]
############################################################################
intronlist = _filter_introns_on_pssm_entropy_combination(intronlist)
# get unique list of donors & acceptors
donor = olba(list(Set([intron.donor for intron in intronlist])),
order_by='pos')
accep = olba(list(Set([intron.acceptor for intron in intronlist])),
order_by='pos')
############################################################################
if verbose:
print "dQ1", [d.pos for d in donor], "aQ1", [a.pos for a in accep]
############################################################################
filtered_intron_list = []
for intron in intronlist:
intron.assign_bp_and_ppts()
if intron.branchpoint and (intron.ppt5p or intron.ppt3p):
filtered_intron_list.append(intron)
else:
pass
# check if list is emptied due to branchpoint filtering
# in that case, filter for either branchpoint OR polyppt
if not filtered_intron_list and intronlist:
for intron in intronlist:
if intron.branchpoint or (intron.ppt5p or intron.ppt3p):
filtered_intron_list.append(intron)
# return list of filtered introns
return filtered_intron_list
def merge_pacbporfs_with_query_intron_bridgeing(pacbporfD,pacbporfA,verbose=False,**kwargs):
"""
Merge query Orfs in PacbPORF by **best** intron
@attention: see orfs.merge_orfs_with_intron for **kwargs
@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 **kwargs dictionary for some forced attributes
_update_kwargs(kwargs,KWARGS_MAPPED_INTRON)
if not kwargs.has_key('aligned_site_max_triplet_distance'):
kwargs['aligned_site_max_triplet_distance'] = kwargs['max_aa_offset']
# calculate maximal/minimal donor/acceptor site position based on alignment
ELEGIABLE_SPLICE_SITE_AA_RANGE = 75
qdr = pacbporfD.alignment_dna_range_query()
qar = pacbporfA.alignment_dna_range_query()
min_donor_query_pos = max([ min(qdr), max(qdr)-(ELEGIABLE_SPLICE_SITE_AA_RANGE*3) ])
max_accep_query_pos = min([ max(qar), min(qar)+(ELEGIABLE_SPLICE_SITE_AA_RANGE*3) ])
# get list of introns
intronlist = merge_orfs_with_intron(pacbporfD.orfQ,pacbporfA.orfQ,
min_donor_pos =min_donor_query_pos,
max_acceptor_pos=max_accep_query_pos,**kwargs)
# filter on entropy
# settings for minimal alignment entropy score
if min([pacbporfD.identityscore,pacbporfA.identityscore]) > 0.55:
min_donor_site_entropy = 0.01
min_acceptor_site_entropy = 0.01
intronlist = _filter_introns_on_entropy(intronlist,pacbporfD,pacbporfA,
min_donor_site_entropy=min_donor_site_entropy,
min_acceptor_site_entropy=min_acceptor_site_entropy)
else:
# do not filter, but do not forget to store apps data to intron(s)
for intron in intronlist:
succes = set_apps_intron_query(intron,pacbporfD,pacbporfA)
for intron in intronlist:
intron._distance = 0 # ??
# set GFF fsource attribute for recognition of intron sources
intron._gff['fsource'] = 'ABGPbridgeing'
# get unique list of donors & acceptors
donor = olba( list(Set([intron.donor for intron in intronlist ])), order_by='pos')
accep = olba( list(Set([intron.acceptor for intron in intronlist ])), order_by='pos')
############################################################################
if verbose: print "dQ1",[d.pos for d in donor],"aQ1",[a.pos for a in accep]
############################################################################
intronlist = _filter_introns_on_pssm_entropy_combination(intronlist)
# get unique list of donors & acceptors
donor = olba( list(Set([intron.donor for intron in intronlist ])), order_by='pos')
accep = olba( list(Set([intron.acceptor for intron in intronlist ])), order_by='pos')
############################################################################
if verbose: print "dQ1",[d.pos for d in donor],"aQ1",[a.pos for a in accep]
############################################################################
filtered_intron_list = []
for intron in intronlist:
intron.assign_bp_and_ppts()
if intron.branchpoint and (intron.ppt5p or intron.ppt3p):
filtered_intron_list.append( intron )
else:
pass
# check if list is emptied due to branchpoint filtering
# in that case, filter for either branchpoint OR polyppt
if not filtered_intron_list and intronlist:
for intron in intronlist:
if intron.branchpoint or (intron.ppt5p or intron.ppt3p):
filtered_intron_list.append( intron )
# return list of filtered introns
return filtered_intron_list
def _merge_pacbporfs_by_two_tinyexons(pacbporfD,pacbporfA,
orfSetObject,queryorsbjct,verbose = False, **kwargs):
""" """
# edit **kwargs dictionary for some forced attributes
_update_kwargs(kwargs,KWARGS_PROJECTED_TINYEXON)
tinyexons = []
sposD = pacbporfD._get_original_alignment_pos_start()
eposD = pacbporfD._get_original_alignment_pos_end()
sposA = pacbporfA._get_original_alignment_pos_start()
eposA = pacbporfA._get_original_alignment_pos_end()
if queryorsbjct == "query":
donorOrf = pacbporfD.orfQ
accepOrf = pacbporfA.orfQ
prjctOrf = pacbporfD.orfS
dStart,dEnd = sposD.query_dna_start, eposD.query_dna_end
aStart,aEnd = sposA.query_dna_start, eposA.query_dna_end
elif queryorsbjct == "sbjct":
donorOrf = pacbporfD.orfS
accepOrf = pacbporfA.orfS
prjctOrf = pacbporfD.orfQ
dStart,dEnd = sposD.sbjct_dna_start, eposD.sbjct_dna_end
aStart,aEnd = sposA.sbjct_dna_start, eposA.sbjct_dna_end
else:
message = "'queryorsbjct' (%s), not 'query' or 'sbjct'" % queryorsbjct
raise InproperlyAppliedArgument, message
# get all potential combinations of two tinyexons
tinyexoncombis = merge_orfs_with_two_tinyexons(
donorOrf, accepOrf,
donorOrf._donor_sites,
accepOrf._acceptor_sites,
orfSetObject.orfs,
)
results = []
for dObj in donorOrf._donor_sites:
if queryorsbjct == "query":
(dPos,dPhase) = pacbporfD.dnaposition_query(dObj.pos,forced_return=True)
else:
(dPos,dPhase) = pacbporfD.dnaposition_sbjct(dObj.pos,forced_return=True)
try:
algDobj = pacbporfD._positions[dPos]
except IndexError:
# site out of range of PacbPORF -> break
break
# check if dObj is on pfD;
# introns of tinyexons can be projected outside of pfD/pfA area
if dObj.pos < dStart: continue
for aObj in accepOrf._acceptor_sites:
if queryorsbjct == "query":
(aPos,aPhase) = pacbporfA.dnaposition_query(aObj.pos,forced_return=True)
else:
(aPos,aPhase) = pacbporfA.dnaposition_sbjct(aObj.pos,forced_return=True)
try:
algAobj = pacbporfA._positions[aPos]
except IndexError:
# site out of range of PacbPORF -> break
break
# check if aObj is on pfA;
# introns of tinyexons can be projected outside of pfD/pfA area
if aObj.pos > aEnd: continue
if queryorsbjct == "query":
posDsbjct = algDobj.sbjct_dna_start + dPhase
posAsbjct = algAobj.sbjct_dna_start + aPhase
else:
posDsbjct = algDobj.query_dna_start + dPhase
posAsbjct = algAobj.query_dna_start + aPhase
distance = posAsbjct - posDsbjct
if distance >= (kwargs['max_tinyexon_nt_length']*2):
break
if distance < (kwargs['min_tinyexon_nt_length']*2):
continue
filtered_tinyexoncombis = _filter_tinyexoncombis(tinyexoncombis,
min_length = distance,
max_length = distance,
min_first_acceptor_pos = dObj.pos + kwargs['min_tinyexon_intron_nt_length'],
max_final_donor_pos = aObj.pos - kwargs['min_tinyexon_intron_nt_length'],
phase_final_donor = aObj.phase,
phase_first_acceptor= dObj.phase,
)
if not filtered_tinyexoncombis: continue
####################################################################
if verbose:
print distance, dObj, aObj, len(tinyexoncombis),
print len(filtered_tinyexoncombis)
####################################################################
for exon1,intron,exon2 in filtered_tinyexoncombis:
# make preceding intron
preceding_intron = IntronConnectingOrfs(
dObj,exon1.acceptor,
None,donorOrf,exon1.orf )
# make subsequent intron
subsequent_intron = IntronConnectingOrfs(
exon2.donor, aObj,
None,exon2.orf,accepOrf)
################################################################
if verbose:
print "\t", exon1, exon1.proteinsequence(),
print preceding_intron.phase, exon1.donor.phase,
print subsequent_intron.phase, preceding_intron.shared_aa,
print intron.shared_aa, subsequent_intron.shared_aa
print "\t", exon2, exon2.proteinsequence()
################################################################
# get prjctOrf sequence for comparison
correctionA = 0
if aObj.phase != 0:
# INCLUDE the final AA which is broken by the splicesite
correctionA=1
if queryorsbjct == "query":
startPos,_phase = pacbporfD.dnaposition_query(dObj.pos,forced_return=True)
stopPos,_phase = pacbporfA.dnaposition_query(aObj.pos,forced_return=True)
start = pacbporfD._positions[startPos].sbjct_pos
stop = pacbporfA._positions[stopPos].sbjct_pos + correctionA
else:
startPos,_phase = pacbporfD.dnaposition_sbjct(dObj.pos,forced_return=True)
stopPos,_phase = pacbporfA.dnaposition_sbjct(aObj.pos,forced_return=True)
start = pacbporfD._positions[startPos].query_pos
stop = pacbporfA._positions[stopPos].query_pos + correctionA
if stop <= start:
# tinyexon is so tiny that is does not have a single
# full aligned AA -> discard here
continue
# actually get the prjctOrf sequence
aaseq = prjctOrf.getaas(abs_pos_start=start,abs_pos_end=stop)
# initialize a PacbP for the combination of both tinyexons
# afterwards, check if the indentityscore is > 0.XX
from pacb import PacbP
seqparts = [ preceding_intron.shared_aa,
exon1.proteinsequence(),
intron.shared_aa,
exon2.proteinsequence(),
subsequent_intron.shared_aa ]
################################################################
if verbose or len("".join(seqparts)) != len(aaseq):
print pacbporfD
print exon1.orf, exon2.orf, prjctOrf
print pacbporfA
print seqparts
print aaseq, len(aaseq), len("".join(seqparts)), (start,stop)
print "'%s'" % queryorsbjct,
print "Q", (algDobj.query_pos, algAobj.query_pos),
print "S", (algDobj.sbjct_pos, algAobj.sbjct_pos)
print "distance:", distance, kwargs['max_tinyexon_nt_length'],
print (posDsbjct, posAsbjct),
print "Q-dna:", ( algDobj.query_dna_start, dPhase, algAobj.query_dna_start, aPhase ),
print "S-dna:", ( algDobj.sbjct_dna_start, dPhase, algAobj.sbjct_dna_start, aPhase )
################################################################
# ignore by continue when sequences not identical in length
if len("".join(seqparts)) != len(aaseq): continue
testpacbp = PacbP(input=( "".join(seqparts), aaseq, 0, 0) )
testpacbp.strip_unmatched_ends()
if not ( testpacbp.identityscore > 0.60 and\
(float(testpacbp.length) / len(aaseq)) > 0.70 ):
# not a very convincing alignment
continue
################################################################
if verbose:
print testpacbp
testpacbp.print_protein()
################################################################
# if here, succesfully mapped 2 tiny exons!!
# get all sequences/coordinates in place for
# pacbporf formation
orfQ1 = exon1.orf
orfS1 = prjctOrf
orfQ2 = exon2.orf
orfS2 = prjctOrf
seqQ1 = exon1.proteinsequence()
seqQ2 = exon2.proteinsequence()
coordQ1 = exon1.acceptor.pos / 3
coordS1 = start
coordQ2 = exon2.acceptor.pos / 3
coordS2 = start + len(seqparts[0]) + len(seqparts[1]) + len(seqparts[2])
seqS1 = aaseq[0:(len(seqparts[0])+len(seqparts[1]))]
seqS2 = aaseq[-(len(seqparts[3])+len(seqparts[4])):]
if len(seqparts[0]):
seqS1 = seqS1[1:]
coordS1 += 1
if len(seqparts[4]):
seqS2 = seqS2[:-1]
if queryorsbjct == "sbjct":
# swap query <-> sbjct
orfQ1,orfS1 = orfS1,orfQ1
orfQ2,orfS2 = orfS2,orfQ2
seqQ1,seqS1 = seqS1,seqQ1
seqQ2,seqS2 = seqS2,seqQ2
coordQ1,coordS1 = coordS1,coordQ1
coordQ2,coordS2 = coordS2,coordQ2
################################################################
if verbose:
print "tinypacbporf1:", seqQ1, seqQ2, coordQ1, coordQ2
print "tinypacbporf2:", seqS1, seqS2, coordS1, coordS2
################################################################
# make pacbporfs
pacbp1 = PacbP(input=( seqQ1, seqS1, coordQ1, coordS1) )
pacbp1.strip_unmatched_ends()
tinypacbporf1 = pacbp2pacbporf(pacbp1,orfQ1,orfS1)
tinypacbporf1.extend_pacbporf_after_stops()
pacbp2 = PacbP(input=( seqQ2, seqS2, coordQ2, coordS2) )
pacbp2.strip_unmatched_ends()
tinypacbporf2 = pacbp2pacbporf(pacbp2,orfQ2,orfS2)
tinypacbporf2.extend_pacbporf_after_stops()
################################################################
if verbose:
print tinypacbporf1
tinypacbporf1.print_protein_and_dna()
print tinypacbporf2
tinypacbporf2.print_protein_and_dna()
################################################################
################################################################
# set some meta-data properties to the intron objects
################################################################
# add distance score to intron
preceding_intron._distance = 0
intron._distance = 0
subsequent_intron._distance = 0
# add Alignment Positional Periphery Score into objects
if queryorsbjct == "query":
succes = set_apps_intron_query(preceding_intron,pacbporfD,tinypacbporf1)
succes = set_apps_intron_query(intron,tinypacbporf1,tinypacbporf2)
succes = set_apps_intron_query(subsequent_intron,tinypacbporf2,pacbporfA)
else:
succes = set_apps_intron_sbjct(preceding_intron,pacbporfD,tinypacbporf1)
succes = set_apps_intron_sbjct(intron,tinypacbporf1,tinypacbporf2)
succes = set_apps_intron_sbjct(subsequent_intron,tinypacbporf2,pacbporfA)
# set GFF fsource attribute for recognition of intron sources
preceding_intron._gff['fsource'] = "ABGPprojectingTE"
intron._gff['fsource'] = "ABGPprojectingTE"
subsequent_intron._gff['fsource'] = "ABGPprojectingTE"
# create _linked_to_xxx attributes
preceding_intron._linked_to_pacbporfs = [ tinypacbporf1, tinypacbporf2 ]
intron._linked_to_pacbporfs = [ tinypacbporf1, tinypacbporf2 ]
subsequent_intron._linked_to_pacbporfs = [ tinypacbporf1, tinypacbporf2 ]
preceding_intron._linked_to_introns = [ intron,subsequent_intron ]
intron._linked_to_introns = [ preceding_intron,subsequent_intron ]
subsequent_intron._linked_to_introns = [ intron,preceding_intron ]
################################################################
# append to results
################################################################
results.append( (
preceding_intron,
intron,
subsequent_intron,
tinypacbporf1,
tinypacbporf2,
) )
# return 3 introns and 2 intermediate tinyexon PacbPORFs (per row)
return results
def _merge_pacbporfs_by_intron(pfD,pfA,queryorsbjct,verbose=False,**kwargs):
"""
Project splicesites from SBJCT intron on continious QUERY PacbPORFs
@type pfD: PacbPORF object
@param pfD: PacbPORF object that has to deliver (aligned) donor sites
@type pfA: PacbPORF object
@param pfA: PacbPORF object that has to deliver (aligned) acceptor sites
@type queryorsbjct: string
@param queryorsbjct: literal string 'query' or 'sbjct'
@type verbose: Boolean
@param verbose: print debugging info to STDOUT when True
@attention: see pacb.connecting.merge_orfs_with_intron for **kwargs)
@rtype: list
@return: list with ProjectedIntrons (from Sbjct on Query)
"""
# input validation
IsPacbPORF(pfD)
IsPacbPORF(pfA)
# edit **kwargs dictionary for some forced attributes
_update_kwargs(kwargs,KWARGS_PROJECTED_INTRON)
### if not kwargs.has_key('projected_intron_max_nt_offset'):
### kwargs['projected_intron_max_nt_offset'] = PROJECTED_INTRON_MAX_NT_OFFSET
### if not kwargs.has_key('projected_intron_max_aa_offset'):
### kwargs['projected_intron_max_aa_offset'] = PROJECTED_INTRON_MAX_AA_OFFSET
# settings for minimal alignment entropy score
min_donor_site_alignment_entropy = 0.0
min_acceptor_site_alignment_entropy = 0.0
ELEGIABLE_SPLICE_SITE_AA_RANGE = 75
sposD = pfD._get_original_alignment_pos_start()
eposD = pfD._get_original_alignment_pos_end()
sposA = pfA._get_original_alignment_pos_start()
eposA = pfA._get_original_alignment_pos_end()
if queryorsbjct == "query":
# Orfs of SBJCT must be identical
IsIdenticalOrfs(pfD.orfS,pfA.orfS)
donorOrf = pfD.orfQ
accepOrf = pfA.orfQ
prjctOrf = pfD.orfS # pfD.orfS == pfA.orfS
dStart = sposD.query_dna_start # ALIGNED start of donorPacbPORF
dEnd = pfD.query_dna_end # ABSOLUTE end of donorPacbPORF
aStart = pfA.query_dna_start # ABSOLUTE start of acceptorPacbPORF
aEnd = eposA.query_dna_end # ALIGNED end of acceptorPacbPORF
outOfAlignmentAttribute = "sbjct_dna_start"
# calculate elegiable splice site range
qdr = pfD.alignment_dna_range_query()
qar = pfA.alignment_dna_range_query()
min_donor_pos = max([ min(qdr), max(qdr)-(ELEGIABLE_SPLICE_SITE_AA_RANGE*3) ])
max_accep_pos = min([ max(qar), min(qar)+(ELEGIABLE_SPLICE_SITE_AA_RANGE*3) ])
elif queryorsbjct == "sbjct":
# Orfs of QUERY must be identical
IsIdenticalOrfs(pfD.orfQ,pfA.orfQ)
donorOrf = pfD.orfS
accepOrf = pfA.orfS
prjctOrf = pfD.orfQ # pfD.orfQ == pfA.orfQ
dStart = sposD.sbjct_dna_start # ALIGNED start of donorPacbPORF
dEnd = pfD.sbjct_dna_end # ABSOLUTE end of donorPacbPORF
aStart = pfA.sbjct_dna_start # ABSOLUTE start of acceptorPacbPORF
aEnd = eposA.sbjct_dna_end # ALIGNED end of acceptorPacbPORF
outOfAlignmentAttribute = "query_dna_start"
# calculate elegiable splice site range
sdr = pfD.alignment_dna_range_sbjct()
sar = pfA.alignment_dna_range_sbjct()
min_donor_pos = max([ min(sdr), max(sdr)-(ELEGIABLE_SPLICE_SITE_AA_RANGE*3) ])
max_accep_pos = min([ max(sar), min(sar)+(ELEGIABLE_SPLICE_SITE_AA_RANGE*3) ])
else:
message = "'queryorsbjct' (%s), not 'query' or 'sbjct'" % queryorsbjct
raise InproperlyAppliedArgument, message
# predict introns only in `queryorsbjct` Orfs
# introns is a list of IntronConnectingOrfs objects
introns = merge_orfs_with_intron(donorOrf,accepOrf,
min_donor_pos=min_donor_pos,
max_acceptor_pos=max_accep_pos,
order_by='length',**kwargs)
# return list with projected introns
projected_introns = []
# gather unique donor and acceptor positions from list
# of IntronConnectingOrfs
for intron in introns:
# break if intron is to large
if kwargs['max_intron_nt_length'] and intron.length > kwargs['max_intron_nt_length']: break
# continue if intron is to small
if kwargs['min_intron_nt_length'] and intron.length < kwargs['min_intron_nt_length']: continue
# continue if intron has non-canonical features
# check if intron.start is on pfD;
# inframe-introns can be projected outside of pfD/pfA area
if intron.start <= dStart: continue
if intron.start >= dEnd: continue
# check if intron.end is on pfA;
# inframe-introns can be projected outside of pfD/pfA area
if intron.end <= aStart: continue
if intron.end >= aEnd: continue
if queryorsbjct == "sbjct":
# get positions of donor & acceptor in the PacbPORF alignment
donorPositionPos, phaseD = pfD.dnaposition_sbjct(intron.donor.pos,forced_return=True)
accepPositionPos, phaseA = pfA.dnaposition_sbjct(intron.acceptor.pos,forced_return=True)
# calculate projected distance on QUERY
posDposQuery = pfD._positions[donorPositionPos].query_pos
posAposQuery = pfA._positions[accepPositionPos].query_pos
aaDistance = posAposQuery - posDposQuery
else:
# get positions of donor & acceptor in the PacbPORF alignment
donorPositionPos, phaseD = pfD.dnaposition_query(intron.donor.pos,forced_return=True)
accepPositionPos, phaseA = pfA.dnaposition_query(intron.acceptor.pos,forced_return=True)
# calculate binary entropy from projected position on SBJCT
posDposSbjct = pfD._positions[donorPositionPos].sbjct_pos
posAposSbjct = pfA._positions[accepPositionPos].sbjct_pos
aaDistance = posAposSbjct - posDposSbjct
# calculate binary entropy score
entropyDonorSbjct = pfD.alignment_entropy(donorPositionPos,method='donor')
entropyAcceptorSbjct= pfA.alignment_entropy(accepPositionPos,method='acceptor')
# do distance check upon (projected) intron acceptance
if abs(aaDistance) <= kwargs['max_aa_offset']:
# check if we've runned out of the aligned part
outofalignedpacbporf = False
# get the projected donor position; mind the gap on this spot ;-)
while pfD._positions[donorPositionPos].isa_gap and donorPositionPos > 0 :
donorPositionPos -= 1
else:
projected_donor_position = getattr(pfD._positions[donorPositionPos],outOfAlignmentAttribute) + phaseD
if donorPositionPos == 0 and pfD._positions[donorPositionPos].isa_gap:
print "WarningThatIsTackled::outofalignedpacbporf::donor"
outofalignedpacbporf = True
# get the projected acceptor position; mind the gap on this spot ;-)
while pfA._positions[accepPositionPos].isa_gap and len(pfA._positions) > accepPositionPos+1:
accepPositionPos += 1
else:
projected_accep_position = getattr(pfA._positions[accepPositionPos],outOfAlignmentAttribute) + phaseA
if accepPositionPos == len(pfA._positions)-1 and pfA._positions[accepPositionPos].isa_gap:
print "WarningThatIsTackled::outofalignedpacbporf::acceptor"
outofalignedpacbporf = True
if not outofalignedpacbporf:
################################################################
# set some meta-data properties to the intron object
################################################################
# add distance score to intron
intron._distance = abs(aaDistance)*3
# add Alignment Positional Periphery Score into objects
if queryorsbjct == "query":
succes = set_apps_intron_query(intron,pfD,pfA)
else:
succes = set_apps_intron_sbjct(intron,pfD,pfA)
# set GFF fsource attribute for recognition of intron sources
intron._gff['fsource'] = "ABGPprojecting"
# make a ProjectedIntronConnectingOrfs object
pico = ProjectedIntronConnectingOrfs(prjctOrf,
projected_donor_position,
projected_accep_position)
intron.binary_entropy_donor = entropyDonorSbjct
intron.binary_entropy_acceptor = entropyAcceptorSbjct
pico.add_projected_intron( intron )
pico.phase = intron.phase
projected_introns.append( pico )
################################################################
if verbose:
print "PROJ::", intron._distance,
print (pfD.orfQ.id, pfA.orfQ.id),
print (pfD.orfS.id, pfA.orfS.id),
print "%s-%snt" % (intron.donor.pos, intron.acceptor.pos),
print "%2.1f,%2.1f" % (intron.donor.pssm_score, intron.acceptor.pssm_score),
print "%2.1f,%2.1f" % (intron.binary_entropy_donor,intron.binary_entropy_acceptor)
################################################################
if aaDistance > kwargs['max_aa_offset']:
# break out; ordered by length can never result in
# a proper projected intron
break
# filter out less relevant ones compared to complete set of results
projected_introns = _filter_projected_introns(projected_introns)
# and return a list of ProjectedIntronConnectingOrfs
return projected_introns
def _merge_pacbporfs_by_tinyexon_and_two_introns(pacbporfD,pacbporfA,
orfSetObject,queryorsbjct,verbose = False, **kwargs):
"""
Merge 2 PacbPORF objects by introns
@attention: see pacb.connecting.merge_orfs_with_intron for **kwargs)
@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 orfSetObject: object with elegiable Orfs
@param orfSetObject: object with elegiable Orfs
@type queryorsbjct: string
@param queryorsbjct: literal string 'query' or 'sbjct'
@type verbose: Boolean
@param verbose: print debugging info to STDOUT when True
@rtype: list
@return: list with ( intron, ExonOnOrf, intron ) on the query sequence
"""
# input validation
IsPacbPORF(pacbporfD)
IsPacbPORF(pacbporfA)
# edit **kwargs dictionary for some forced attributes
_update_kwargs(kwargs,KWARGS_PROJECTED_TINYEXON)
MAX_TINYEXON_NT_LENGTH = 33
MIN_TINYEXON_NT_LENGTH = 6
tinyexons = []
if queryorsbjct == "query":
donorOrf = pacbporfD.orfQ
accepOrf = pacbporfA.orfQ
prjctOrf = pacbporfD.orfS
alignedDonorRange = pacbporfD.alignment_dna_range_query()
alignedAccepRange = pacbporfA.alignment_dna_range_query()
elif queryorsbjct == "sbjct":
donorOrf = pacbporfD.orfS
accepOrf = pacbporfA.orfS
prjctOrf = pacbporfD.orfQ
alignedDonorRange = pacbporfD.alignment_dna_range_sbjct()
alignedAccepRange = pacbporfA.alignment_dna_range_sbjct()
else:
message = "'queryorsbjct' (%s), not 'query' or 'sbjct'" % queryorsbjct
raise InproperlyAppliedArgument, message
for dObj in donorOrf._donor_sites:
# do not make a projection OVER the aligned area
if dObj.pos < min(alignedDonorRange): continue
if queryorsbjct == "query":
(dPos,dPhase) = pacbporfD.dnaposition_query(dObj.pos,forced_return=True)
else:
(dPos,dPhase) = pacbporfD.dnaposition_sbjct(dObj.pos,forced_return=True)
try:
algDobj = pacbporfD._positions[dPos]
except IndexError:
# site out of range of PacbPORF -> break
break
for aObj in accepOrf._acceptor_sites:
# do not make a projection OVER the aligned area
if aObj.pos > max(alignedAccepRange): continue
if queryorsbjct == "query":
(aPos,aPhase) = pacbporfA.dnaposition_query(aObj.pos,forced_return=True)
else:
(aPos,aPhase) = pacbporfA.dnaposition_sbjct(aObj.pos,forced_return=True)
try:
algAobj = pacbporfA._positions[aPos]
except IndexError:
# site out of range of PacbPORF -> break
break
if queryorsbjct == "query":
posDsbjct = algDobj.sbjct_dna_start + dPhase
posAsbjct = algAobj.sbjct_dna_start + aPhase
else:
posDsbjct = algDobj.query_dna_start + dPhase
posAsbjct = algAobj.query_dna_start + aPhase
distance = posAsbjct - posDsbjct
if distance >= MAX_TINYEXON_NT_LENGTH:
break
if distance < MIN_TINYEXON_NT_LENGTH:
continue
####################################################
# generate a ScanForMatches pattern file
####################################################
# example pattern: 6...6 AG NNGNNANNANNGN[2,0,0] GT 3...3
query = list(prjctOrf.inputgenomicsequence[posDsbjct:posAsbjct])
# mask all non-phase0 nucleotides to N residues;
# this represents the regularexpression for a specific
# peptide sequence
firstphasepositions = range( 3-dPhase % 3, len(query), 3)
for pos in range(0,len(query)):
if pos not in firstphasepositions:
query[pos] = "N"
# calculate a ~50% mismatch number
mismatches = max([ 0, (len(query) - query.count("N"))/2 ])
# write the pattern to string and subsequently to file
# example pattern: 6...6 AG NNGNNANNANNGN[2,0,0] GT 3...3
if kwargs['allow_non_canonical_donor']:
sfmpat = "%s...%s AG %s[%s,0,0] G (T | C) %s...%s" % (
AUSO,AUSO,"".join(query),mismatches,DDSO,DDSO)
else:
sfmpat = "%s...%s AG %s[%s,0,0] GT %s...%s" % (
AUSO,AUSO,"".join(query),mismatches,DDSO,DDSO)
####################################################
if verbose:
print (pacbporfD.orfQ.id,pacbporfA.orfQ.id),
print distance, dObj, aObj
print sfmpat
####################################################
fname = "sfmpat_tinyexon_%s_%s_%s_%s" % (
donorOrf.id,
accepOrf.id,
posDsbjct,
posAsbjct,
)
fh = open(fname,'w')
fh.write(sfmpat+"\n")
fh.close()
####################################################
# run ScanForMatches
####################################################
command = """echo ">myseq\n%s" | %s %s | tr "[,]" "\t\t#" | """ +\
"""tr -d "\n " | sed "s/>/\\n>/g" | tr "#" "\t" | """ +\
"""awk -F'\t' '{ if (NF==4 && $2>%s && $3<%s) """ +\
"""{ print $1"["$2","$3"]\\n"$4 } }' """
command = command % (
donorOrf.inputgenomicsequence,
EXECUTABLE_SFM,fname,
dObj.pos+(kwargs['min_intron_nt_length']-3),
aObj.pos-(kwargs['min_intron_nt_length']-3) )
co = osPopen(command)
matches = parseFasta(co.readlines())
co.close()
# filter matches for:
# (1) correct donor & acceptor phase
# (2) high enough donor & acceptor site scores
for hdr,seqmatch in matches.iteritems():
startQ,stopQ = [ int(item) for item in hdr.split(":")[1][1:-1].split(",") ]
exonQstart = startQ + AUSO + 2 - 1
exonQstop = stopQ - DDSO - 2
####################################
# get Orf object of tinyexon
####################################
tinyexonorf = None
# select the Orf on which the tinyexon is located
for orfObj in orfSetObject.get_elegiable_orfs(
max_orf_start=exonQstart,min_orf_end=exonQstop):
orfPhase = (exonQstart - orfObj.startPY) % 3
if orfPhase == dPhase:
tinyexonorf = orfObj
break
else:
# No tinyexonorf assigned!! Iin case a regex matched
# over a STOP-codon or the regex length is smaller
# then the smallest Orf, no Orf can be assigned
continue
# filter for donor & acceptor score
dScore = _score_splice_site(seqmatch[-9:],splicetype='donor')
aScore = _score_splice_site(seqmatch[0:11],splicetype='acceptor')
if dScore < kwargs['min_donor_pssm_score']:
continue
if aScore < kwargs['min_acceptor_pssm_score']:
continue
# scan Orf for splicesites
tinyexonorf.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'])
tinyexonorf.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'])
# get 1th intron donor object
intron1_aObj = None
for a in tinyexonorf._acceptor_sites:
if a.pos == exonQstart:
intron1_aObj = a
break
else:
# pseudo-acceptorsite as found be SFM regex
# is not a valid acceptor site of high enough score
# continue to next iteration of (hdr,seqmatch) pair
continue
# get 2th intron donor object
intron2_dObj = None
for d in tinyexonorf._donor_sites:
if d.pos == exonQstop:
intron2_dObj = d
break
else:
# pseudo-donorsite as found be SFM regex
# is not a valid acceptor site of high enough score
# continue to next iteration of (hdr,seqmatch) pair
continue
# check if introns are of elegiable lengths
if (intron1_aObj.pos-dObj.pos) > kwargs['max_intron_nt_length']:
continue
if (aObj.pos-intron2_dObj.pos) > kwargs['max_intron_nt_length']:
continue
####################################################
if True or verbose:
# if here, a candidate!!!
print (pacbporfD.orfQ.id,tinyexonorf.id,pacbporfA.orfQ.id),
print hdr, dScore, aScore
print seqmatch
####################################################
# append to found tinyexons
query_data = ( tinyexonorf, exonQstart, exonQstop )
sbjct_data = ( prjctOrf, posDsbjct, posAsbjct )
splicesite_data = ( dObj,intron1_aObj, intron2_dObj, aObj )
tinyexons.append( ( query_data, sbjct_data, splicesite_data ) )
# file cleanup
osRemove(fname)
# return - End Of Function - if no tinyexons are found
if not tinyexons:
return []
####################################
# select the **best** tinyexon
####################################
(query_data,sbjct_data,splicesite_data) = tinyexons[0]
orfQ,query_dna_start,query_dna_end = query_data
orfS,sbjct_dna_start,sbjct_dna_end = sbjct_data
(intron1_dObj,intron1_aObj,intron2_dObj,intron2_aObj) = splicesite_data
####################################################
if verbose:
print "tinyexon orf:", orfQ
print "tinyexon orf:", intron1_aObj
print "tinyexon orf:", intron2_dObj
####################################################
####################################
# make tinyexon PacbPORF
####################################
startQaa = orfQ.dnapos2aapos(query_dna_start) -1
startSaa = orfS.dnapos2aapos(sbjct_dna_start) -1
stopQaa = orfQ.dnapos2aapos(query_dna_end) +1
stopSaa = orfS.dnapos2aapos(sbjct_dna_end) +1
# check for directly leading stop codon on tinyexon
while startQaa <= orfQ.protein_startPY:
startQaa+=1
startSaa+=1
query_dna_start+=3
sbjct_dna_start+=3
while startSaa <= orfS.protein_startPY:
startQaa+=1
startSaa+=1
query_dna_start+=3
sbjct_dna_start+=3
# check for directly tailing stop codon on tinyexon
while stopQaa > orfQ.protein_endPY:
stopQaa-=1
stopSaa-=1
query_dna_end-=3
sbjct_dna_end-=3
while stopSaa > orfS.protein_endPY:
stopQaa-=1
stopSaa-=1
query_dna_end-=3
sbjct_dna_end-=3
# get sequences
qAAseq = orfQ.getaas(abs_pos_start=startQaa,abs_pos_end=stopQaa)
sAAseq = orfS.getaas(abs_pos_start=startSaa,abs_pos_end=stopSaa)
####################################################
if verbose or len(qAAseq) != len(sAAseq):
# if unequal lengths, error will be raised upon PacbP.__init__()
print orfQ, qAAseq, startQaa, stopQaa, (stopQaa-startQaa),
print (query_dna_start,query_dna_end)
print orfS, sAAseq, startSaa, stopSaa, (stopSaa-startSaa),
print (sbjct_dna_start,sbjct_dna_end)
print orfQ.inputgenomicsequence[query_dna_start-2:query_dna_end+2]
print orfS.inputgenomicsequence[sbjct_dna_start-2:sbjct_dna_end+2]
####################################################
# initialize extended tinyexon PacbPORF
from pacb import PacbP
pacbp = PacbP(input=( qAAseq, sAAseq, startQaa, startSaa ) )
pacbp.strip_unmatched_ends()
pacbporf = pacbp2pacbporf(pacbp,orfQ,orfS)
pacbporf.extend_pacbporf_after_stops()
pacbporf.source = 'ABGPprojectingTE'
####################################
# make introns
####################################
intron1 = IntronConnectingOrfs(
intron1_dObj, intron1_aObj, None,
donorOrf,pacbporf.orfQ )
intron2 = IntronConnectingOrfs(
intron2_dObj, intron2_aObj, None,
pacbporf.orfQ, accepOrf )
################################################################
# set some meta-data properties to the intron objects
################################################################
# add distance score to intron
intron1._distance = 0
intron2._distance = 0
# add Alignment Positional Periphery Score into objects
if queryorsbjct == "query":
succes = set_apps_intron_query(intron1,pacbporfD,pacbporf)
succes = set_apps_intron_query(intron2,pacbporf,pacbporfA)
else:
succes = set_apps_intron_sbjct(intron1,pacbporfD,pacbporf)
succes = set_apps_intron_sbjct(intron2,pacbporf,pacbporfA)
# set GFF fsource attribute for recognition of intron sources
intron1._gff['fsource'] = "ABGPprojectingTE"
intron2._gff['fsource'] = "ABGPprojectingTE"
# create _linked_to_xxx attributes
intron1._linked_to_pacbporfs = [ pacbporf ]
intron2._linked_to_pacbporfs = [ pacbporf ]
intron1._linked_to_introns = [ intron2 ]
intron2._linked_to_introns = [ intron1 ]
####################################################
if verbose:
print pacbporf
pacbporf.print_protein_and_dna()
print intron1
print intron2
if False:
# printing data when this function needs to be debugged:
print ""
print intron1
print intron2
print ""
print pacbporfD
pacbporfD.print_protein_and_dna()
print ""
print pacbporf
pacbporf.print_protein_and_dna()
print ""
print pacbporfA
pacbporfA.print_protein_and_dna()
import sys
sys.exit()
####################################################
# return introns and intermediate tinyexon PacbPORF
return [(intron1,intron2,pacbporf)]
def merge_pacbporfs_with_introns(pacbporfD,pacbporfA,verbose=False,**kwargs):
"""
Merge 2 PacbPORF objects by introns
@attention: see orfs.merge_orfs_with_intron for **kwargs
@attention: see functions._filter_for_alignable_splice_sites for **kwargs
@attention: see functions._filter_for_entropy for **kwargs
@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 **kwargs dictionary for some forced attributes
_update_kwargs(kwargs,KWARGS_MAPPED_INTRON)
if not kwargs.has_key('aligned_site_max_triplet_distance'):
kwargs['aligned_site_max_triplet_distance'] = kwargs['max_aa_offset']
# settings for minimal alignment entropy score
min_donor_site_alignment_entropy = 0.0
min_acceptor_site_alignment_entropy = 0.0
# calculate maximal/minimal donor/acceptor site position based on alignment
ELEGIABLE_SPLICE_SITE_AA_RANGE = 75
qdr = pacbporfD.alignment_dna_range_query()
qar = pacbporfA.alignment_dna_range_query()
min_donor_query_pos = max([ min(qdr), max(qdr)-(ELEGIABLE_SPLICE_SITE_AA_RANGE*3) ])
max_accep_query_pos = min([ max(qar), min(qar)+(ELEGIABLE_SPLICE_SITE_AA_RANGE*3) ])
sdr = pacbporfD.alignment_dna_range_sbjct()
sar = pacbporfA.alignment_dna_range_sbjct()
min_donor_sbjct_pos = max([ min(sdr), max(sdr)-(ELEGIABLE_SPLICE_SITE_AA_RANGE*3) ])
max_accep_sbjct_pos = min([ max(sar), min(sar)+(ELEGIABLE_SPLICE_SITE_AA_RANGE*3) ])
# get list of introns
#intronsQ = merge_orfs_with_intron(pacbporfD.orfQ,pacbporfA.orfQ,
# min_donor_pos =min_donor_query_pos,
# max_acceptor_pos=max_accep_query_pos,**kwargs)
#intronsS = merge_orfs_with_intron(pacbporfD.orfS,pacbporfA.orfS,
# min_donor_pos =min_donor_sbjct_pos,
# max_acceptor_pos=max_accep_sbjct_pos,**kwargs)
# get list of introns
intronsQ = merge_orfs_with_intron(pacbporfD.orfQ,pacbporfA.orfQ,**kwargs)
intronsS = merge_orfs_with_intron(pacbporfD.orfS,pacbporfA.orfS,**kwargs)
# get unique list of donors & acceptors
donorQ = olba( list(Set([inQ.donor for inQ in intronsQ ])), order_by='pos')
donorS = olba( list(Set([inS.donor for inS in intronsS ])), order_by='pos')
accepQ = olba( list(Set([inQ.acceptor for inQ in intronsQ ])), order_by='pos')
accepS = olba( list(Set([inS.acceptor for inS in intronsS ])), order_by='pos')
############################################################################
if verbose:
print "dQ1", [ d.pos for d in donorQ ], "aQ1", [ a.pos for a in accepQ ]
print "dS1", [ d.pos for d in donorS ], "aS1", [ a.pos for a in accepS ]
############################################################################
# filter for alignable donor & acceptor sites
kwargs['allow_non_canonical'] = kwargs['allow_non_canonical_donor']
algdonors = _filter_for_alignable_splice_sites(donorQ,donorS,pacbporfD,**kwargs)
kwargs['allow_non_canonical'] = kwargs['allow_non_canonical_acceptor']
algacceps = _filter_for_alignable_splice_sites(accepQ,accepS,pacbporfA,**kwargs)
############################################################################
if verbose:
print "dQ2", [ _dq.pos for (_dq,_ds) in algdonors ],
print "aQ2", [ _aq.pos for (_aq,_as) in algacceps ]
print "dS2", [ _ds.pos for (_dq,_ds) in algdonors ],
print "aS2", [ _as.pos for (_aq,_as) in algacceps ]
############################################################################
# remove sites with to low alignment entropy
algdonors = _filter_for_entropy(algdonors,pacbporfD,'donor',
min_alignment_entropy=min_donor_site_alignment_entropy)
algacceps = _filter_for_entropy(algacceps,pacbporfA,'acceptor',
min_alignment_entropy=min_acceptor_site_alignment_entropy)
############################################################################
if verbose:
print "dQ3", [ _dq.pos for (_dq,_ds) in algdonors ],
print "aQ3", [ _aq.pos for (_aq,_as) in algacceps ]
print "dS3", [ _ds.pos for (_dq,_ds) in algdonors ],
print "aS3", [ _as.pos for (_aq,_as) in algacceps ]
############################################################################
# make unique position lists for quick lookup in intron lists
dQpl = Set([ dQ.pos for dQ,dS in algdonors ])
dSpl = Set([ dS.pos for dQ,dS in algdonors ])
aQpl = Set([ aQ.pos for aQ,aS in algacceps ])
aSpl = Set([ aS.pos for aQ,aS in algacceps ])
# check exterior boundaries of PacbPORFs
sposD = pacbporfD._get_original_alignment_pos_start()
eposD = pacbporfD._get_original_alignment_pos_end()
sposA = pacbporfA._get_original_alignment_pos_start()
eposA = pacbporfA._get_original_alignment_pos_end()
# now make list of aligable introns
algintrons = []
for intQ in intronsQ:
# check if intron falls within the PacbPORF aligned area
if intQ.donor.pos <= sposD.query_dna_start: continue
if intQ.acceptor.pos >= eposA.query_dna_end: continue
if intQ.donor.pos in dQpl and intQ.acceptor.pos in aQpl:
# Query intron occurs in list of alignable splice sites!
for intS in intronsS:
# check if intron falls within the PacbPORF aligned area
if intS.donor.pos <= sposD.sbjct_dna_start: continue
if intS.acceptor.pos >= eposA.sbjct_dna_end: continue
if intS.donor.pos in dSpl and intS.acceptor.pos in aSpl:
# Sbjct intron occurs as well in alignable splice sites!
if (intQ.donor,intS.donor) in algdonors and\
(intQ.acceptor,intS.acceptor) in algacceps:
# Sbjct & Query Donor & Acceptor are alignable!
algintrons.append( ( intQ, intS ) )
############################################################################
# set some meta-data properties to the intron objects
############################################################################
for intQ,intS in algintrons:
distDnt = pacbporfD.get_distance_aligned_nucleotide_positions(
query = intQ.donor.pos, sbjct = intS.donor.pos
)
distAnt = pacbporfA.get_distance_aligned_nucleotide_positions(
query = intQ.acceptor.pos, sbjct = intS.acceptor.pos
)
# final distance check. kwargs['aligned_site_max_triplet_distance']
# is applied on donor and acceptor site. This distance measured on the
# protein sequence can be DOUBLED in case distDnt / distAnt are
# opposite (+ and -). Check here if the protein sequence gap is
# as well <= kwargs['aligned_site_max_triplet_distance'].
if abs(distAnt - distDnt) > kwargs['aligned_site_max_triplet_distance']*3:
continue
# add distance score to introns
intQ._distance = abs(distDnt) + abs(distAnt)
intS._distance = abs(distDnt) + abs(distAnt)
# add Alignment Positional Periphery Score into objects
succes = set_apps_intron_query(intQ,pacbporfD,pacbporfA)
succes = set_apps_intron_sbjct(intS,pacbporfD,pacbporfA)
# set GFF fsource attribute for recognition of intron sources
intQ._gff['fsource'] = "ABGPmapping"
intS._gff['fsource'] = "ABGPmapping"
########################################################################
if verbose:
# some printing....
print "Aligned introns:", ( intQ.donor.pos, intQ.acceptor.pos ) ,
print ( intS.donor.pos, intS.acceptor.pos ),
print "DIST:", distDnt, distAnt,
print "[%s]" % kwargs['aligned_site_max_triplet_distance'],
print "ENTROPY: %1.2f %1.2f" % (intQ._apps_donor, intQ._apps_accep),
print "PSSM: (%1.2f %1.2f) (%1.2f %1.2f)" % (
intQ.donor.pssm_score, intS.donor.pssm_score,
intQ.acceptor.pssm_score, intS.acceptor.pssm_score,
)
########################################################################
# return lists of aligned introns
return algintrons
def merge_pacbporfs_with_closeby_independant_introns(pacbporfD,pacbporfA,
verbose=False,**kwargs):
"""
Merge 2 PacbPORF objects by closeby independant gained introns
@attention: see pacb.connecting.merge_orfs_with_intron for **kwargs)
@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 ( intronQ, intronS, CIGexonPacbPORF )
"""
# input validation
IsPacbPORF(pacbporfD)
IsPacbPORF(pacbporfA)
# edit **kwargs dictionary for some forced attributes
kwargs['allow_phase_shift'] = True
_update_kwargs(kwargs,KWARGS_CLOSEBY_INDEPENDANT_INTRON_GAIN)
if not kwargs.has_key('aligned_site_max_triplet_distance'):
kwargs['aligned_site_max_triplet_distance'] = kwargs['cig_max_aa_length']
# run regular merge_pacbporfs_with_introns function
alg_introns = merge_pacbporfs_with_introns(pacbporfD,pacbporfA,verbose=verbose,**kwargs)
cig_introns = []
if verbose:
print "introns::", len(alg_introns), "cig_max_aa_length:", kwargs['cig_max_aa_length'], kwargs['aligned_site_max_triplet_distance']
# check if there is length congruence between the cig_introns
for intQ,intS in alg_introns:
dQpos, dQphase = pacbporfD.dnaposition_query(intQ.donor.pos,forced_return=True)
dSpos, dSphase = pacbporfD.dnaposition_sbjct(intS.donor.pos,forced_return=True)
aQpos, aQphase = pacbporfA.dnaposition_query(intQ.acceptor.pos,forced_return=True)
aSpos, aSphase = pacbporfA.dnaposition_sbjct(intS.acceptor.pos,forced_return=True)
distDnt = (dQpos*3 + dQphase) - (dSpos*3 + dSphase)
distAnt = (aQpos*3 + aQphase) - (aSpos*3 + aSphase)
########################################################################
if verbose:
print (intQ.donor.pos, intQ.acceptor.pos),
print (intS.donor.pos, intS.acceptor.pos),
print distDnt, distAnt, kwargs['max_nt_offset']
########################################################################
if abs(distDnt-distAnt) > kwargs['max_nt_offset']:
# intermediate ciigPacbPORF has query vs sbjct length discrepancy
# *3 for AA2nt coordinate conversion, +2 to allow different phases
# e.g. phase difference can give 1AA+2nt difference
continue
if intQ.donor.phase == intS.donor.phase and\
(distDnt/3) <= kwargs['aligned_site_max_triplet_distance']:
# a regularly merged intron combination
continue
if intQ.acceptor.phase == intS.acceptor.phase and\
(distAnt/3) <= kwargs['aligned_site_max_triplet_distance']:
# a regularly merged intron combination
continue
if abs(distDnt) <= 5 or abs(distDnt) <= 5:
# most likely a splice site phase shift, not a c.i.g.
continue
if abs(distDnt/3) >= kwargs['cig_min_aa_length'] and\
abs(distAnt/3) >= kwargs['cig_min_aa_length'] and\
abs(distDnt/3) <= kwargs['cig_max_aa_length'] and\
abs(distAnt/3) <= kwargs['cig_max_aa_length']:
# putatively a closeby independant (intron) gain
cig_introns.append( ( intQ, intS ) )
############################################################################
if verbose:
for intQ,intS in cig_introns:
print "cig?:", (intQ.donor.pos, intQ.acceptor.pos),
print (intS.donor.pos, intS.acceptor.pos)
############################################################################
# return variable to store found positive cases of CIG into
found_cig_list = []
# check if there is some sequence similarity
for intQ,intS in cig_introns:
# get alignment positions around query & sbjcts splice sites
dQpos, dQphase = pacbporfD.dnaposition_query(intQ.donor.pos,forced_return=True)
dSpos, dSphase = pacbporfD.dnaposition_sbjct(intS.donor.pos,forced_return=True)
aQpos, aQphase = pacbporfA.dnaposition_query(intQ.acceptor.pos,forced_return=True)
aSpos, aSphase = pacbporfA.dnaposition_sbjct(intS.acceptor.pos,forced_return=True)
distD = dQpos - dSpos
distA = aQpos - aSpos
distDnt = (dQpos*3 + dQphase) - (dSpos*3 + dSphase)
distAnt = (aQpos*3 + aQphase) - (aSpos*3 + aSphase)
if distDnt > 0: # then, distAnt is as well > 0
# QUERY is extended on the donor side
#mode = "SQ"
#qStart = pacbporfD._positions[dSpos].query_pos
#qEnd = qStart + distD
#sStart = pacbporfA._positions[aSpos].sbjct_pos
#sEnd = sStart + distD
#qSeq = pacbporfD.orfQ.getaas(abs_pos_start=qStart,abs_pos_end=qEnd)
#sSeq = pacbporfA.orfS.getaas(abs_pos_start=sStart,abs_pos_end=sEnd)
mode = "SQ"
qEnd = pacbporfD.orfQ.dnapos2aapos(intQ.donor.pos)
qStart= qEnd - max([distA,distD])
sStart= pacbporfA.orfS.dnapos2aapos(intS.acceptor.pos)
sEnd = sStart + max([distA,distD])
qSeq = pacbporfD.orfQ.getaas(abs_pos_start=qStart,abs_pos_end=qEnd)
sSeq = pacbporfA.orfS.getaas(abs_pos_start=sStart,abs_pos_end=sEnd)
else: # distDnt and distAnt are < 0
## SBJCT is extended on the donor site
#mode = "QS"
#qStart = pacbporfA._positions[aQpos].query_pos
#qEnd = qStart - distA
#sStart = pacbporfD._positions[dQpos].sbjct_pos
#sEnd = sStart - distA
#qSeq = pacbporfA.orfQ.getaas(abs_pos_start=qStart, abs_pos_end=qEnd)
#sSeq = pacbporfD.orfS.getaas(abs_pos_start=sStart, abs_pos_end=sEnd)
mode = "QS"
qStart= pacbporfA.orfQ.dnapos2aapos(intQ.acceptor.pos)
qEnd = qStart - min([distA,distD])
sEnd = pacbporfD.orfS.dnapos2aapos(intS.donor.pos)
sStart= sEnd + min([distA,distD])
qSeq = pacbporfA.orfQ.getaas(abs_pos_start=qStart,abs_pos_end=qEnd)
sSeq = pacbporfD.orfS.getaas(abs_pos_start=sStart,abs_pos_end=sEnd)
headerQ = "query_%s_%s_%s" % (qStart,qEnd,qSeq)
headerS = "sbjct_%s_%s_%s" % (sStart,sEnd,sSeq)
headerQ = headerQ[0:20] # truncate to prevent error
headerS = headerS[0:20] # truncate to prevent error
if verbose:
print mode, (distD,distA), qSeq, sSeq, headerQ, headerS, distDnt, distAnt,
print dQpos, aQpos, dSpos, aSpos
if not qSeq: continue # superfluous check-doublecheck for sequence
if not sSeq: continue # superfluous check-doublecheck for sequence
####################################################
# make PacbPORF with ClustalW
####################################################
# align the sequences with clustalw
seqs = { headerQ: qSeq, headerS: sSeq }
(alignedseqs,alignment) = clustalw(seqs=seqs)
# make pacbp from clustalw alignment
pacbp = pacbp_from_clustalw(
alignment=(
alignedseqs[headerQ],
alignment,
alignedseqs[headerS]
),
coords=(qStart,qEnd,sStart,sEnd)
)
if not pacbp: continue
# strip unaligned fraction of this pacbp object, then check length
pacbp.strip_unmatched_ends()
if len(pacbp) < kwargs['cig_min_aa_length']:
continue
if len(pacbp) > kwargs['cig_max_aa_length']:
continue
if pacbp:
# initialize extended tiny PacbPORF caused by c.i.g.
if distDnt > 0:
cig_pacbporf = pacbp2pacbporf(pacbp,pacbporfD.orfQ,pacbporfA.orfS)
else:
cig_pacbporf = pacbp2pacbporf(pacbp,pacbporfA.orfQ,pacbporfD.orfS)
cig_pacbporf.extend_pacbporf_after_stops()
####################################################################
if verbose:
print pacbp, len(pacbp)
print cig_pacbporf
print "CIG:", intQ
print "CIG:", intS
print distD, distA, distDnt, distAnt
cig_pacbporf.print_protein_and_dna()
####################################################################
####################################################################
# set some meta-data properties to the intron objects
####################################################################
# add distance score to introns
# The distance set in merge_pacbporfs_with_introns is large;
# it is the actual distance between the splice sites. In CIG,
# the measure for distance is the length difference between
# the offset between query and sbjct measured on the cig_pacbporf
intQ._distance = abs(distDnt-distAnt)
intS._distance = abs(distDnt-distAnt)
if distDnt > 0: # then, distAnt is as well > 0
# QUERY is extended on the donor side
# add Alignment Positional Periphery Score into objects
succes = set_apps_intron_query(intQ,cig_pacbporf,pacbporfA)
succes = set_apps_intron_sbjct(intS,pacbporfD,cig_pacbporf)
else:
# SBJCT is extended on the donor side
# add Alignment Positional Periphery Score into objects
succes = set_apps_intron_query(intQ,pacbporfD,cig_pacbporf)
succes = set_apps_intron_sbjct(intS,cig_pacbporf,pacbporfA)
# set GFF fsource attribute for recognition of intron sources
intQ._gff['fsource'] = "ABGPcig"
intS._gff['fsource'] = "ABGPcig"
# create _linked_to_xxx attributes
intQ._linked_to_pacbporfs = [ cig_pacbporf ]
intS._linked_to_pacbporfs = [ cig_pacbporf ]
# append to found_cig_list
found_cig_list.append( ( intQ, intS, cig_pacbporf ) )
else:
# no alignment possible -> try next
continue
# return lists of closeby_independant_introns
return found_cig_list
def _merge_pacbporfs_by_two_tinyexons(pacbporfD,
pacbporfA,
orfSetObject,
queryorsbjct,
verbose=False,
**kwargs):
""" """
# edit **kwargs dictionary for some forced attributes
_update_kwargs(kwargs, KWARGS_PROJECTED_TINYEXON)
tinyexons = []
sposD = pacbporfD._get_original_alignment_pos_start()
eposD = pacbporfD._get_original_alignment_pos_end()
sposA = pacbporfA._get_original_alignment_pos_start()
eposA = pacbporfA._get_original_alignment_pos_end()
if queryorsbjct == "query":
donorOrf = pacbporfD.orfQ
accepOrf = pacbporfA.orfQ
prjctOrf = pacbporfD.orfS
dStart, dEnd = sposD.query_dna_start, eposD.query_dna_end
aStart, aEnd = sposA.query_dna_start, eposA.query_dna_end
elif queryorsbjct == "sbjct":
donorOrf = pacbporfD.orfS
accepOrf = pacbporfA.orfS
prjctOrf = pacbporfD.orfQ
dStart, dEnd = sposD.sbjct_dna_start, eposD.sbjct_dna_end
aStart, aEnd = sposA.sbjct_dna_start, eposA.sbjct_dna_end
else:
message = "'queryorsbjct' (%s), not 'query' or 'sbjct'" % queryorsbjct
raise InproperlyAppliedArgument, message
# get all potential combinations of two tinyexons
tinyexoncombis = merge_orfs_with_two_tinyexons(
donorOrf,
accepOrf,
donorOrf._donor_sites,
accepOrf._acceptor_sites,
orfSetObject.orfs,
)
results = []
for dObj in donorOrf._donor_sites:
if queryorsbjct == "query":
(dPos, dPhase) = pacbporfD.dnaposition_query(dObj.pos,
forced_return=True)
else:
(dPos, dPhase) = pacbporfD.dnaposition_sbjct(dObj.pos,
forced_return=True)
try:
algDobj = pacbporfD._positions[dPos]
except IndexError:
# site out of range of PacbPORF -> break
break
# check if dObj is on pfD;
# introns of tinyexons can be projected outside of pfD/pfA area
if dObj.pos < dStart: continue
for aObj in accepOrf._acceptor_sites:
if queryorsbjct == "query":
(aPos,
aPhase) = pacbporfA.dnaposition_query(aObj.pos,
forced_return=True)
else:
(aPos,
aPhase) = pacbporfA.dnaposition_sbjct(aObj.pos,
forced_return=True)
try:
algAobj = pacbporfA._positions[aPos]
except IndexError:
# site out of range of PacbPORF -> break
break
# check if aObj is on pfA;
# introns of tinyexons can be projected outside of pfD/pfA area
if aObj.pos > aEnd: continue
if queryorsbjct == "query":
posDsbjct = algDobj.sbjct_dna_start + dPhase
posAsbjct = algAobj.sbjct_dna_start + aPhase
else:
posDsbjct = algDobj.query_dna_start + dPhase
posAsbjct = algAobj.query_dna_start + aPhase
distance = posAsbjct - posDsbjct
if distance >= (kwargs['max_tinyexon_nt_length'] * 2):
break
if distance < (kwargs['min_tinyexon_nt_length'] * 2):
continue
filtered_tinyexoncombis = _filter_tinyexoncombis(
tinyexoncombis,
min_length=distance,
max_length=distance,
min_first_acceptor_pos=dObj.pos +
kwargs['min_tinyexon_intron_nt_length'],
max_final_donor_pos=aObj.pos -
kwargs['min_tinyexon_intron_nt_length'],
phase_final_donor=aObj.phase,
phase_first_acceptor=dObj.phase,
)
if not filtered_tinyexoncombis: continue
####################################################################
if verbose:
print distance, dObj, aObj, len(tinyexoncombis),
print len(filtered_tinyexoncombis)
####################################################################
for exon1, intron, exon2 in filtered_tinyexoncombis:
# make preceding intron
preceding_intron = IntronConnectingOrfs(
dObj, exon1.acceptor, None, donorOrf, exon1.orf)
# make subsequent intron
subsequent_intron = IntronConnectingOrfs(
exon2.donor, aObj, None, exon2.orf, accepOrf)
################################################################
if verbose:
print "\t", exon1, exon1.proteinsequence(),
print preceding_intron.phase, exon1.donor.phase,
print subsequent_intron.phase, preceding_intron.shared_aa,
print intron.shared_aa, subsequent_intron.shared_aa
print "\t", exon2, exon2.proteinsequence()
################################################################
# get prjctOrf sequence for comparison
correctionA = 0
if aObj.phase != 0:
# INCLUDE the final AA which is broken by the splicesite
correctionA = 1
if queryorsbjct == "query":
startPos, _phase = pacbporfD.dnaposition_query(
dObj.pos, forced_return=True)
stopPos, _phase = pacbporfA.dnaposition_query(
aObj.pos, forced_return=True)
start = pacbporfD._positions[startPos].sbjct_pos
stop = pacbporfA._positions[stopPos].sbjct_pos + correctionA
else:
startPos, _phase = pacbporfD.dnaposition_sbjct(
dObj.pos, forced_return=True)
stopPos, _phase = pacbporfA.dnaposition_sbjct(
aObj.pos, forced_return=True)
start = pacbporfD._positions[startPos].query_pos
stop = pacbporfA._positions[stopPos].query_pos + correctionA
if stop <= start:
# tinyexon is so tiny that is does not have a single
# full aligned AA -> discard here
continue
# actually get the prjctOrf sequence
aaseq = prjctOrf.getaas(abs_pos_start=start, abs_pos_end=stop)
# initialize a PacbP for the combination of both tinyexons
# afterwards, check if the indentityscore is > 0.XX
from pacb import PacbP
seqparts = [
preceding_intron.shared_aa,
exon1.proteinsequence(), intron.shared_aa,
exon2.proteinsequence(), subsequent_intron.shared_aa
]
################################################################
if verbose or len("".join(seqparts)) != len(aaseq):
print pacbporfD
print exon1.orf, exon2.orf, prjctOrf
print pacbporfA
print seqparts
print aaseq, len(aaseq), len("".join(seqparts)), (start,
stop)
print "'%s'" % queryorsbjct,
print "Q", (algDobj.query_pos, algAobj.query_pos),
print "S", (algDobj.sbjct_pos, algAobj.sbjct_pos)
print "distance:", distance, kwargs[
'max_tinyexon_nt_length'],
print(posDsbjct, posAsbjct),
print "Q-dna:", (algDobj.query_dna_start, dPhase,
algAobj.query_dna_start, aPhase),
print "S-dna:", (algDobj.sbjct_dna_start, dPhase,
algAobj.sbjct_dna_start, aPhase)
################################################################
# ignore by continue when sequences not identical in length
if len("".join(seqparts)) != len(aaseq): continue
testpacbp = PacbP(input=("".join(seqparts), aaseq, 0, 0))
testpacbp.strip_unmatched_ends()
if not ( testpacbp.identityscore > 0.60 and\
(float(testpacbp.length) / len(aaseq)) > 0.70 ):
# not a very convincing alignment
continue
################################################################
if verbose:
print testpacbp
testpacbp.print_protein()
################################################################
# if here, succesfully mapped 2 tiny exons!!
# get all sequences/coordinates in place for
# pacbporf formation
orfQ1 = exon1.orf
orfS1 = prjctOrf
orfQ2 = exon2.orf
orfS2 = prjctOrf
seqQ1 = exon1.proteinsequence()
seqQ2 = exon2.proteinsequence()
coordQ1 = exon1.acceptor.pos / 3
coordS1 = start
coordQ2 = exon2.acceptor.pos / 3
coordS2 = start + len(seqparts[0]) + len(seqparts[1]) + len(
seqparts[2])
seqS1 = aaseq[0:(len(seqparts[0]) + len(seqparts[1]))]
seqS2 = aaseq[-(len(seqparts[3]) + len(seqparts[4])):]
if len(seqparts[0]):
seqS1 = seqS1[1:]
coordS1 += 1
if len(seqparts[4]):
seqS2 = seqS2[:-1]
if queryorsbjct == "sbjct":
# swap query <-> sbjct
orfQ1, orfS1 = orfS1, orfQ1
orfQ2, orfS2 = orfS2, orfQ2
seqQ1, seqS1 = seqS1, seqQ1
seqQ2, seqS2 = seqS2, seqQ2
coordQ1, coordS1 = coordS1, coordQ1
coordQ2, coordS2 = coordS2, coordQ2
################################################################
if verbose:
print "tinypacbporf1:", seqQ1, seqQ2, coordQ1, coordQ2
print "tinypacbporf2:", seqS1, seqS2, coordS1, coordS2
################################################################
# make pacbporfs
pacbp1 = PacbP(input=(seqQ1, seqS1, coordQ1, coordS1))
pacbp1.strip_unmatched_ends()
tinypacbporf1 = pacbp2pacbporf(pacbp1, orfQ1, orfS1)
tinypacbporf1.extend_pacbporf_after_stops()
pacbp2 = PacbP(input=(seqQ2, seqS2, coordQ2, coordS2))
pacbp2.strip_unmatched_ends()
tinypacbporf2 = pacbp2pacbporf(pacbp2, orfQ2, orfS2)
tinypacbporf2.extend_pacbporf_after_stops()
################################################################
if verbose:
print tinypacbporf1
tinypacbporf1.print_protein_and_dna()
print tinypacbporf2
tinypacbporf2.print_protein_and_dna()
################################################################
################################################################
# set some meta-data properties to the intron objects
################################################################
# add distance score to intron
preceding_intron._distance = 0
intron._distance = 0
subsequent_intron._distance = 0
# add Alignment Positional Periphery Score into objects
if queryorsbjct == "query":
succes = set_apps_intron_query(preceding_intron, pacbporfD,
tinypacbporf1)
succes = set_apps_intron_query(intron, tinypacbporf1,
tinypacbporf2)
succes = set_apps_intron_query(subsequent_intron,
tinypacbporf2, pacbporfA)
else:
succes = set_apps_intron_sbjct(preceding_intron, pacbporfD,
tinypacbporf1)
succes = set_apps_intron_sbjct(intron, tinypacbporf1,
tinypacbporf2)
succes = set_apps_intron_sbjct(subsequent_intron,
tinypacbporf2, pacbporfA)
# set GFF fsource attribute for recognition of intron sources
preceding_intron._gff['fsource'] = "ABGPprojectingTE"
intron._gff['fsource'] = "ABGPprojectingTE"
subsequent_intron._gff['fsource'] = "ABGPprojectingTE"
# create _linked_to_xxx attributes
preceding_intron._linked_to_pacbporfs = [
tinypacbporf1, tinypacbporf2
]
intron._linked_to_pacbporfs = [tinypacbporf1, tinypacbporf2]
subsequent_intron._linked_to_pacbporfs = [
tinypacbporf1, tinypacbporf2
]
preceding_intron._linked_to_introns = [
intron, subsequent_intron
]
intron._linked_to_introns = [
preceding_intron, subsequent_intron
]
subsequent_intron._linked_to_introns = [
intron, preceding_intron
]
################################################################
# append to results
################################################################
results.append((
preceding_intron,
intron,
subsequent_intron,
tinypacbporf1,
tinypacbporf2,
))
# return 3 introns and 2 intermediate tinyexon PacbPORFs (per row)
return results
def _merge_pacbporfs_by_tinyexon_and_two_introns(pacbporfD,
pacbporfA,
orfSetObject,
queryorsbjct,
verbose=False,
**kwargs):
"""
Merge 2 PacbPORF objects by introns
@attention: see pacb.connecting.merge_orfs_with_intron for **kwargs)
@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 orfSetObject: object with elegiable Orfs
@param orfSetObject: object with elegiable Orfs
@type queryorsbjct: string
@param queryorsbjct: literal string 'query' or 'sbjct'
@type verbose: Boolean
@param verbose: print debugging info to STDOUT when True
@rtype: list
@return: list with ( intron, ExonOnOrf, intron ) on the query sequence
"""
# input validation
IsPacbPORF(pacbporfD)
IsPacbPORF(pacbporfA)
# edit **kwargs dictionary for some forced attributes
_update_kwargs(kwargs, KWARGS_PROJECTED_TINYEXON)
MAX_TINYEXON_NT_LENGTH = 33
MIN_TINYEXON_NT_LENGTH = 6
tinyexons = []
if queryorsbjct == "query":
donorOrf = pacbporfD.orfQ
accepOrf = pacbporfA.orfQ
prjctOrf = pacbporfD.orfS
alignedDonorRange = pacbporfD.alignment_dna_range_query()
alignedAccepRange = pacbporfA.alignment_dna_range_query()
elif queryorsbjct == "sbjct":
donorOrf = pacbporfD.orfS
accepOrf = pacbporfA.orfS
prjctOrf = pacbporfD.orfQ
alignedDonorRange = pacbporfD.alignment_dna_range_sbjct()
alignedAccepRange = pacbporfA.alignment_dna_range_sbjct()
else:
message = "'queryorsbjct' (%s), not 'query' or 'sbjct'" % queryorsbjct
raise InproperlyAppliedArgument, message
for dObj in donorOrf._donor_sites:
# do not make a projection OVER the aligned area
if dObj.pos < min(alignedDonorRange): continue
if queryorsbjct == "query":
(dPos, dPhase) = pacbporfD.dnaposition_query(dObj.pos,
forced_return=True)
else:
(dPos, dPhase) = pacbporfD.dnaposition_sbjct(dObj.pos,
forced_return=True)
try:
algDobj = pacbporfD._positions[dPos]
except IndexError:
# site out of range of PacbPORF -> break
break
for aObj in accepOrf._acceptor_sites:
# do not make a projection OVER the aligned area
if aObj.pos > max(alignedAccepRange): continue
if queryorsbjct == "query":
(aPos,
aPhase) = pacbporfA.dnaposition_query(aObj.pos,
forced_return=True)
else:
(aPos,
aPhase) = pacbporfA.dnaposition_sbjct(aObj.pos,
forced_return=True)
try:
algAobj = pacbporfA._positions[aPos]
except IndexError:
# site out of range of PacbPORF -> break
break
if queryorsbjct == "query":
posDsbjct = algDobj.sbjct_dna_start + dPhase
posAsbjct = algAobj.sbjct_dna_start + aPhase
else:
posDsbjct = algDobj.query_dna_start + dPhase
posAsbjct = algAobj.query_dna_start + aPhase
distance = posAsbjct - posDsbjct
if distance >= MAX_TINYEXON_NT_LENGTH:
break
if distance < MIN_TINYEXON_NT_LENGTH:
continue
####################################################
# generate a ScanForMatches pattern file
####################################################
# example pattern: 6...6 AG NNGNNANNANNGN[2,0,0] GT 3...3
query = list(prjctOrf.inputgenomicsequence[posDsbjct:posAsbjct])
# mask all non-phase0 nucleotides to N residues;
# this represents the regularexpression for a specific
# peptide sequence
firstphasepositions = range(3 - dPhase % 3, len(query), 3)
for pos in range(0, len(query)):
if pos not in firstphasepositions:
query[pos] = "N"
# calculate a ~50% mismatch number
mismatches = max([0, (len(query) - query.count("N")) / 2])
# write the pattern to string and subsequently to file
# example pattern: 6...6 AG NNGNNANNANNGN[2,0,0] GT 3...3
if kwargs['allow_non_canonical_donor']:
sfmpat = "%s...%s AG %s[%s,0,0] G (T | C) %s...%s" % (
AUSO, AUSO, "".join(query), mismatches, DDSO, DDSO)
else:
sfmpat = "%s...%s AG %s[%s,0,0] GT %s...%s" % (
AUSO, AUSO, "".join(query), mismatches, DDSO, DDSO)
####################################################
if verbose:
print(pacbporfD.orfQ.id, pacbporfA.orfQ.id),
print distance, dObj, aObj
print sfmpat
####################################################
fname = "sfmpat_tinyexon_%s_%s_%s_%s" % (
donorOrf.id,
accepOrf.id,
posDsbjct,
posAsbjct,
)
fh = open(fname, 'w')
fh.write(sfmpat + "\n")
fh.close()
####################################################
# run ScanForMatches
####################################################
command = """echo ">myseq\n%s" | %s %s | tr "[,]" "\t\t#" | """ +\
"""tr -d "\n " | sed "s/>/\\n>/g" | tr "#" "\t" | """ +\
"""awk -F'\t' '{ if (NF==4 && $2>%s && $3<%s) """ +\
"""{ print $1"["$2","$3"]\\n"$4 } }' """
command = command % (donorOrf.inputgenomicsequence, EXECUTABLE_SFM,
fname, dObj.pos +
(kwargs['min_intron_nt_length'] - 3),
aObj.pos -
(kwargs['min_intron_nt_length'] - 3))
co = osPopen(command)
matches = parseFasta(co.readlines())
co.close()
# filter matches for:
# (1) correct donor & acceptor phase
# (2) high enough donor & acceptor site scores
for hdr, seqmatch in matches.iteritems():
startQ, stopQ = [
int(item) for item in hdr.split(":")[1][1:-1].split(",")
]
exonQstart = startQ + AUSO + 2 - 1
exonQstop = stopQ - DDSO - 2
####################################
# get Orf object of tinyexon
####################################
tinyexonorf = None
# select the Orf on which the tinyexon is located
for orfObj in orfSetObject.get_eligible_orfs(
max_orf_start=exonQstart, min_orf_end=exonQstop):
orfPhase = (exonQstart - orfObj.startPY) % 3
if orfPhase == dPhase:
tinyexonorf = orfObj
break
else:
# No tinyexonorf assigned!! Iin case a regex matched
# over a STOP-codon or the regex length is smaller
# then the smallest Orf, no Orf can be assigned
continue
# filter for donor & acceptor score
dScore = _score_splice_site(seqmatch[-9:], splicetype='donor')
aScore = _score_splice_site(seqmatch[0:11],
splicetype='acceptor')
if dScore < kwargs['min_donor_pssm_score']:
continue
if aScore < kwargs['min_acceptor_pssm_score']:
continue
# scan Orf for splicesites
tinyexonorf.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'])
tinyexonorf.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'])
# get 1th intron donor object
intron1_aObj = None
for a in tinyexonorf._acceptor_sites:
if a.pos == exonQstart:
intron1_aObj = a
break
else:
# pseudo-acceptorsite as found be SFM regex
# is not a valid acceptor site of high enough score
# continue to next iteration of (hdr,seqmatch) pair
continue
# get 2th intron donor object
intron2_dObj = None
for d in tinyexonorf._donor_sites:
if d.pos == exonQstop:
intron2_dObj = d
break
else:
# pseudo-donorsite as found be SFM regex
# is not a valid acceptor site of high enough score
# continue to next iteration of (hdr,seqmatch) pair
continue
# check if introns are of elegiable lengths
if (intron1_aObj.pos -
dObj.pos) > kwargs['max_intron_nt_length']:
continue
if (aObj.pos -
intron2_dObj.pos) > kwargs['max_intron_nt_length']:
continue
####################################################
if True or verbose:
# if here, a candidate!!!
print(pacbporfD.orfQ.id, tinyexonorf.id,
pacbporfA.orfQ.id),
print hdr, dScore, aScore
print seqmatch
####################################################
# append to found tinyexons
query_data = (tinyexonorf, exonQstart, exonQstop)
sbjct_data = (prjctOrf, posDsbjct, posAsbjct)
splicesite_data = (dObj, intron1_aObj, intron2_dObj, aObj)
tinyexons.append((query_data, sbjct_data, splicesite_data))
# file cleanup
osRemove(fname)
# return - End Of Function - if no tinyexons are found
if not tinyexons:
return []
####################################
# select the **best** tinyexon
####################################
(query_data, sbjct_data, splicesite_data) = tinyexons[0]
orfQ, query_dna_start, query_dna_end = query_data
orfS, sbjct_dna_start, sbjct_dna_end = sbjct_data
(intron1_dObj, intron1_aObj, intron2_dObj, intron2_aObj) = splicesite_data
####################################################
if verbose:
print "tinyexon orf:", orfQ
print "tinyexon orf:", intron1_aObj
print "tinyexon orf:", intron2_dObj
####################################################
####################################
# make tinyexon PacbPORF
####################################
startQaa = orfQ.dnapos2aapos(query_dna_start) - 1
startSaa = orfS.dnapos2aapos(sbjct_dna_start) - 1
stopQaa = orfQ.dnapos2aapos(query_dna_end) + 1
stopSaa = orfS.dnapos2aapos(sbjct_dna_end) + 1
# check for directly leading stop codon on tinyexon
while startQaa <= orfQ.protein_startPY:
startQaa += 1
startSaa += 1
query_dna_start += 3
sbjct_dna_start += 3
while startSaa <= orfS.protein_startPY:
startQaa += 1
startSaa += 1
query_dna_start += 3
sbjct_dna_start += 3
# check for directly tailing stop codon on tinyexon
while stopQaa > orfQ.protein_endPY:
stopQaa -= 1
stopSaa -= 1
query_dna_end -= 3
sbjct_dna_end -= 3
while stopSaa > orfS.protein_endPY:
stopQaa -= 1
stopSaa -= 1
query_dna_end -= 3
sbjct_dna_end -= 3
# get sequences
qAAseq = orfQ.getaas(abs_pos_start=startQaa, abs_pos_end=stopQaa)
sAAseq = orfS.getaas(abs_pos_start=startSaa, abs_pos_end=stopSaa)
####################################################
if verbose or len(qAAseq) != len(sAAseq):
# if unequal lengths, error will be raised upon PacbP.__init__()
print orfQ, qAAseq, startQaa, stopQaa, (stopQaa - startQaa),
print(query_dna_start, query_dna_end)
print orfS, sAAseq, startSaa, stopSaa, (stopSaa - startSaa),
print(sbjct_dna_start, sbjct_dna_end)
print orfQ.inputgenomicsequence[query_dna_start - 2:query_dna_end + 2]
print orfS.inputgenomicsequence[sbjct_dna_start - 2:sbjct_dna_end + 2]
####################################################
# initialize extended tinyexon PacbPORF
from pacb import PacbP
pacbp = PacbP(input=(qAAseq, sAAseq, startQaa, startSaa))
pacbp.strip_unmatched_ends()
pacbporf = pacbp2pacbporf(pacbp, orfQ, orfS)
pacbporf.extend_pacbporf_after_stops()
pacbporf.source = 'ABGPprojectingTE'
####################################
# make introns
####################################
intron1 = IntronConnectingOrfs(intron1_dObj, intron1_aObj, None, donorOrf,
pacbporf.orfQ)
intron2 = IntronConnectingOrfs(intron2_dObj, intron2_aObj, None,
pacbporf.orfQ, accepOrf)
################################################################
# set some meta-data properties to the intron objects
################################################################
# add distance score to intron
intron1._distance = 0
intron2._distance = 0
# add Alignment Positional Periphery Score into objects
if queryorsbjct == "query":
succes = set_apps_intron_query(intron1, pacbporfD, pacbporf)
succes = set_apps_intron_query(intron2, pacbporf, pacbporfA)
else:
succes = set_apps_intron_sbjct(intron1, pacbporfD, pacbporf)
succes = set_apps_intron_sbjct(intron2, pacbporf, pacbporfA)
# set GFF fsource attribute for recognition of intron sources
intron1._gff['fsource'] = "ABGPprojectingTE"
intron2._gff['fsource'] = "ABGPprojectingTE"
# create _linked_to_xxx attributes
intron1._linked_to_pacbporfs = [pacbporf]
intron2._linked_to_pacbporfs = [pacbporf]
intron1._linked_to_introns = [intron2]
intron2._linked_to_introns = [intron1]
####################################################
if verbose:
print pacbporf
pacbporf.print_protein_and_dna()
print intron1
print intron2
if False:
# printing data when this function needs to be debugged:
print ""
print intron1
print intron2
print ""
print pacbporfD
pacbporfD.print_protein_and_dna()
print ""
print pacbporf
pacbporf.print_protein_and_dna()
print ""
print pacbporfA
pacbporfA.print_protein_and_dna()
import sys
sys.exit()
####################################################
# return introns and intermediate tinyexon PacbPORF
return [(intron1, intron2, pacbporf)]
def _merge_pacbporfs_by_intron(pfD,
pfA,
queryorsbjct,
verbose=False,
**kwargs):
"""
Project splicesites from SBJCT intron on continious QUERY PacbPORFs
@type pfD: PacbPORF object
@param pfD: PacbPORF object that has to deliver (aligned) donor sites
@type pfA: PacbPORF object
@param pfA: PacbPORF object that has to deliver (aligned) acceptor sites
@type queryorsbjct: string
@param queryorsbjct: literal string 'query' or 'sbjct'
@type verbose: Boolean
@param verbose: print debugging info to STDOUT when True
@attention: see pacb.connecting.merge_orfs_with_intron for **kwargs)
@rtype: list
@return: list with ProjectedIntrons (from Sbjct on Query)
"""
# input validation
IsPacbPORF(pfD)
IsPacbPORF(pfA)
# edit **kwargs dictionary for some forced attributes
_update_kwargs(kwargs, KWARGS_PROJECTED_INTRON)
### if not kwargs.has_key('projected_intron_max_nt_offset'):
### kwargs['projected_intron_max_nt_offset'] = PROJECTED_INTRON_MAX_NT_OFFSET
### if not kwargs.has_key('projected_intron_max_aa_offset'):
### kwargs['projected_intron_max_aa_offset'] = PROJECTED_INTRON_MAX_AA_OFFSET
# settings for minimal alignment entropy score
min_donor_site_alignment_entropy = 0.0
min_acceptor_site_alignment_entropy = 0.0
ELEGIABLE_SPLICE_SITE_AA_RANGE = 75
sposD = pfD._get_original_alignment_pos_start()
eposD = pfD._get_original_alignment_pos_end()
sposA = pfA._get_original_alignment_pos_start()
eposA = pfA._get_original_alignment_pos_end()
if queryorsbjct == "query":
# Orfs of SBJCT must be identical
IsIdenticalOrfs(pfD.orfS, pfA.orfS)
donorOrf = pfD.orfQ
accepOrf = pfA.orfQ
prjctOrf = pfD.orfS # pfD.orfS == pfA.orfS
dStart = sposD.query_dna_start # ALIGNED start of donorPacbPORF
dEnd = pfD.query_dna_end # ABSOLUTE end of donorPacbPORF
aStart = pfA.query_dna_start # ABSOLUTE start of acceptorPacbPORF
aEnd = eposA.query_dna_end # ALIGNED end of acceptorPacbPORF
outOfAlignmentAttribute = "sbjct_dna_start"
# calculate elegiable splice site range
qdr = pfD.alignment_dna_range_query()
qar = pfA.alignment_dna_range_query()
min_donor_pos = max(
[min(qdr),
max(qdr) - (ELEGIABLE_SPLICE_SITE_AA_RANGE * 3)])
max_accep_pos = min(
[max(qar),
min(qar) + (ELEGIABLE_SPLICE_SITE_AA_RANGE * 3)])
elif queryorsbjct == "sbjct":
# Orfs of QUERY must be identical
IsIdenticalOrfs(pfD.orfQ, pfA.orfQ)
donorOrf = pfD.orfS
accepOrf = pfA.orfS
prjctOrf = pfD.orfQ # pfD.orfQ == pfA.orfQ
dStart = sposD.sbjct_dna_start # ALIGNED start of donorPacbPORF
dEnd = pfD.sbjct_dna_end # ABSOLUTE end of donorPacbPORF
aStart = pfA.sbjct_dna_start # ABSOLUTE start of acceptorPacbPORF
aEnd = eposA.sbjct_dna_end # ALIGNED end of acceptorPacbPORF
outOfAlignmentAttribute = "query_dna_start"
# calculate elegiable splice site range
sdr = pfD.alignment_dna_range_sbjct()
sar = pfA.alignment_dna_range_sbjct()
min_donor_pos = max(
[min(sdr),
max(sdr) - (ELEGIABLE_SPLICE_SITE_AA_RANGE * 3)])
max_accep_pos = min(
[max(sar),
min(sar) + (ELEGIABLE_SPLICE_SITE_AA_RANGE * 3)])
else:
message = "'queryorsbjct' (%s), not 'query' or 'sbjct'" % queryorsbjct
raise InproperlyAppliedArgument, message
# predict introns only in `queryorsbjct` Orfs
# introns is a list of IntronConnectingOrfs objects
introns = merge_orfs_with_intron(donorOrf,
accepOrf,
min_donor_pos=min_donor_pos,
max_acceptor_pos=max_accep_pos,
order_by='length',
**kwargs)
# return list with projected introns
projected_introns = []
# gather unique donor and acceptor positions from list
# of IntronConnectingOrfs
for intron in introns:
# break if intron is to large
if kwargs['max_intron_nt_length'] and intron.length > kwargs[
'max_intron_nt_length']:
break
# continue if intron is to small
if kwargs['min_intron_nt_length'] and intron.length < kwargs[
'min_intron_nt_length']:
continue
# continue if intron has non-canonical features
# check if intron.start is on pfD;
# inframe-introns can be projected outside of pfD/pfA area
if intron.start <= dStart: continue
if intron.start >= dEnd: continue
# check if intron.end is on pfA;
# inframe-introns can be projected outside of pfD/pfA area
if intron.end <= aStart: continue
if intron.end >= aEnd: continue
if queryorsbjct == "sbjct":
# get positions of donor & acceptor in the PacbPORF alignment
donorPositionPos, phaseD = pfD.dnaposition_sbjct(
intron.donor.pos, forced_return=True)
accepPositionPos, phaseA = pfA.dnaposition_sbjct(
intron.acceptor.pos, forced_return=True)
# calculate projected distance on QUERY
posDposQuery = pfD._positions[donorPositionPos].query_pos
posAposQuery = pfA._positions[accepPositionPos].query_pos
aaDistance = posAposQuery - posDposQuery
else:
# get positions of donor & acceptor in the PacbPORF alignment
donorPositionPos, phaseD = pfD.dnaposition_query(
intron.donor.pos, forced_return=True)
accepPositionPos, phaseA = pfA.dnaposition_query(
intron.acceptor.pos, forced_return=True)
# calculate binary entropy from projected position on SBJCT
posDposSbjct = pfD._positions[donorPositionPos].sbjct_pos
posAposSbjct = pfA._positions[accepPositionPos].sbjct_pos
aaDistance = posAposSbjct - posDposSbjct
# calculate binary entropy score
entropyDonorSbjct = pfD.alignment_entropy(donorPositionPos,
method='donor')
entropyAcceptorSbjct = pfA.alignment_entropy(accepPositionPos,
method='acceptor')
# do distance check upon (projected) intron acceptance
if abs(aaDistance) <= kwargs['max_aa_offset']:
# check if we've runned out of the aligned part
outofalignedpacbporf = False
# get the projected donor position; mind the gap on this spot ;-)
while pfD._positions[
donorPositionPos].isa_gap and donorPositionPos > 0:
donorPositionPos -= 1
else:
projected_donor_position = getattr(
pfD._positions[donorPositionPos],
outOfAlignmentAttribute) + phaseD
if donorPositionPos == 0 and pfD._positions[
donorPositionPos].isa_gap:
print "WarningThatIsTackled::outofalignedpacbporf::donor"
outofalignedpacbporf = True
# get the projected acceptor position; mind the gap on this spot ;-)
while pfA._positions[accepPositionPos].isa_gap and len(
pfA._positions) > accepPositionPos + 1:
accepPositionPos += 1
else:
projected_accep_position = getattr(
pfA._positions[accepPositionPos],
outOfAlignmentAttribute) + phaseA
if accepPositionPos == len(
pfA._positions
) - 1 and pfA._positions[accepPositionPos].isa_gap:
print "WarningThatIsTackled::outofalignedpacbporf::acceptor"
outofalignedpacbporf = True
if not outofalignedpacbporf:
################################################################
# set some meta-data properties to the intron object
################################################################
# add distance score to intron
intron._distance = abs(aaDistance) * 3
# add Alignment Positional Periphery Score into objects
if queryorsbjct == "query":
succes = set_apps_intron_query(intron, pfD, pfA)
else:
succes = set_apps_intron_sbjct(intron, pfD, pfA)
# set GFF fsource attribute for recognition of intron sources
intron._gff['fsource'] = "ABGPprojecting"
# make a ProjectedIntronConnectingOrfs object
pico = ProjectedIntronConnectingOrfs(prjctOrf,
projected_donor_position,
projected_accep_position)
intron.binary_entropy_donor = entropyDonorSbjct
intron.binary_entropy_acceptor = entropyAcceptorSbjct
pico.add_projected_intron(intron)
pico.phase = intron.phase
projected_introns.append(pico)
################################################################
if verbose:
print "PROJ::", intron._distance,
print(pfD.orfQ.id, pfA.orfQ.id),
print(pfD.orfS.id, pfA.orfS.id),
print "%s-%snt" % (intron.donor.pos, intron.acceptor.pos),
print "%2.1f,%2.1f" % (intron.donor.pssm_score,
intron.acceptor.pssm_score),
print "%2.1f,%2.1f" % (intron.binary_entropy_donor,
intron.binary_entropy_acceptor)
################################################################
if aaDistance > kwargs['max_aa_offset']:
# break out; ordered by length can never result in
# a proper projected intron
break
# filter out less relevant ones compared to complete set of results
projected_introns = _filter_projected_introns(projected_introns)
# and return a list of ProjectedIntronConnectingOrfs
return projected_introns
def merge_pacbporfs_with_closeby_independant_introns(pacbporfD,
pacbporfA,
verbose=False,
**kwargs):
"""
Merge 2 PacbPORF objects by closeby independant gained introns
@attention: see pacb.connecting.merge_orfs_with_intron for **kwargs)
@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 ( intronQ, intronS, CIGexonPacbPORF )
"""
# input validation
IsPacbPORF(pacbporfD)
IsPacbPORF(pacbporfA)
# edit **kwargs dictionary for some forced attributes
kwargs['allow_phase_shift'] = True
_update_kwargs(kwargs, KWARGS_CLOSEBY_INDEPENDANT_INTRON_GAIN)
if not kwargs.has_key('aligned_site_max_triplet_distance'):
kwargs['aligned_site_max_triplet_distance'] = kwargs[
'cig_max_aa_length']
# run regular merge_pacbporfs_with_introns function
alg_introns = merge_pacbporfs_with_introns(pacbporfD,
pacbporfA,
verbose=verbose,
**kwargs)
cig_introns = []
if verbose:
print "introns::", len(alg_introns), "cig_max_aa_length:", kwargs[
'cig_max_aa_length'], kwargs['aligned_site_max_triplet_distance']
# check if there is length congruence between the cig_introns
for intQ, intS in alg_introns:
dQpos, dQphase = pacbporfD.dnaposition_query(intQ.donor.pos,
forced_return=True)
dSpos, dSphase = pacbporfD.dnaposition_sbjct(intS.donor.pos,
forced_return=True)
aQpos, aQphase = pacbporfA.dnaposition_query(intQ.acceptor.pos,
forced_return=True)
aSpos, aSphase = pacbporfA.dnaposition_sbjct(intS.acceptor.pos,
forced_return=True)
distDnt = (dQpos * 3 + dQphase) - (dSpos * 3 + dSphase)
distAnt = (aQpos * 3 + aQphase) - (aSpos * 3 + aSphase)
########################################################################
if verbose:
print(intQ.donor.pos, intQ.acceptor.pos),
print(intS.donor.pos, intS.acceptor.pos),
print distDnt, distAnt, kwargs['max_nt_offset']
########################################################################
if abs(distDnt - distAnt) > kwargs['max_nt_offset']:
# intermediate ciigPacbPORF has query vs sbjct length discrepancy
# *3 for AA2nt coordinate conversion, +2 to allow different phases
# e.g. phase difference can give 1AA+2nt difference
continue
if intQ.donor.phase == intS.donor.phase and\
(distDnt/3) <= kwargs['aligned_site_max_triplet_distance']:
# a regularly merged intron combination
continue
if intQ.acceptor.phase == intS.acceptor.phase and\
(distAnt/3) <= kwargs['aligned_site_max_triplet_distance']:
# a regularly merged intron combination
continue
if abs(distDnt) <= 5 or abs(distDnt) <= 5:
# most likely a splice site phase shift, not a c.i.g.
continue
if abs(distDnt/3) >= kwargs['cig_min_aa_length'] and\
abs(distAnt/3) >= kwargs['cig_min_aa_length'] and\
abs(distDnt/3) <= kwargs['cig_max_aa_length'] and\
abs(distAnt/3) <= kwargs['cig_max_aa_length']:
# putatively a closeby independant (intron) gain
cig_introns.append((intQ, intS))
############################################################################
if verbose:
for intQ, intS in cig_introns:
print "cig?:", (intQ.donor.pos, intQ.acceptor.pos),
print(intS.donor.pos, intS.acceptor.pos)
############################################################################
# return variable to store found positive cases of CIG into
found_cig_list = []
# check if there is some sequence similarity
for intQ, intS in cig_introns:
# get alignment positions around query & sbjcts splice sites
dQpos, dQphase = pacbporfD.dnaposition_query(intQ.donor.pos,
forced_return=True)
dSpos, dSphase = pacbporfD.dnaposition_sbjct(intS.donor.pos,
forced_return=True)
aQpos, aQphase = pacbporfA.dnaposition_query(intQ.acceptor.pos,
forced_return=True)
aSpos, aSphase = pacbporfA.dnaposition_sbjct(intS.acceptor.pos,
forced_return=True)
distD = dQpos - dSpos
distA = aQpos - aSpos
distDnt = (dQpos * 3 + dQphase) - (dSpos * 3 + dSphase)
distAnt = (aQpos * 3 + aQphase) - (aSpos * 3 + aSphase)
if distDnt > 0: # then, distAnt is as well > 0
# QUERY is extended on the donor side
#mode = "SQ"
#qStart = pacbporfD._positions[dSpos].query_pos
#qEnd = qStart + distD
#sStart = pacbporfA._positions[aSpos].sbjct_pos
#sEnd = sStart + distD
#qSeq = pacbporfD.orfQ.getaas(abs_pos_start=qStart,abs_pos_end=qEnd)
#sSeq = pacbporfA.orfS.getaas(abs_pos_start=sStart,abs_pos_end=sEnd)
mode = "SQ"
qEnd = pacbporfD.orfQ.dnapos2aapos(intQ.donor.pos)
qStart = qEnd - max([distA, distD])
sStart = pacbporfA.orfS.dnapos2aapos(intS.acceptor.pos)
sEnd = sStart + max([distA, distD])
qSeq = pacbporfD.orfQ.getaas(abs_pos_start=qStart,
abs_pos_end=qEnd)
sSeq = pacbporfA.orfS.getaas(abs_pos_start=sStart,
abs_pos_end=sEnd)
else: # distDnt and distAnt are < 0
## SBJCT is extended on the donor site
#mode = "QS"
#qStart = pacbporfA._positions[aQpos].query_pos
#qEnd = qStart - distA
#sStart = pacbporfD._positions[dQpos].sbjct_pos
#sEnd = sStart - distA
#qSeq = pacbporfA.orfQ.getaas(abs_pos_start=qStart, abs_pos_end=qEnd)
#sSeq = pacbporfD.orfS.getaas(abs_pos_start=sStart, abs_pos_end=sEnd)
mode = "QS"
qStart = pacbporfA.orfQ.dnapos2aapos(intQ.acceptor.pos)
qEnd = qStart - min([distA, distD])
sEnd = pacbporfD.orfS.dnapos2aapos(intS.donor.pos)
sStart = sEnd + min([distA, distD])
qSeq = pacbporfA.orfQ.getaas(abs_pos_start=qStart,
abs_pos_end=qEnd)
sSeq = pacbporfD.orfS.getaas(abs_pos_start=sStart,
abs_pos_end=sEnd)
headerQ = "query_%s_%s_%s" % (qStart, qEnd, qSeq)
headerS = "sbjct_%s_%s_%s" % (sStart, sEnd, sSeq)
headerQ = headerQ[0:20] # truncate to prevent error
headerS = headerS[0:20] # truncate to prevent error
if verbose:
print mode, (
distD, distA), qSeq, sSeq, headerQ, headerS, distDnt, distAnt,
print dQpos, aQpos, dSpos, aSpos
if not qSeq: continue # superfluous check-doublecheck for sequence
if not sSeq: continue # superfluous check-doublecheck for sequence
####################################################
# make PacbPORF with ClustalW
####################################################
# align the sequences with clustalw
seqs = {headerQ: qSeq, headerS: sSeq}
(alignedseqs, alignment) = clustalw(seqs=seqs)
# make pacbp from clustalw alignment
pacbp = pacbp_from_clustalw(alignment=(alignedseqs[headerQ], alignment,
alignedseqs[headerS]),
coords=(qStart, qEnd, sStart, sEnd))
if not pacbp: continue
# strip unaligned fraction of this pacbp object, then check length
pacbp.strip_unmatched_ends()
if len(pacbp) < kwargs['cig_min_aa_length']:
continue
if len(pacbp) > kwargs['cig_max_aa_length']:
continue
if pacbp:
# initialize extended tiny PacbPORF caused by c.i.g.
if distDnt > 0:
cig_pacbporf = pacbp2pacbporf(pacbp, pacbporfD.orfQ,
pacbporfA.orfS)
else:
cig_pacbporf = pacbp2pacbporf(pacbp, pacbporfA.orfQ,
pacbporfD.orfS)
cig_pacbporf.extend_pacbporf_after_stops()
####################################################################
if verbose:
print pacbp, len(pacbp)
print cig_pacbporf
print "CIG:", intQ
print "CIG:", intS
print distD, distA, distDnt, distAnt
cig_pacbporf.print_protein_and_dna()
####################################################################
####################################################################
# set some meta-data properties to the intron objects
####################################################################
# add distance score to introns
# The distance set in merge_pacbporfs_with_introns is large;
# it is the actual distance between the splice sites. In CIG,
# the measure for distance is the length difference between
# the offset between query and sbjct measured on the cig_pacbporf
intQ._distance = abs(distDnt - distAnt)
intS._distance = abs(distDnt - distAnt)
if distDnt > 0: # then, distAnt is as well > 0
# QUERY is extended on the donor side
# add Alignment Positional Periphery Score into objects
succes = set_apps_intron_query(intQ, cig_pacbporf, pacbporfA)
succes = set_apps_intron_sbjct(intS, pacbporfD, cig_pacbporf)
else:
# SBJCT is extended on the donor side
# add Alignment Positional Periphery Score into objects
succes = set_apps_intron_query(intQ, pacbporfD, cig_pacbporf)
succes = set_apps_intron_sbjct(intS, cig_pacbporf, pacbporfA)
# set GFF fsource attribute for recognition of intron sources
intQ._gff['fsource'] = "ABGPcig"
intS._gff['fsource'] = "ABGPcig"
# create _linked_to_xxx attributes
intQ._linked_to_pacbporfs = [cig_pacbporf]
intS._linked_to_pacbporfs = [cig_pacbporf]
# append to found_cig_list
found_cig_list.append((intQ, intS, cig_pacbporf))
else:
# no alignment possible -> try next
continue
# return lists of closeby_independant_introns
return found_cig_list
def merge_pacbporfs_with_introns(pacbporfD,
pacbporfA,
verbose=False,
**kwargs):
"""
Merge 2 PacbPORF objects by introns
@attention: see orfs.merge_orfs_with_intron for **kwargs
@attention: see functions._filter_for_alignable_splice_sites for **kwargs
@attention: see functions._filter_for_entropy for **kwargs
@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 **kwargs dictionary for some forced attributes
_update_kwargs(kwargs, KWARGS_MAPPED_INTRON)
if not kwargs.has_key('aligned_site_max_triplet_distance'):
kwargs['aligned_site_max_triplet_distance'] = kwargs['max_aa_offset']
# settings for minimal alignment entropy score
min_donor_site_alignment_entropy = 0.0
min_acceptor_site_alignment_entropy = 0.0
# calculate maximal/minimal donor/acceptor site position based on alignment
ELEGIABLE_SPLICE_SITE_AA_RANGE = 75
qdr = pacbporfD.alignment_dna_range_query()
qar = pacbporfA.alignment_dna_range_query()
min_donor_query_pos = max(
[min(qdr), max(qdr) - (ELEGIABLE_SPLICE_SITE_AA_RANGE * 3)])
max_accep_query_pos = min(
[max(qar), min(qar) + (ELEGIABLE_SPLICE_SITE_AA_RANGE * 3)])
sdr = pacbporfD.alignment_dna_range_sbjct()
sar = pacbporfA.alignment_dna_range_sbjct()
min_donor_sbjct_pos = max(
[min(sdr), max(sdr) - (ELEGIABLE_SPLICE_SITE_AA_RANGE * 3)])
max_accep_sbjct_pos = min(
[max(sar), min(sar) + (ELEGIABLE_SPLICE_SITE_AA_RANGE * 3)])
# get list of introns
#intronsQ = merge_orfs_with_intron(pacbporfD.orfQ,pacbporfA.orfQ,
# min_donor_pos =min_donor_query_pos,
# max_acceptor_pos=max_accep_query_pos,**kwargs)
#intronsS = merge_orfs_with_intron(pacbporfD.orfS,pacbporfA.orfS,
# min_donor_pos =min_donor_sbjct_pos,
# max_acceptor_pos=max_accep_sbjct_pos,**kwargs)
# get list of introns
intronsQ = merge_orfs_with_intron(pacbporfD.orfQ, pacbporfA.orfQ, **kwargs)
intronsS = merge_orfs_with_intron(pacbporfD.orfS, pacbporfA.orfS, **kwargs)
# get unique list of donors & acceptors
donorQ = olba(list(Set([inQ.donor for inQ in intronsQ])), order_by='pos')
donorS = olba(list(Set([inS.donor for inS in intronsS])), order_by='pos')
accepQ = olba(list(Set([inQ.acceptor for inQ in intronsQ])),
order_by='pos')
accepS = olba(list(Set([inS.acceptor for inS in intronsS])),
order_by='pos')
############################################################################
if verbose:
print "dQ1", [d.pos for d in donorQ], "aQ1", [a.pos for a in accepQ]
print "dS1", [d.pos for d in donorS], "aS1", [a.pos for a in accepS]
############################################################################
# filter for alignable donor & acceptor sites
kwargs['allow_non_canonical'] = kwargs['allow_non_canonical_donor']
algdonors = _filter_for_alignable_splice_sites(donorQ, donorS, pacbporfD,
**kwargs)
kwargs['allow_non_canonical'] = kwargs['allow_non_canonical_acceptor']
algacceps = _filter_for_alignable_splice_sites(accepQ, accepS, pacbporfA,
**kwargs)
############################################################################
if verbose:
print "dQ2", [_dq.pos for (_dq, _ds) in algdonors],
print "aQ2", [_aq.pos for (_aq, _as) in algacceps]
print "dS2", [_ds.pos for (_dq, _ds) in algdonors],
print "aS2", [_as.pos for (_aq, _as) in algacceps]
############################################################################
# remove sites with to low alignment entropy
algdonors = _filter_for_entropy(
algdonors,
pacbporfD,
'donor',
min_alignment_entropy=min_donor_site_alignment_entropy)
algacceps = _filter_for_entropy(
algacceps,
pacbporfA,
'acceptor',
min_alignment_entropy=min_acceptor_site_alignment_entropy)
############################################################################
if verbose:
print "dQ3", [_dq.pos for (_dq, _ds) in algdonors],
print "aQ3", [_aq.pos for (_aq, _as) in algacceps]
print "dS3", [_ds.pos for (_dq, _ds) in algdonors],
print "aS3", [_as.pos for (_aq, _as) in algacceps]
############################################################################
# make unique position lists for quick lookup in intron lists
dQpl = Set([dQ.pos for dQ, dS in algdonors])
dSpl = Set([dS.pos for dQ, dS in algdonors])
aQpl = Set([aQ.pos for aQ, aS in algacceps])
aSpl = Set([aS.pos for aQ, aS in algacceps])
# check exterior boundaries of PacbPORFs
sposD = pacbporfD._get_original_alignment_pos_start()
eposD = pacbporfD._get_original_alignment_pos_end()
sposA = pacbporfA._get_original_alignment_pos_start()
eposA = pacbporfA._get_original_alignment_pos_end()
# now make list of aligable introns
algintrons = []
for intQ in intronsQ:
# check if intron falls within the PacbPORF aligned area
if intQ.donor.pos <= sposD.query_dna_start: continue
if intQ.acceptor.pos >= eposA.query_dna_end: continue
if intQ.donor.pos in dQpl and intQ.acceptor.pos in aQpl:
# Query intron occurs in list of alignable splice sites!
for intS in intronsS:
# check if intron falls within the PacbPORF aligned area
if intS.donor.pos <= sposD.sbjct_dna_start: continue
if intS.acceptor.pos >= eposA.sbjct_dna_end: continue
if intS.donor.pos in dSpl and intS.acceptor.pos in aSpl:
# Sbjct intron occurs as well in alignable splice sites!
if (intQ.donor,intS.donor) in algdonors and\
(intQ.acceptor,intS.acceptor) in algacceps:
# Sbjct & Query Donor & Acceptor are alignable!
algintrons.append((intQ, intS))
############################################################################
# set some meta-data properties to the intron objects
############################################################################
for intQ, intS in algintrons:
distDnt = pacbporfD.get_distance_aligned_nucleotide_positions(
query=intQ.donor.pos, sbjct=intS.donor.pos)
distAnt = pacbporfA.get_distance_aligned_nucleotide_positions(
query=intQ.acceptor.pos, sbjct=intS.acceptor.pos)
# final distance check. kwargs['aligned_site_max_triplet_distance']
# is applied on donor and acceptor site. This distance measured on the
# protein sequence can be DOUBLED in case distDnt / distAnt are
# opposite (+ and -). Check here if the protein sequence gap is
# as well <= kwargs['aligned_site_max_triplet_distance'].
if abs(distAnt -
distDnt) > kwargs['aligned_site_max_triplet_distance'] * 3:
continue
# add distance score to introns
intQ._distance = abs(distDnt) + abs(distAnt)
intS._distance = abs(distDnt) + abs(distAnt)
# add Alignment Positional Periphery Score into objects
succes = set_apps_intron_query(intQ, pacbporfD, pacbporfA)
succes = set_apps_intron_sbjct(intS, pacbporfD, pacbporfA)
# set GFF fsource attribute for recognition of intron sources
intQ._gff['fsource'] = "ABGPmapping"
intS._gff['fsource'] = "ABGPmapping"
########################################################################
if verbose:
# some printing....
print "Aligned introns:", (intQ.donor.pos, intQ.acceptor.pos),
print(intS.donor.pos, intS.acceptor.pos),
print "DIST:", distDnt, distAnt,
print "[%s]" % kwargs['aligned_site_max_triplet_distance'],
print "ENTROPY: %1.2f %1.2f" % (intQ._apps_donor,
intQ._apps_accep),
print "PSSM: (%1.2f %1.2f) (%1.2f %1.2f)" % (
intQ.donor.pssm_score,
intS.donor.pssm_score,
intQ.acceptor.pssm_score,
intS.acceptor.pssm_score,
)
########################################################################
# return lists of aligned introns
return algintrons
