def check_lsrcbgs_for_inframe_introns(self,verbose=False):
"""
Check the lsrCBGs in the GSG and see if these regions can better be explained by an inframe intron
"""
INFRAME_INTRONS_PREDICTED = 0
LSR_RECREATED = 0
for cbgpos in range(len(self)-1,-1,-1):
cbg = self.codingblockgraphs[cbgpos]
if cbg.__class__.__name__ != 'LowSimilarityRegionCodingBlockGraph':
continue
# do the inframe intron analyses on a lsrCBG
inframeintrons = cbg.potentially_contains_inframe_intron(verbose=verbose)
# aparantly it seems possible to create one or more introns in the lsrCBG
if inframeintrons:
# get the bordering CBGs
prev = self.codingblockgraphs[cbgpos-1]
next = self.codingblockgraphs[cbgpos+1]
# make CBGInterface between prev and next;
# reset the _IS_SPLITTED tags!
prev._splicedonorgraph = None
prev._CBGinterface3p = None
prev._forced_3p_ends = {}
prev.IS_3P_SPLITTED = False
prev.IS_SPLITTED = prev.IS_5P_SPLITTED
next._spliceacceptorgraph = None
next._CBGinterface5p = None
next._forced_5p_ends = {}
next.IS_5P_SPLITTED = False
next.IS_SPLITTED = next.IS_3P_SPLITTED
# create an actual CBGInterface of both CBGs around the lsrCBG
cbgIF = CodingBlockGraphInterface(prev,next)
if verbose: print cbgIF
# re-harvest splice sites; store ALL the intron-projected sites
cbgIF.harvest_splice_sites(allow_phase_shift=False,store_all_projected_sites=True)
if verbose: print cbgIF
# now remove all non-projected splice-sites in organisms that
# are not reported to have a potential inframe intron
cbgIF.allow_intron_in_organisms(inframeintrons)
cbgIF.find_conserved_splice_sites()
if verbose:
print cbgIF
print "compatible:", cbgIF.is_compatible(), "optimal:", cbgIF.is_optimal()
print cbgIF._optimal_aligned_donor
print cbgIF._optimal_aligned_acceptor
# yes, this is what we expect; a compatible CBGInterface!
# this very likely represents an inframe intron!
if cbgIF.is_compatible():
# remove the lsrCBG from the GSG
lsrCBG = self.codingblockgraphs.pop(cbgpos)
# set the CBGInterface object in next and prev CBG
prev._CBGinterface3p = cbgIF
next._CBGinterface5p = cbgIF
# increase the counter of number of inframe introns predicted
INFRAME_INTRONS_PREDICTED+=1
############################################################
if verbose: print "INFRAME INTRON PREDICTED!!"
############################################################
else:
# nope, this does not seem like a proper inframe intron
# reset the CBGs and the lsrCBG objects as they were!
# If this point is reached, `first` and `second` are CBGs with exactly the same nodes
# create intermediate lsrCBG
prev.IS_SPLITTED = True
prev.IS_3P_SPLITTED = True
next.IS_SPLITTED = True
next.IS_5P_SPLITTED = True
lsrCBG = create_intermediate_lowsimilarity_region(prev,next)
self.codingblockgraphs[cbgpos] = lsrCBG
# recreate the CBGInterfaces (I)
cbgIFa = CodingBlockGraphInterface(prev,lsrCBG)
cbgIFa.harvest_splice_sites()
cbgIFa.find_conserved_splice_sites()
# set the interface object to the CBGs in GSG
prev._CBGinterface3p = cbgIFa
lsrCBG._CBGinterface5p = cbgIFa
# recreate the CBGInterfaces (II)
cbgIFb = CodingBlockGraphInterface(lsrCBG,next)
cbgIFb.harvest_splice_sites()
cbgIFb.find_conserved_splice_sites()
# set the interface object to the CBGs in GSG
lsrCBG._CBGinterface3p = cbgIFb
next._CBGinterface5p = cbgIFb
############################################################
if verbose: print "NO COMPATIBLE SITE!"
############################################################
###for org in inframeintrons:
### print org, "NO COMPATIBLE SITES FOUND!"
### print prev
### print cbgIF
### print next
### theorf = next.get_orfs_of_graph(organism = org )[0]
### print theorf
### theorf.printproteinanddna()
### for donor in theorf._donor_sites: print donor
### for acceptor in theorf._acceptor_sites: print acceptor
# return number of found inframe introns
return INFRAME_INTRONS_PREDICTED
def construct_final_tiny_cbg(self,
max_exon_nt_length=SHORT_TAILINGEXON_MAX_NT_LENGTH,
max_intron_nt_length=SHORT_TAILINGEXON_MAX_INTRON_NT_LENGTH,
take_max_best_acceptors=SHORT_TAILINGEXON_TAKE_MAX_BEST_ACCEPTORS,
take_max_best_ecgs=SHORT_TAILINGEXON_TAKE_MAX_BEST_ECGS,
take_max_best_cbgs=SHORT_TAILINGEXON_TAKE_MAX_BEST_CBGS,
maximal_current_stopcodongraph_average_weight=0.90,
minimal_last_vs_new_identity_ratio=0.80,
maximal_cexpander_cbg_tail_uniformity_aa_length=3,
elegiable_donor_omsr_nt_offset=21,
verbose=False):
"""
Make a tiny final CBG by ``shooting tiny exons into the deep``
"""
# get current last CBG
last = self.get_final_cbg()
# check if final tail of this CBG is uniformaly alignable
cxpdrOutput = cexpanderanalyses_omsr2orfend(last)
IS_UNIFORMLY_ALIGNED = True
for trf in cxpdrOutput._transferblocks:
if trf.binarystring[-maximal_cexpander_cbg_tail_uniformity_aa_length:].count("0"):
IS_UNIFORMLY_ALIGNED = False
break
############################################################
if verbose:
print "Cexpander uniformaly aligned:",
print maximal_cexpander_cbg_tail_uniformity_aa_length,
print "->", IS_UNIFORMLY_ALIGNED
print "omsr: ", last._cexpander.projected_on,
print last._cexpander.binarystring
trf = cxpdrOutput.get_transfer_of_projected_on(
last._cexpander.projected_on)
if trf and trf != True:
print "omsr2orfend:", last._cexpander.projected_on,
print trf.binarystring
############################################################
if IS_UNIFORMLY_ALIGNED:
# break out of this function. Chance of overpredicting
# a final tiny exon is bigger then finding a True one!
return False
# check if the stopcodongraph is not (very) good already
if last._stopcodongraph.average_weight() >=\
maximal_current_stopcodongraph_average_weight:
# break out of this function. Chance of overpredicting
# a final tiny exon is bigger then finding a True existing one
return False
# start the timer (performance benchmark in verbose mode)
stw = StopWatch(name='stwFinalECG')
stw.start()
# get FinalExons on elegiable Orfs based on distance towards OMSR of
# current last CBG and minimal acceptor site score
omsr = last.overall_minimal_spanning_range()
maxsr = last.maximal_spanning_range()
ECG = ExonCollectionGraph()
################################################################
if verbose:
print "currentLAST", last
print last._stopcodongraph
print last._stopcodongraph.is_optimal()
for org in last.organism_set():
print org, last._stopcodongraph.is_optimal(organism=org)
for organism in last.organism_set():
node = last.node_by_organism(organism)
theorf = last.get_orfs_of_graph(organism=organism)[0]
print organism, "\t", node, "\t", max(omsr[node]), "\t",
print max(maxsr[node]), theorf.endPY/3
################################################################
for organism in last.organism_set():
node = last.node_by_organism(organism)
# calculate an offset for the acceptor position
# variable elegiable_acceptor_omsr_nt_offset is needed to
# enlarge the OMSR definded offset. When the OMSR is by chance
# a few nt or aa larger than the actual exon length, the true
# acceptor position can be erroneously abandoned.
offset = max(omsr[node]) * 3 - elegiable_donor_omsr_nt_offset
theorf = last.get_orfs_of_graph(organism=organism)[0]
# check if this final orf is self can serve as a final extension
remaining_orf_nt_length = (theorf.protein_endPY - max(omsr[node])) * 3
remaining_maxsr_nt_length = (max(maxsr[node]) - max(omsr[node])) * 3
remaining_maxsr_tostop_nt_length = (theorf.protein_endPY - max(maxsr[node])) * 3
FIND_NEW_FINAL_ORFS = True
STORE_CURRENT_ORF_AS_FIOO = False
if remaining_maxsr_nt_length >= max_exon_nt_length:
# exceptionally large maxsr on rigth side of omsr
# store as FIOO but to NOT search for an orf extension!
### FIND_NEW_FINAL_ORFS = False # discarded 17/09/2009; when poos maxsr present, overruled!
STORE_CURRENT_ORF_AS_FIOO = True
elif remaining_maxsr_tostop_nt_length <= 18:
# maxsr is less then 6 AA apart from stop on current orf
#FIND_NEW_FINAL_ORFS = False
STORE_CURRENT_ORF_AS_FIOO = True
elif remaining_orf_nt_length < max_exon_nt_length:
# final piece of unaligned sequence is a perfect HMM seed
STORE_CURRENT_ORF_AS_FIOO = True
else:
pass
if STORE_CURRENT_ORF_AS_FIOO:
cbs = CodingBlockStart( theorf.aapos2dnapos( max(omsr[node]) ) )
# set pssm_score to (very) high; this rewards
# using the current Orf as the last Orf
cbs.pssm_score = 20.0
fioo = FinalExonOnOrf(cbs,theorf.endPY,theorf)
node = (organism,theorf.id,fioo.start,fioo.end)
ECG.add_node_and_object(node,fioo)
################################################################
if verbose:
print organism,theorf.id,"self==potential last exon", remaining_orf_nt_length
print organism, theorf.id, fioo, fioo.start,fioo.end, theorf.endPY
################################################################
if not FIND_NEW_FINAL_ORFS:
# quit here -> no orf extension of this CBG
continue
# get elegiable (new) final orfs
orflist = self.input[organism]['orfs'].get_elegiable_orfs(
max_orf_start=offset+max_intron_nt_length,
min_orf_end=offset )
################################################################
if verbose:
print organism, [ orf.id for orf in orflist ], "offset:", offset, offset/3
################################################################
for orf in orflist:
results = find_tailing_exon_on_orf(
theorf,orf,
current_donor_pos=offset,
max_tailingexon_nt_length=max_exon_nt_length,
max_tailingexon_intron_nt_length=max_intron_nt_length,
)
for exon,intron in results:
node = (organism,orf.id,exon.start,exon.end)
if node not in ECG.get_nodes():
ECG.add_node_and_object(node,exon)
if verbose: print organism, node, exon
if verbose: print stw.lap(), "Exon objects gathered", ECG.node_count()
# now take only the best `take_max_best_acceptors`
# because there can be quite some of them!
for organism in ECG.organism_set():
objects = ordering.order_list_by_attribute( ECG.get_organism_objects(organism), order_by='pssm_score', reversed=True )
for obj in objects[take_max_best_acceptors:]:
node = (organism,obj.orf.id,obj.start,obj.end)
ECG.del_node(node)
if verbose: print "deleted:", node, obj.orf.id, obj.pssm_score
########################################################################
if verbose:
print stw.lap(), ">take_max_best_acceptors DELETED"
for organism in ECG.organism_set():
for obj in ordering.order_list_by_attribute(
ECG.get_organism_objects(organism),
order_by='pssm_score', reversed=True
):
print "remaining", organism, obj.orf.id, obj.length, obj
########################################################################
# only continue if all organisms are represented in the ECG
if last.organism_set_size() > ECG.organism_set_size():
if verbose: print "To few organisms/genes present -> return False"
return False
# create edges in the ECG between compatible phases and
# exon length, then make pacbps for these edges
ECG.create_edges()
ECG.make_pacbps_for_edges()
if verbose:
print stw.lap(), "edges + PACBPS created:", ECG.edge_count(), ECG.node_count(), len(ECG.pacbps)
# search for complete graphs in this
last_exon_graphs = ECG.find_fully_connected_subgraphs()
########################################################################
if verbose:
print stw.lap(), "duration of ECG.find_fully_connected_subgraphs()",
print len(last_exon_graphs)
########################################################################
# only continue if there is an perfectly aligned last exon graph
if not (last_exon_graphs and last_exon_graphs[0].connectivitysaturation() == 1.0):
####################################################################
if verbose: print "no perfect aligned last exon graph -> return False"
####################################################################
return False
# convert to CodingBlockGraphs
new_last_cbgs = []
for leg in last_exon_graphs[0:take_max_best_ecgs]:
cbg = ExonCollectionGraph2CodingBlockGraph(leg,is_last=True,lastCBG=last)
if cbg != False and cbg != None and cbg.organism_set_size() == last.organism_set_size():
# create cache of CBG and do final check on quality
cbg.create_cache()
if (cbg.total_weight() < 0 or cbg.omsrlength() <= 10) and\
cbg._cexpander.binarystring.find("1") == -1:
# discard hardly alignable CBGs
continue
# if here, then append this cbg as a possible novel final CBG
new_last_cbgs.append( cbg )
################################################################
if verbose: print "LEGcbg", cbg
################################################################
########################################################################
if verbose: print stw.lap(), "ECGs converted to CBGs", len(new_last_cbgs)
########################################################################
if not new_last_cbgs:
####################################################################
if verbose: print "no ecgs convertable to CBGs -> return False"
####################################################################
return False
# order by total weight, get the optimal CBG and its corresponding ECG
new_last_cbgs = ordering.order_graphlist_by_total_weight(new_last_cbgs)
theNewLastCbg = None
cbgIF = None
# check all interfaces between the novel final CBGs and the previous
# CBG. The best interface is added to the GSG!
cbgif_accepted_new_last_cbgs = []
already_checked_node_sets = []
for newcbg in new_last_cbgs[0:take_max_best_cbgs]:
lastExonGraph = newcbg._ExonCollectionGraph
del( newcbg._ExonCollectionGraph )
# check if it is not the extention of the current
# last CBG (identical nodes)
if len(last.node_set().symmetric_difference(newcbg.node_set())) == 0:
if verbose: print "newCBG is the extention of current last CBG!!"
continue
# check if this combination of nodes (orfs) has not been tried already
if newcbg.get_ordered_nodes() in already_checked_node_sets:
###############################################################
if verbose:
print "newCBG node set done earlier:",
print newcbg.get_ordered_nodes()
###############################################################
continue
else:
# append this set of nodes (as a list) to checklist
already_checked_node_sets.append( newcbg.get_ordered_nodes() )
# check if this new final tinyexon graph has a compatible interface
# with the current last one
cbgIF = CodingBlockGraphInterface(last,newcbg)
cbgIF.harvest_splice_sites()
distinct_orgs = []
for node in lastExonGraph.get_nodes():
exon = lastExonGraph.get_node_object(node)
if exon.acceptor.__class__.__name__ == 'SpliceAcceptor':
distinct_orgs.append( lastExonGraph.organism_by_node(node) )
cbgIF.allow_intron_in_organisms(distinct_orgs)
cbgIF.find_conserved_splice_sites()
# do NOT optimize -> consumes a lot of time and is helpfull
# only in extreme cases...
#cbgIF.optimize()
if not cbgIF.is_compatible():
################################################################
if verbose:
print "newCBG not a is_compatible() cbgIF"
print newcbg
################################################################
continue
# append to cbgif_accepted_new_last_cbgs
newcbg._CBGinterface5p = cbgIF
cbgif_accepted_new_last_cbgs.append(
(
cbgIF.optimalitycheck().count(True),
newcbg.total_weight(),
newcbg
)
)
########################################################################
if verbose:
print stw.lap(), "cbgIFs checked %s/%s" % (
len(cbgif_accepted_new_last_cbgs),
len(new_last_cbgs[0:take_max_best_cbgs])
)
########################################################################
# now start by adding the highest scoring newcbg first
cbgif_accepted_new_last_cbgs.sort()
cbgif_accepted_new_last_cbgs.reverse()
########################################################################
if verbose:
print "candidate novel final CBGs:", len(cbgif_accepted_new_last_cbgs)
for (true_cnt,totalwt,newcbg) in cbgif_accepted_new_last_cbgs:
print true_cnt,totalwt,newcbg._CBGinterface5p
print newcbg
########################################################################
for (true_cnt,totalwt,newcbg) in cbgif_accepted_new_last_cbgs:
# get the already created cbgIF from the newcbg graph
cbgIF = newcbg._CBGinterface5p
# now check 4 criteria:
# (1) cbgIF.is_optimal() (2) >GTG.identity
# (3) >STG.totalweight (4) <STG.distance
criteria = []
criteria.append( cbgIF.is_optimal() )
criteria.append( newcbg._stopcodongraph.total_weight() > last._stopcodongraph.total_weight() )
criteria.append( newcbg.genetree().identity() > last.genetree().identity() )
criteria.append( newcbg._stopcodongraph.stopcodon2omsrdistance() <= last._stopcodongraph.stopcodon2omsrdistance() )
####################################################################
if verbose:
print "TRYING ADDITION of final newcbg", criteria
print true_cnt,totalwt,newcbg._CBGinterface5p
print newcbg
####################################################################
# check if there is only a single different node/orf changed in the newcbg
# this is recognized by a symmetric_difference of size 2
# in this case, be very strict! This easily causes overprediction (FP) tiny exons
if len(last.node_set().symmetric_difference(newcbg.node_set())) == 2:
# check if 4 criteria are valid;
# a single False results in not accepting this new last tiny cbg
if False in criteria:
if verbose: print "# NOVEL lastTinyExon discarded; single orf extension, criteria", criteria
# continue -> no new tiny CBG
continue
# now start check the criteria.
# if criteria[0] == True, means a fully is_optimal interface!
# do not perform any additional check, just add!
if criteria[0] == True:
theNewLastCbg = newcbg
break
# total weight criterion -> new.tw() > last.tw()
if criteria[1] == False:
##########################################################################
if verbose:
print "# NOVEL lastTinyExon discarded; to low total weight"
print "#", newcbg._stopcodongraph
##########################################################################
# continue -> no new tiny CBG
continue
# identity criterion -> allow a ratio i.s.o. new.id() > last.id()
# this strict criterion (>) is applied for single-new-orf-CBGs
if criteria[2] == False:
ratio = newcbg.genetree().identity() / last.genetree().identity()
if ratio < minimal_last_vs_new_identity_ratio:
######################################################################
if verbose:
print "# NOVEL lastTinyExon discarded; to low identity"
print "#", newcbg._stopcodongraph, newcbg.genetree().identity()
######################################################################
# continue -> no new tiny CBG
continue
if criteria[3] == False:
##########################################################################
if verbose:
print "# NOVEL lastTinyExon discarded; higher stopcodon2omsrdistance"
print "#", newcbg._stopcodongraph
##########################################################################
# continue -> no new tiny CBG
continue
# if this point is reached, a new tiny last CBG has been found!
theNewLastCbg = newcbg
# break out of the for loop; store into the genestructure
break
# all okay -> ready for inserting the new CBG
if theNewLastCbg and verbose:
################################################################################
print "NEW FINAL TINY EXON FOUND!!"
print theNewLastCbg
print cbgIF, cbgIF.is_optimal(), cbgIF.is_acceptable()
print cbgIF._optimal_aligned_donor, cbgIF.donor_phase()
print cbgIF._optimal_aligned_acceptor, cbgIF.acceptor_phase()
################################################################################
# hard-insert into the genestructure
# using add_codingblock is likely to cause problems
# because of the tinyness of the CBG
if theNewLastCbg:
for pos in range(0,len(self)):
if self.codingblockgraphs[pos].IS_IGNORED: continue
if self.codingblockgraphs[pos].IS_LAST:
thelast = self.codingblockgraphs[pos]
thelast.IS_LAST = False
newcbg.IS_LAST = True
self.codingblockgraphs.insert(pos+1,theNewLastCbg)
# set the CBGInterface object in next and prev CBG
self.codingblockgraphs[pos]._CBGinterface3p = cbgIF
self.codingblockgraphs[pos+1]._CBGinterface5p = cbgIF
# break out; end of this function
break
# done! return a True because newcbg is created & inserted
return True
else:
# no newLastCbg found
return False