def remove_repeats_from_pacbp_list(pacbplist, overlap_ratio=0.85):
"""
"""
if not pacbplist: return pacbplist
# order pacbplist by `bits` attribute, highest first
ordered = pacb.ordering.order_list_by_attribute(pacbplist,
order_by='bits',
reversed=True)
# make upper cross of element indexes in ordered list of pacbps
pairs = recombination.pairwise(range(0, len(ordered)))
# loop over all pacbp combis, calculate overlap and store the
# index to `toberemoved` when higher than `overlap_ratio`
toberemoved = []
for (posA, posB) in pairs:
if posA in toberemoved: continue
if posB in toberemoved: continue
pacbpA = ordered[posA]
pacbpB = ordered[posB]
if ordering.overlap(pacbpA, pacbpB) >= overlap_ratio:
toberemoved.append(posB)
# order `toberemoved` and pop the (pacbp) elements from the ordered input list
toberemoved.sort()
toberemoved.reverse()
for pos in toberemoved:
ordered.pop(pos)
# return the remainder of the odered input list
return ordered
def remove_repeats_from_pacbp_list(pacbplist, overlap_ratio=0.85):
"""
"""
if not pacbplist:
return pacbplist
# order pacbplist by `bits` attribute, highest first
ordered = pacb.ordering.order_list_by_attribute(pacbplist, order_by="bits", reversed=True)
# make upper cross of element indexes in ordered list of pacbps
pairs = recombination.pairwise(range(0, len(ordered)))
# loop over all pacbp combis, calculate overlap and store the
# index to `toberemoved` when higher than `overlap_ratio`
toberemoved = []
for (posA, posB) in pairs:
if posA in toberemoved:
continue
if posB in toberemoved:
continue
pacbpA = ordered[posA]
pacbpB = ordered[posB]
if ordering.overlap(pacbpA, pacbpB) >= overlap_ratio:
toberemoved.append(posB)
# order `toberemoved` and pop the (pacbp) elements from the ordered input list
toberemoved.sort()
toberemoved.reverse()
for pos in toberemoved:
ordered.pop(pos)
# return the remainder of the odered input list
return ordered
def resolve_microsyntheny(
self,
absolute_max_intron_nt_length=ABSOLUTE_MAX_INTRON_NT_LENGTH,
max_intron_nt_length=MAX_INTRON_NT_LENGTH,
max_intergenic_min_nt_length=MAX_INTERGENIC_MIN_NT_LENGTH,
average_intergenic_min_nt_length=AVERAGE_INTERGENIC_MIN_NT_LENGTH,
min_intergenic_nt_length=MIN_INTERGENIC_NT_LENGTH,
apply_tcode_check=False,
verbose=False):
"""
Assign codingblocks outside of *the* genestructure that belong to another gene (in a synthenic region)
@type max_intron_nt_length: integer (positive)
@param max_intron_nt_length: maximal intron size -> any larger distance MUST be CBGs of 2 distinct genes
@type min_intergenic_nt_length: integer (positive)
@param min_intergenic_nt_length: minimum intergenic size -> any distance smaller MUST be CBGs of a single gene
@type max_intergenic_min_nt_distance: integer (positive)
@param max_intergenic_min_nt_distance: represent the upper border of a small intergenic region
@attention: *the* genestructure is supposed to be the most central one in case of doubt
"""
# List of list of position id's of CBGs together are (part of a) gene
# When a distance is large enough for an intergenic region, the structure will
# be something like [ [ 0,1,2], [3,4,5,6,7] ]. The first 3 CBGs are assigned to
# another, frontal placed gene.
structures = []
for pos in range(0, len(self) - 1):
this = self.codingblockgraphs[pos]
next = self.codingblockgraphs[pos + 1]
(mindist, maxdist,
avdist) = _cbg_intergenic_distance_analyses(this, next)
# check which nodes are mutual
mutual = this.mutual_nodes(next)
########################################################
if verbose:
print pos, pos + 1,
print "%s - %s - %s" % (mindist, avdist, maxdist),
print mutual, "cbgIFopt?:",
try:
print this._CBGinterface3p.optimalitycheck()
except:
print "NO cbgIF!!"
########################################################
if len(mutual) >= 1:
# orf node(s) are shared -> this MUST be the same gene!
pass
elif maxdist > absolute_max_intron_nt_length:
# largest distance is larger than the largest possible intron
if not structures: structures.append(range(0, pos + 1))
else: structures.append(range(structures[-1][-1] + 1, pos + 1))
elif maxdist > max_intron_nt_length:
# largest distance is larger than what is likely a very large intron
# in this case: check the cbgIF
if this._CBGinterface3p and this._CBGinterface3p.is_optimal() and\
not next.have_all_starts_upstream_of_omsr():
# interface is optimal and 2th CBG is not a first TSS CBG.
# do not break the genestructure here.
pass
else:
# break the genestructure in 2 parts
if not structures: structures.append(range(0, pos + 1))
else:
structures.append(
range(structures[-1][-1] + 1, pos + 1))
elif mindist > min_intergenic_nt_length and maxdist > max_intergenic_min_nt_length:
# the ``grey zone``, but very likely to be intergenic
if this._CBGinterface3p and this._CBGinterface3p.is_compatible() and\
this._CBGinterface3p.optimalitycheck().count(True) >= 2 and\
not next.have_all_starts_upstream_of_omsr():
pass
else:
if not structures: structures.append(range(0, pos + 1))
else:
structures.append(
range(structures[-1][-1] + 1, pos + 1))
elif avdist > average_intergenic_min_nt_length:
# very likely intergenic!
if this._CBGinterface3p and this._CBGinterface3p.is_compatible() and\
this._CBGinterface3p.optimalitycheck().count(True) >= 2 and\
not next.have_all_starts_upstream_of_omsr():
pass
else:
if not structures: structures.append(range(0, pos + 1))
else:
structures.append(
range(structures[-1][-1] + 1, pos + 1))
elif maxdist <= min_intergenic_nt_length:
# largest distance is smaller than ``smallest possible`` intergenic region
pass
else:
# all other cases...many of these are spurious intergenic
# but can as well be putative long introns. Do, if requested
# for, the tcode_check. If not-> pass (and keep in the GSG)
if apply_tcode_check:
# calculate TCODE averages
tcodescore = intergenecity_tcode_analyses(
this, next, self.input)
averages = [0.0, 0.0, 0.0, 0.0]
for org, data in tcodescore.iteritems():
for i in range(0, len(data)):
averages[i] += data[i]
averages = [
item / len(tcodescore.keys()) for item in averages
]
omsrdists = this.omsr_distance_between_codingblocks(next)
lengthvar = [
float(a) / float(b)
for a, b in recombination.pairwise(omsrdists.values())
]
lengthvar = sum(lengthvar) / len(lengthvar)
########################################################
if verbose:
for org, data in tcodescore.iteritems():
print org, "\t", data
print "AVER:\t", averages, "*graAV:",
print this._stopcodongraph.average_weight(),
print "lenghtvar:", lengthvar
print this._CBGinterface3p
########################################################
if averages[1] < INTERGENIC_TCODE_MAX_LOWEST_WINDOW and\
averages[2] < INTERGENIC_TCODE_MAX_AVERAGE_WINDOW and\
this._stopcodongraph.average_weight() >=\
INTERGENIC_TCODE_MIN_STGRA_AV_WT and\
(not this._CBGinterface3p or not this._CBGinterface3p.is_compatible()):
# yes, a somewhat less obvious intergenic boundary
if not structures: structures.append(range(0, pos + 1))
else:
structures.append(
range(structures[-1][-1] + 1, pos + 1))
else:
pass
else:
pass
else:
if not structures: structures.append(range(0, len(self)))
else: structures.append(range(structures[-1][-1] + 1, len(self)))
# now deal with the results
if len(structures) > 1:
# hmmmm... most likely a - rare(!?) - region of microsyntheny
# in all species. Get the best structure out of these
best_structure = self._define_best_structure(structures,
verbose=verbose)
self._update_best_structure_in_gsg(best_structure)
####################################################
if verbose:
print "microsyntheny", structures,
print "MAX-intron:", max_intron_nt_length
print "BEST:", best_structure
