def map2region(self, sg, type):
"""get annotations for the regions spaned by a SpliceGraph
returns the annotation dictionary for all element within the specified region
with complete information, such as chr, strand, start, stop etc...
--> (dict)
"""
if not isinstance(sg, SpliceGraph.SpliceGraph) and os.path.exists(sg):
sg = SpliceGraph.SpliceGraph(filename=sg)
if isinstance(sg, SpliceGraph.SpliceGraph):
# get annotation
if not self.annotationFiles.has_key(type): # give up
self.__inform(
"ERROR in map2region: unknown annotation type [%s]" % type)
raise Errors.ArgumentError(
"map2region", "unknown annotation type [%s]" % type)
elif not self.exonInfo.has_key(type): # parse it
self.parseAnnotation(type)
# get region
#regStart, regEnd = sg.genomicRange()
ex = sg.allExons()
regStart = ex[0][0]
regEnd = ex[-1][1]
# get overlap
genes = {}
(overlapGns, overlapExons) = self.overlappingGenesExons(type,
regStart,
regEnd,
detailed=1)
for overlapGn in overlapGns:
if genes.has_key(overlapGn):
genes[overlapGn] += 1
else:
genes[overlapGn] = 1
return genes, overlapExons
def parseAnnotation(self, type):
"parse and store annotation files from MetaData"
if type not in self.annotationFiles.keys():
raise Errors.ArgumentError(
'Mapper.parseAnnotation',
'no annotation file for type "%s"' % type)
elif type == 'ensembl' or type == 'vega' or type == 'genrate' or type == "HuExonStv2":
versionPattern = re.compile('\.\d+$')
self.geneInfo[type] = {}
self.ssInfo[type] = {}
self.exonInfo[type] = {}
nb = 0
fh = gzip.GzipFile(self.annotationFiles[type], 'r')
while 1:
line = fh.readline()
if not line:
break
elif line.startswith('#') or line.startswith('Chromosome'):
continue
else:
line = line.strip('\n')
(chr, strand, gnId, txId, extGnId, biotype, exId, start,
end) = line.split('\t')
if not chr.startswith('chr'):
chr = "chr%s" % chr
strand = ((strand == '1') and '+' or '-')
exId = versionPattern.sub('', exId)
# store in self.geneInfo, self.ssInfo and self.exonInfo
if not self.geneInfo[type].has_key(gnId):
self.geneInfo[type][gnId] = {
'extGnId': extGnId,
'biotype': biotype
}
if not self.ssInfo[type].has_key(chr):
self.ssInfo[type][chr] = {'+': {}, '-': {}}
self.ssInfo[type][chr][strand][start] = (gnId, exId)
self.ssInfo[type][chr][strand][end] = (gnId, exId)
if not self.exonInfo[type].has_key(chr):
self.exonInfo[type][chr] = {'+': {}, '-': {}}
if not self.exonInfo[type][chr][strand].has_key(start):
self.exonInfo[type][chr][strand][start] = {}
self.exonInfo[type][chr][strand][start][end] = (gnId, exId)
nb += 1
self.__inform(
"just stored %s -> %s : %s\n" % (start, end, gnId), 5)
self.__inform(
"\t%s,%s,%s,%s\n" % (type, chr, strand, start), 7)
fh.close()
self.__inform(
"parseAnnotation: successfully parsed gene association of %i %s exons\n"
% (nb, type))
elif type == 'U133target' or type == 'gnf1m' or type == 'u133v2':
self.geneInfo[type] = {}
self.ssInfo[type] = {}
self.exonInfo[type] = {}
nb = 0
fh = gzip.GzipFile(self.annotationFiles[type], 'r')
while 1:
line = fh.readline()
if not line:
break
elif line.startswith('#'):
continue
else:
line = line.strip('\n')
(probesetId, chr, start, end, strand) = line.split('\t')
# store in self.exonInfo
if not self.exonInfo[type].has_key(chr):
self.exonInfo[type][chr] = {'+': {}, '-': {}}
if not self.exonInfo[type][chr][strand].has_key(start):
self.exonInfo[type][chr][strand][start] = {}
self.exonInfo[type][chr][strand][start][end] = (probesetId,
probesetId)
nb += 1
self.__inform(
"just stored %s -> %s : %s\n" %
(start, end, probesetId), 5)
fh.close()
self.__inform(
"parseAnnotation: successfully parsed gene association of %i %s exons\n"
% (nb, type))
elif type == 'hgu95av2':
#versionPattern = re.compile('\.\d+$')
self.geneInfo[type] = {}
self.ssInfo[type] = {}
self.exonInfo[type] = {}
nb = 0
fh = gzip.GzipFile(self.annotationFiles[type], 'r')
while 1:
line = fh.readline()
if not line:
break
else:
line = line.strip('\n')
blocks = line.split('\t')
(probeId, map) = blocks[0].split('::')
(chr, start, end, strand) = map.split(':')
if not self.ssInfo[type].has_key(chr):
self.ssInfo[type][chr] = {'+': {}, '-': {}}
self.ssInfo[type][chr][strand][start] = (probeId, probeId)
self.ssInfo[type][chr][strand][end] = (probeId, probeId)
if not self.exonInfo[type].has_key(chr):
self.exonInfo[type][chr] = {'+': {}, '-': {}}
if not self.exonInfo[type][chr][strand].has_key(start):
self.exonInfo[type][chr][strand][start] = {}
self.exonInfo[type][chr][strand][start][end] = (probeId,
probeId)
nb += 1
self.__inform(
"just stored %s -> %s : %s\n" % (start, end, probeId), 5)
fh.close()
self.__inform(
"parseAnnotation: successfully parsed gene association of %i %s exons\n"
% (nb, type))
def mapEvents(self, event, event_type, type, outFile=None, mode="within"):
"""maps a list of events (e.g. CE or SE) in the raw text format stored in *_events files
to annotation type using the specifid mode, by default within (to use for microarray probeset regions"""
if isinstance(event, basestring):
if os.path.exists(event):
f = open(event, "r")
event = f.readlines()
f.close()
if not isinstance(event, list):
raise Errors.ArgumentError(
"Mapper.mapEvents",
"event argument must either be a filename or list of events (strings)"
)
# get annotation
if not self.annotationFiles.has_key(type): # give up
self.__inform(
"ERROR in Mapper.map2gene: unknown annotation type '%s'" %
type)
raise Errors.ArgumentError("Mapper.map2gene",
"unknown annotation type '%s'" % type)
elif not self.exonInfo.has_key(type): # parse it
self.parseAnnotation(type)
genes = {} #format: genes[gnId] = nb_of_exons
exons = {
} #format: exons[(sg.name,sg.exon)] = (mapped.gene, mapped.exon) #where sg.exon=element1:E:element2
# open outFile fh
if outFile is None:
outFile = "%s.mapped_%s" % (event_type, type)
fh = open(outFile, "w")
if event_type == "SE" or event_type == "CE" or event_type == "CI" or event_type == "RI":
fh.write("#gnId\texStart\texEnd\tExon_id\tExon_coordinates\n")
for ev in event:
if ev.startswith("#"): continue
line = ev.strip().replace('\n', '')
if event_type == "SE":
gnId, exStart, exEnd, skCoverage, incCoverage = line.split(
'\t')
elif event_type == "CE" or event_type == "CI":
gnId, exStart, exEnd, Coverage = line.split('\t')
elif event_type == "RI":
gnId, exStart, exEnd, retainedCoverage, splicedCoverage = line.split(
'\t')
elif event_type == "A5SS" or event_type == "A3SS":
gnId, nbASS, altSS, Coverage, anotherSS, yetanotherSS = line.split(
'\t')
if nbASS == 2:
exStart, exEnd = altSS.split(',')
else:
continue # try next event from the list
else:
sys.stderr.write(
"Error. Mapper.MapEvents. event not implemented: %s" %
event_type)
# remember: exStart/exEnd are biological, not always exStart<exEnd --> flip
(exChromosome, exStartCoord, exStrand) = exStart.split(':')
exEndCoord = exEnd.split(':')[1]
if exStrand == '-':
exStartCoord, exEndCoord = exEndCoord, exStartCoord
# if correspondance is found with annotation, store gene and exon IDs
if mode == "exon" and \
self.exonInfo[type].has_key(exChromosome) and \
self.exonInfo[type][exChromosome].has_key(exStrand) and \
self.exonInfo[type][exChromosome][exStrand].has_key(exStartCoord) and \
self.exonInfo[type][exChromosome][exStrand][exStartCoord].has_key(exEndCoord):
if genes.has_key(self.exonInfo[type][exChromosome]
[exStrand][exStartCoord][exEndCoord][0]):
genes[self.exonInfo[type][exChromosome][exStrand]
[exStartCoord][exEndCoord][0]] += 1
else:
genes[self.exonInfo[type][exChromosome][exStrand]
[exStartCoord][exEndCoord][0]] = 1
exons[(gnId, exStart + ":E:" + exEnd)] = self.exonInfo[
type][exChromosome][exStrand][exStartCoord][exEndCoord]
elif mode == "bothSS" and \
self.ssInfo[type].has_key(exChromosome) and \
self.ssInfo[type][exChromosome].has_key(exStrand) and \
self.ssInfo[type][exChromosome][exStrand].has_key(exStartCoord) and \
self.ssInfo[type][exChromosome][exStrand].has_key(exEndCoord) and \
self.ssInfo[type][exChromosome][exStrand][exStartCoord] == self.ssInfo[type][exChromosome][exStrand][exEndCoord]:
if genes.has_key(self.ssInfo[type][exChromosome][exStrand]
[exStartCoord][0]):
genes[self.ssInfo[type][exChromosome][exStrand]
[exStartCoord][0]] += 1
else:
genes[self.ssInfo[type][exChromosome][exStrand]
[exStartCoord][0]] = 1
exons[(gnId, exStart + ":E:" + exEnd)] = self.ssInfo[type][
exChromosome][exStrand][exStartCoord]
elif mode == "singleSS" and \
self.ssInfo[type].has_key(exChromosome) and \
self.ssInfo[type][exChromosome].has_key(exStrand) and \
( self.ssInfo[type][exChromosome][exStrand].has_key(exStartCoord) or \
self.ssInfo[type][exChromosome][exStrand].has_key(exEndCoord) ):
ss = self.ssInfo[type][exChromosome][exStrand].has_key(
exStartCoord) and exStartCoord or exEndCoord
if genes.has_key(
self.ssInfo[type][exChromosome][exStrand][ss][0]):
genes[self.ssInfo[type][exChromosome][exStrand][ss]
[0]] += 1
else:
genes[self.ssInfo[type][exChromosome][exStrand][ss]
[0]] = 1
exons[(
gnId, exStart + ":E:" +
exEnd)] = self.ssInfo[type][exChromosome][exStrand][ss]
elif mode == "overlap":
(overlapGns, overlapExons) = self.overlappingGenesExons(
type, exStart, exEnd)
for overlapGn in overlapGns:
if genes.has_key(overlapGn):
genes[overlapGn] += 1
else:
genes[overlapGn] = 1
for overlapExon in overlapExons.iterkeys():
exons[(gnId, exStart + ":E:" +
exEnd)] = (overlapExons[overlapExon],
overlapExon)
fh.write("%s\t%s\t%s\t%s\t%s\n" %
(gnId, exStart, exEnd,
overlapExons[overlapExon], overlapExon))
elif mode == "within":
(withinGns, withinExons) = self.withinExons(type,
exStart,
exEnd,
detailed=1)
for withinGn in withinGns:
if genes.has_key(withinGn):
genes[withinGn] += 1
else:
genes[withinGn] = 1
for withinExon in withinExons.iterkeys():
exons[(gnId, exStart + ":E:" +
exEnd)] = (withinExons[withinExon], withinExon)
if len(withinExons.keys()) > 0:
fh.write("%s\t%s\t%s\t%s\t%s\n" % (gnId, exStart, exEnd,\
#",".join(str(withinExons[withinExon]) for withinExon in withinExons),\
",".join("%s:%s:%s" % withinExons[withinExon] for withinExon in withinExons),\
",".join(withinExon for withinExon in withinExons)))
#",".join("%s:%s:%s" % withinExons[withinExon] for withinExon in withinExons),\
elif mode not in [
"bothSS", "singleSS", "overlap", "exon", "within"
]:
self.__inform("map2gene: Ignoring unknown mode %s\n" %
mode)
elif event_type == "A5SS" or event_type == "A3SS":
pass
elif event_type == "MXE":
pass
fh.close()
def map2gene(self, sg, type, mode="singleSS"):
"""map a SpliceGraph to a gene according to the specified exon matching mode
returns a (gene-dict,exon-dict)-tuple, where
gene-dict is a dictionary with mapped gene ids as keys and the number of matching exons as values
exon-dict is a dictionary with (sg.name, sg.exon_ids)-tuples as keys and the corresponding (gnId, exId)-tuples as values
--> (dict, dict)
"""
genes = {} #format: genes[gnId] = nb_of_exons
exons = {
} #format: exons[(sg.name,sg.exon)] = (mapped.gene, mapped.exon) #where sg.exon=element1:E:element2
if not isinstance(sg, SpliceGraph.SpliceGraph) and os.path.exists(sg):
sg = SpliceGraph.SpliceGraph(filename=sg)
if isinstance(sg, SpliceGraph.SpliceGraph):
# get annotation
if not self.annotationFiles.has_key(type): # give up
self.__inform(
"ERROR in Mapper.map2gene: unknown annotation type '%s'" %
type)
raise Errors.ArgumentError(
"Mapper.map2gene", "unknown annotation type '%s'" % type)
elif not self.exonInfo.has_key(type): # parse it
self.parseAnnotation(type)
# for each exon, get associated gene
for exStart in sg.allElements():
if sg.is3ss(exStart) or sg.isTSS(exStart):
# look for a corresponding exon end (5ss element)
for exEnd in sg.downstreamConnectedElements(exStart):
# make sure exEnd is a 5ss element
if sg.is5ss(exEnd) or sg.isTER(exEnd):
# remember: exStart/exEnd are biological, not always exStart<exEnd --> flip
(exChromosome, exStartCoord,
exStrand) = exStart.split(':')
exEndCoord = exEnd.split(':')[1]
if exStrand == '-':
exStartCoord, exEndCoord = exEndCoord, exStartCoord
# if correspondance is found with annotation, store gene and exon IDs
if mode == "exon" and \
self.exonInfo[type].has_key(exChromosome) and \
self.exonInfo[type][exChromosome].has_key(exStrand) and \
self.exonInfo[type][exChromosome][exStrand].has_key(exStartCoord) and \
self.exonInfo[type][exChromosome][exStrand][exStartCoord].has_key(exEndCoord):
if genes.has_key(
self.exonInfo[type][exChromosome]
[exStrand][exStartCoord][exEndCoord][0]):
genes[self.exonInfo[type][exChromosome]
[exStrand][exStartCoord][exEndCoord]
[0]] += 1
else:
genes[self.exonInfo[type][exChromosome]
[exStrand][exStartCoord][exEndCoord]
[0]] = 1
exons[(sg.name, exStart + ":E:" + exEnd
)] = self.exonInfo[type][exChromosome][
exStrand][exStartCoord][exEndCoord]
elif mode == "bothSS" and \
self.ssInfo[type].has_key(exChromosome) and \
self.ssInfo[type][exChromosome].has_key(exStrand) and \
self.ssInfo[type][exChromosome][exStrand].has_key(exStartCoord) and \
self.ssInfo[type][exChromosome][exStrand].has_key(exEndCoord) and \
self.ssInfo[type][exChromosome][exStrand][exStartCoord] == self.ssInfo[type][exChromosome][exStrand][exEndCoord]:
if genes.has_key(
self.ssInfo[type][exChromosome]
[exStrand][exStartCoord][0]):
genes[self.ssInfo[type][exChromosome]
[exStrand][exStartCoord][0]] += 1
else:
genes[self.ssInfo[type][exChromosome]
[exStrand][exStartCoord][0]] = 1
exons[(
sg.name, exStart + ":E:" +
exEnd)] = self.ssInfo[type][exChromosome][
exStrand][exStartCoord]
elif mode == "singleSS" and \
self.ssInfo[type].has_key(exChromosome) and \
self.ssInfo[type][exChromosome].has_key(exStrand) and \
( self.ssInfo[type][exChromosome][exStrand].has_key(exStartCoord) or \
self.ssInfo[type][exChromosome][exStrand].has_key(exEndCoord) ):
ss = self.ssInfo[type][exChromosome][
exStrand].has_key(
exStartCoord
) and exStartCoord or exEndCoord
if genes.has_key(
self.ssInfo[type][exChromosome]
[exStrand][ss][0]):
genes[self.ssInfo[type][exChromosome]
[exStrand][ss][0]] += 1
else:
genes[self.ssInfo[type][exChromosome]
[exStrand][ss][0]] = 1
exons[(sg.name,
exStart + ":E:" + exEnd)] = self.ssInfo[
type][exChromosome][exStrand][ss]
elif mode == "overlap":
(overlapGns,
overlapExons) = self.overlappingGenesExons(
type, exStart, exEnd)
for overlapGn in overlapGns:
if genes.has_key(overlapGn):
genes[overlapGn] += 1
else:
genes[overlapGn] = 1
for overlapExon in overlapExons.iterkeys():
exons[(sg.name,
exStart + ":E:" + exEnd)] = (
overlapExons[overlapExon],
overlapExon)
elif mode == "within":
(overlapGns, overlapExons) = self.withinExons(
type, exStart, exEnd)
for overlapGn in overlapGns:
if genes.has_key(overlapGn):
genes[overlapGn] += 1
else:
genes[overlapGn] = 1
for overlapExon in overlapExons.iterkeys():
exons[(sg.name,
exStart + ":E:" + exEnd)] = (
overlapExons[overlapExon],
overlapExon)
elif mode not in [
"bothSS", "singleSS", "overlap", "exon",
"within"
]:
self.__inform(
"map2gene: Ignoring unknown mode %s\n" %
mode)
else:
self.__inform(
"ERROR in map2gene: 1st argument must either be filename or instance of SpliceGraph"
)
raise Errors.ArgumentError(
"Mapper.map2gene",
"1st argument must either be filename or instance of SpliceGraph"
)
return genes, exons
