def shift_sites(self, sites):
"""
Calculate the list of splice sites on the mutated string, given a list
of splice sites on the original string.
@arg sites: List of splice sites on the original string.
@type sites: list(int)
@return: List of splice sites on the mutated string.
@rtype: list(int)
Example 1 (DNA): NG_012772.1(BRCA2_v001)
...---------[=========]----------...
^ ^
18964 19013
Variant Expected new location for splice site 18964
g.18963del 18963
g.18964del 18964
g.18963_18964ins 18964
g.18964_18965ins 18964
Variant Expected new location for splice site 19013
g.19013del 19012
g.19014del 19013
g.19013_19014ins 19014
Example 2 (RNA): NM_000088.3
...============][==============...
/\
229 230
Variant Expected new location for splice sites 229,230
n.228del 228,229
n.229del 228,229
n.230del 229,230
n.231del 229,230
n.228_229ins 230,231
n.229_230ins 229,230 or 230,231
n.230_231ins 229,230
"""
# We use shiftpos(i+1)-1 instead of shiftpos(i) (and its mirror)
# to make sure insertions directly before or after an exon are
# placed inside the exon.
#
# Example:
#
# -----SPLICE[======]SPLICE----------SPLICE[=======]SPLICE-----
# ^ ^
# ins ins
#
# These two insertions should be mapped inside the exons because
# they are before and after (respectively) their exons and don't
# hit the (biological) splice sites.
#
# This also makes sure deletions of the last exon base are really
# removed from the exon. The problem is that positions following
# (but not including) the deletion get a shift, but the splice site
# is stored by the position of the last exon base. So the splice
# site position would not be decremented without the +1-1 dance.
new_sites = []
prev_donor = None
filtered_sites = [s for s in sites if s not in self._removed_sites]
for acceptor, donor in util.grouper(filtered_sites):
# We don't want to do the -1+1 dance if
# 1) there is a deletion directly before the exon, or
# 2) there is another exon directly before this exon, or
# 3) this is the first site in the list.
#
# A consequence of check 2) is that insertions between two
# directly adjacent exons are seen as insertions in the first
# exon.
#
# Condition 3) makes sure we don't include insertions directly
# in front of CDS start in the CDS. It also affects translation
# start, but this should be no problem.
if not prev_donor or prev_donor == acceptor - 1 or \
self._shift_minus_at(acceptor):
new_sites.append(self.shift(acceptor))
else:
new_sites.append(self.shift(acceptor - 1) + 1)
# Should never happen since splice sites come in pairs.
if not donor: continue
# We don't want to do the +1-1 dance if this is the last site
# in the list. This makes sure we don't include insertions
# directly at CDS end in the CDS. It also affects translation
# end, but this should be no problem.
if donor == sites[-1]:
new_sites.append(self.shift(donor))
else:
new_sites.append(self.shift(donor + 1) - 1)
prev_donor = donor
return new_sites
def shift_sites(self, sites):
"""
Calculate the list of splice sites on the mutated string, given a list
of splice sites on the original string.
@arg sites: List of splice sites on the original string.
@type sites: list(int)
@return: List of splice sites on the mutated string.
@rtype: list(int)
Example 1 (DNA): NG_012772.1(BRCA2_v001)
...---------[=========]----------...
^ ^
18964 19013
Variant Expected new location for splice site 18964
g.18963del 18963
g.18964del 18964
g.18963_18964ins 18964
g.18964_18965ins 18964
Variant Expected new location for splice site 19013
g.19013del 19012
g.19014del 19013
g.19013_19014ins 19014
Example 2 (RNA): NM_000088.3
...============][==============...
/\
229 230
Variant Expected new location for splice sites 229,230
n.228del 228,229
n.229del 228,229
n.230del 229,230
n.231del 229,230
n.228_229ins 230,231
n.229_230ins 229,230 or 230,231
n.230_231ins 229,230
"""
# We use shiftpos(i+1)-1 instead of shiftpos(i) (and its mirror)
# to make sure insertions directly before or after an exon are
# placed inside the exon.
#
# Example:
#
# -----SPLICE[======]SPLICE----------SPLICE[=======]SPLICE-----
# ^ ^
# ins ins
#
# These two insertions should be mapped inside the exons because
# they are before and after (respectively) their exons and don't
# hit the (biological) splice sites.
#
# This also makes sure deletions of the last exon base are really
# removed from the exon. The problem is that positions following
# (but not including) the deletion get a shift, but the splice site
# is stored by the position of the last exon base. So the splice
# site position would not be decremented without the +1-1 dance.
new_sites = []
prev_donor = None
filtered_sites = [s for s in sites if s not in self._removed_sites]
for acceptor, donor in util.grouper(filtered_sites):
# We don't want to do the -1+1 dance if
# 1) there is a deletion directly before the exon, or
# 2) there is another exon directly before this exon, or
# 3) this is the first site in the list.
#
# A consequence of check 2) is that insertions between two
# directly adjacent exons are seen as insertions in the first
# exon.
#
# Condition 3) makes sure we don't include insertions directly
# in front of CDS start in the CDS. It also affects translation
# start, but this should be no problem.
if not prev_donor or prev_donor == acceptor - 1 or \
self._shift_minus_at(acceptor):
new_sites.append(self.shift(acceptor))
else:
new_sites.append(self.shift(acceptor - 1) + 1)
# Should never happen since splice sites come in pairs.
if not donor: continue
# We don't want to do the +1-1 dance if this is the last site
# in the list. This makes sure we don't include insertions
# directly at CDS end in the CDS. It also affects translation
# end, but this should be no problem.
if donor == sites[-1]:
new_sites.append(self.shift(donor))
else:
new_sites.append(self.shift(donor + 1) - 1)
prev_donor = donor
return new_sites
def checkRecord(self):
"""
Check if the record in self.record is compatible with mutalyzer.
Update the mRNA PList with the exon and CDS data.
@todo: This function should really check the record for minimal
requirements
"""
# TODO: This function should really check
# the record for minimal requirements.
for i in self.record.geneList:
"""
if len(i.transcriptList) == 2 :
if i.transcriptList[0].CDS and not i.transcriptList[1].CDS and \
i.transcriptList[1].mRNA and not i.transcriptList[0].mRNA :
i.transcriptList[0].mRNA = i.transcriptList[1].mRNA
if i.transcriptList[1].CDS and not i.transcriptList[0].CDS and \
i.transcriptList[0].mRNA and not i.transcriptList[1].mRNA :
i.transcriptList[0].CDS = i.transcriptList[1].CDS
i.transcriptList = [i.transcriptList[0]]
i.transcriptList[0].transcribe = True
i.transcriptList[0].translate = True
#if
"""
for j in i.transcriptList:
if not j.mRNA:
usableExonList = self.__checkExonList(j.exon, j.CDS)
if self.record.molType == "n" and j.exon:
if not all(p1 + 1 == p2 for p1, p2 in util.grouper(j.exon.positionList[1:-1])):
code = "WEXON_ANNOTATION" if j.current else "WEXON_ANNOTATION_OTHER"
self.__output.addMessage(
__file__,
2,
code,
"Exons for gene %s, transcript variant %s were "
"found not to be adjacent. This signifies a "
"possible problem in the annotation of the "
"reference sequence." % (i.name, j.name),
)
if not j.exon or not usableExonList:
if self.record.molType == "g":
code = "WNOMRNA" if j.current else "WNOMRNA_OTHER"
self.__output.addMessage(
__file__,
2,
code,
"No mRNA field found for gene %s, transcript "
"variant %s in record, constructing "
"it from CDS. Please note that descriptions "
"exceeding CDS boundaries are invalid." % (i.name, j.name),
)
if j.exon and j.exon.positionList and not usableExonList:
code = "WNOMRNA" if j.current else "WNOMRNA_OTHER"
self.__output.addMessage(
__file__,
2,
code,
"Exons were found for gene %s, transcript "
"variant %s but were not usable. "
"Please note that descriptions "
"exceeding CDS boundaries are invalid." % (i.name, j.name),
)
if j.CDS:
if not j.CDS.positionList:
# self.__output.addMessage(__file__, 2,
# "WNOCDSLIST", "No CDS list found for " \
# "gene %s, transcript variant %s in " \
# "record, constructing it from " \
# "CDS location." % (i.name, j.name))
j.mRNA = j.CDS
j.mRNA.positionList = j.CDS.location
# if
else:
j.mRNA = j.CDS
j.linkMethod = "construction"
j.transcribe = True
j.translate = True
# if
else:
self.__output.addMessage(
__file__,
2,
"WNOCDS",
"No CDS found for gene %s, transcript "
"variant %s in record, "
"constructing it from gene location." % (i.name, j.name),
)
j.CDS = None # PList()
# j.CDS.location = i.location
j.mRNA = PList()
j.mRNA.location = i.location
# j.mRNA.positionList = i.location
j.molType = "n"
# else
# if
else:
# self.__output.addMessage(__file__, 2, "WNOMRNA",
# "No mRNA field found for gene %s, transcript " \
# "variant %s in record, constructing " \
# "it from gathered exon information." % (
# i.name, j.name))
j.mRNA = j.exon
# else
# if
# else :
# j.transcribe = True
if not j.mRNA.positionList:
j.mRNA.positionList = j.mRNA.location
if j.mRNA.positionList and j.CDS and j.CDS.positionList != None:
if not j.CDS.positionList:
# self.__output.addMessage(__file__, 2, "WNOCDS",
# "No CDS list found for gene %s, transcript " \
# "variant %s in record, constructing " \
# "it from mRNA list and CDS location." % (i.name,
# j.name))
if j.mRNA.positionList:
j.CDS.positionList = self.__constructCDS(j.mRNA.positionList, j.CDS.location)
else:
j.CDS.positionList = self.__constructCDS(j.mRNA.location, j.CDS.location)
j.transcribe = True
j.translate = True
# if
j.CM = Crossmap.Crossmap(j.mRNA.positionList, j.CDS.location, i.orientation)
# if
else:
j.molType = "n"
if j.mRNA.positionList:
j.CM = Crossmap.Crossmap(j.mRNA.positionList, [], i.orientation)
j.transcribe = True
else:
j.description = "?"
def checkRecord(self):
"""
Check if the record in self.record is compatible with mutalyzer.
Update the mRNA PList with the exon and CDS data.
@todo: This function should really check the record for minimal
requirements
"""
#TODO: This function should really check
# the record for minimal requirements.
for i in self.record.geneList:
"""
if len(i.transcriptList) == 2 :
if i.transcriptList[0].CDS and not i.transcriptList[1].CDS and \
i.transcriptList[1].mRNA and not i.transcriptList[0].mRNA :
i.transcriptList[0].mRNA = i.transcriptList[1].mRNA
if i.transcriptList[1].CDS and not i.transcriptList[0].CDS and \
i.transcriptList[0].mRNA and not i.transcriptList[1].mRNA :
i.transcriptList[0].CDS = i.transcriptList[1].CDS
i.transcriptList = [i.transcriptList[0]]
i.transcriptList[0].transcribe = True
i.transcriptList[0].translate = True
#if
"""
for j in i.transcriptList:
if not j.mRNA:
usableExonList = self.__checkExonList(j.exon, j.CDS)
if self.record.molType == 'n' and j.exon:
if not all(p1 + 1 == p2 for p1, p2 in util.grouper(
j.exon.positionList[1:-1])):
code = 'WEXON_ANNOTATION' if j.current else 'WEXON_ANNOTATION_OTHER'
self.__output.addMessage(
__file__, 2, code,
"Exons for gene %s, transcript variant %s were "
"found not to be adjacent. This signifies a "
"possible problem in the annotation of the "
"reference sequence." % (i.name, j.name))
if not j.exon or not usableExonList:
if self.record.molType == 'g':
code = 'WNOMRNA' if j.current else 'WNOMRNA_OTHER'
self.__output.addMessage(__file__, 2, code,
"No mRNA field found for gene %s, transcript " \
"variant %s in record, constructing " \
"it from CDS. Please note that descriptions "\
"exceeding CDS boundaries are invalid." % (
i.name, j.name))
if j.exon and j.exon.positionList and \
not usableExonList :
code = 'WNOMRNA' if j.current else 'WNOMRNA_OTHER'
self.__output.addMessage(__file__, 2, code,
"Exons were found for gene %s, transcript " \
"variant %s but were not usable. " \
"Please note that descriptions "\
"exceeding CDS boundaries are invalid." % (
i.name, j.name))
if j.CDS:
if not j.CDS.positionList:
#self.__output.addMessage(__file__, 2,
# "WNOCDSLIST", "No CDS list found for " \
# "gene %s, transcript variant %s in " \
# "record, constructing it from " \
# "CDS location." % (i.name, j.name))
j.mRNA = j.CDS
j.mRNA.positionList = j.CDS.location
#if
else:
j.mRNA = j.CDS
j.linkMethod = "construction"
j.transcribe = True
j.translate = True
#if
else:
self.__output.addMessage(__file__, 2, "WNOCDS",
"No CDS found for gene %s, transcript " \
"variant %s in record, " \
"constructing it from gene location." % (
i.name, j.name))
j.CDS = None #PList()
#j.CDS.location = i.location
j.mRNA = PList()
j.mRNA.location = i.location
#j.mRNA.positionList = i.location
j.molType = 'n'
#else
#if
else:
#self.__output.addMessage(__file__, 2, "WNOMRNA",
# "No mRNA field found for gene %s, transcript " \
# "variant %s in record, constructing " \
# "it from gathered exon information." % (
# i.name, j.name))
j.mRNA = j.exon
#else
#if
#else :
# j.transcribe = True
if not j.mRNA.positionList:
j.mRNA.positionList = j.mRNA.location
if j.mRNA.positionList and j.CDS and j.CDS.positionList != None:
if not j.CDS.positionList:
#self.__output.addMessage(__file__, 2, "WNOCDS",
# "No CDS list found for gene %s, transcript " \
# "variant %s in record, constructing " \
# "it from mRNA list and CDS location." % (i.name,
# j.name))
if j.mRNA.positionList:
j.CDS.positionList = self.__constructCDS(
j.mRNA.positionList, j.CDS.location)
else:
j.CDS.positionList = self.__constructCDS(
j.mRNA.location, j.CDS.location)
j.transcribe = True
j.translate = True
#if
j.CM = Crossmap.Crossmap(j.mRNA.positionList,
j.CDS.location, i.orientation)
#if
else:
j.molType = 'n'
if j.mRNA.positionList:
j.CM = Crossmap.Crossmap(j.mRNA.positionList, [],
i.orientation)
j.transcribe = True
else:
j.description = '?'