def _orf_overlap_rank(theorf,orflist,orfpointer):
""" """
subset = [ theorf ]
for orf in orflist[orfpointer+1:]:
if orf.startPY > theorf.endPY:
break
subset.append(orf)
for pointer in range(orfpointer-1,-1,-1):
orf = orflist[pointer]
if orf.endPY < theorf.startPY:
break
subset.insert(0,orf)
# order the subset
subset = order_list_by_attribute(subset,order_by='coding_propensity',reversed=True)
rank=0
for orf in subset:
rank+=1
if orf.startPY == theorf.startPY:
break
# return the rank
return rank
def _orf_overlap_rank(theorf, orflist, orfpointer):
""" """
subset = [theorf]
for orf in orflist[orfpointer + 1:]:
if orf.startPY > theorf.endPY:
break
subset.append(orf)
for pointer in range(orfpointer - 1, -1, -1):
orf = orflist[pointer]
if orf.endPY < theorf.startPY:
break
subset.insert(0, orf)
# order the subset
subset = order_list_by_attribute(subset,
order_by='coding_propensity',
reversed=True)
rank = 0
for orf in subset:
rank += 1
if orf.startPY == theorf.startPY:
break
# return the rank
return rank
def assembleorf(orflist,start,end,max_errors=2,minimum_errors_only=True):
""" """
orflist = order_list_by_attribute(orflist,order_by='length',reversed=True)
orfidcombis = []
for startpos in range(0,len(orflist)):
centralorf = orflist[startpos]
orfset = [ ( centralorf.startPY, centralorf.endPY, centralorf.frame, centralorf ) ]
# correct 'end' orf gff track position with STOP codon length!
minpos = min([ tup[0] for tup in orfset ])
maxpos = max([ tup[1] for tup in orfset ])
while minpos > start or maxpos < end-3:
for pos in range(0,len(orflist)):
#if minpos <= start and maxpos >= end-3: break
orf = orflist[pos]
if orf.id in [ tup[-1].id for tup in orfset ]: continue
if minpos > start and orf.startPY < minpos and orf.endPY >= minpos-3:
orfset.insert(0, ( orf.startPY, orf.endPY, orf.frame, orf ) )
minpos = min([ tup[0] for tup in orfset ])
maxpos = max([ tup[1] for tup in orfset ])
# check if this orf even OVERLAPS ths current group of orfs
if orf.endPY == maxpos:
orfset.append( ( orf.startPY, orf.endPY, orf.frame, orf ) )
# goto next iteration
break
if maxpos < end-3 and orf.endPY > maxpos and orf.startPY <= maxpos+3:
orfset.append( ( orf.startPY, orf.endPY, orf.frame, orf ) )
minpos = min([ tup[0] for tup in orfset ])
maxpos = max([ tup[1] for tup in orfset ])
# check if this orf even OVERLAPS ths current group of orfs
if orf.startPY == minpos:
orfset.insert(0, ( orf.startPY, orf.endPY, orf.frame, orf ) )
# goto next iteration
break
# calculate minimal amount of sequence changes needed
frames = [ tup[2] for tup in orfset ]
distance = _getorfgroupframedistance(frames)
# only store if not to much errors
if not minimum_errors_only and distance[0] > max_errors:
pass
else:
if ( sum(distance), distance, orfset ) not in orfidcombis: orfidcombis.append( ( sum(distance), distance, orfset ) )
# now find the most likely explanation
orfidcombis.sort()
minimum_error_count = None
for (summed,distance,orfset) in orfidcombis:
# define minimum number of sequence errors
if minimum_error_count == None: minimum_error_count=distance[0]
# break when more than minimum sequence errors
if minimum_errors_only and distance[0] > minimum_error_count: break
# if NO sequence errors -> break as well (not an error, but a missed tiny Orf!)
orfids = [ tup[-1].id for tup in orfset ]
frames = [ tup[2] for tup in orfset ]
# oldprinting style, replaced by PotentialSequenceErrorWarning
#print orfids, frames, distance
#for tup in orfset: print tup[-1], tup[-1].frame
# print PotentialSequenceErrorWarning
message = [ str(distance[1:]), "(insertions,deletions,errors)" ]
for tup in orfset: message.append( str(tup[-1]) )
print PotentialSequenceErrorWarning( message )
def order_list_by_attribute(self, order_by='', reversed=False):
"""
@attention: see graphAbgp.ordering.order_list_by_attribute
"""
self.codingblockgraphs = order_list_by_attribute(
self.codingblockgraphs, order_by=order_by, reversed=reversed)
def order_list_by_attribute(self,order_by='',reversed=False):
"""
@attention: see graphAbgp.ordering.order_list_by_attribute
"""
self.codingblockgraphs = order_list_by_attribute(
self.codingblockgraphs,order_by=order_by,reversed=reversed)
print explain()
sysExit()
## TEMPORARILY backwards-compatibility with old input_data_struct.txt file
#input = eval(open('input_data_struct.txt').read().strip())
# do geneconfirmation; this includes rungetorf() function call
input, gene_status = geneconfirmation(input, verbose=True)
# proces tcode data
input = obtaintcodedata(input)
for org in input.keys():
# loop over all the Orf objects and score their coding propensity rank
orflist = input[org]['orfs'].orfs
orflist = order_list_by_attribute(orflist, 'startPY')
for orfpointer in range(0, len(orflist)):
orf = orflist[orfpointer]
# add data to tss object
orf.coding_propensity = orf.tcode_score() * orf.length
for orfpointer in range(0, len(orflist)):
orf = orflist[orfpointer]
# define _orf_overlap_rank
rank = _orf_overlap_rank(orf, orflist, orfpointer)
orf._orf_overlap_rank = rank
# order orflist by coding_propensity and score this rank
orflist = order_list_by_attribute(orflist,
'coding_propensity',
reversed=True)
print explain()
sysExit()
## TEMPORARILY backwards-compatibility with old input_data_struct.txt file
#input = eval(open('input_data_struct.txt').read().strip())
# do geneconfirmation; this includes rungetorf() function call
input,gene_status = geneconfirmation(input,verbose=True)
# proces tcode data
input = obtaintcodedata(input)
for org in input.keys():
# loop over all the Orf objects and score their coding propensity rank
orflist = input[org]['orfs'].orfs
orflist = order_list_by_attribute(orflist,'startPY')
for orfpointer in range(0,len(orflist)):
orf = orflist[orfpointer]
# add data to tss object
orf.coding_propensity = orf.tcode_score() * orf.length
for orfpointer in range(0,len(orflist)):
orf = orflist[orfpointer]
# define _orf_overlap_rank
rank = _orf_overlap_rank(orf,orflist,orfpointer)
orf._orf_overlap_rank = rank
# order orflist by coding_propensity and score this rank
orflist = order_list_by_attribute(orflist,'coding_propensity',reversed=True)
cnt = 1
for orf in orflist:
