def __new__(cls, genome):
from gtrackcore.track.core.GenomeRegion import GenomeRegion
from gtrackcore.metadata.GenomeInfo import GenomeInfo
chrList = GenomeInfo.getChrList(genome)
if len(chrList) > 0:
return [
GenomeRegion(genome,
GenomeInfo.getChrList(genome)[0], 0, 1)
]
def parseRegSpec(regSpec, genome = None, includeExtraChrs = False):
from gtrackcore.track.core.GenomeRegion import GenomeRegion
from gtrackcore.metadata.GenomeInfo import GenomeInfo
class SimpleUserBinSource(list):
pass
regions = []
allRegSpecs = regSpec.strip().split(',')
for curRegSpec in allRegSpecs:
regParts = curRegSpec.strip().split(':')
if genome == None:
genome = regParts[0]
#assert GenomeInfo(genome).isInstalled(), "Specified genome is not installed: %s" % genome
if not (regParts[0]=='*' or regParts[0] in GenomeInfo.getExtendedChrList(genome)):
#if (regParts[0]=='*' or regParts[0].startswith('chr')):
# if genome == None:
# genome = DEFAULT_GENOME
#else:
# assert genome is None or genome == regParts[0], \
assert regParts[0] == genome, \
"Region specification does not start with one of '*' or correct chromosome or genome name. Region specification: %s. Genome: %s" % (curRegSpec, genome)
#genome = regParts[0]
regParts = regParts[1:]
if regParts[0] == '*':
assert len(regParts) == 1, \
"Region specification starts with '*' but continues with ':'. Region specification: %s" % curRegSpec
assert len(allRegSpecs) == 1, \
"Region specification is '*', but is in a list with other region specifications: %s" % regSpec
chrList = GenomeInfo.getExtendedChrList(genome) if includeExtraChrs else GenomeInfo.getChrList(genome)
for chr in chrList:
regions.append(GenomeRegion(genome, chr, 0, GenomeInfo.getChrLen(genome, chr)))
else:
#assert(regParts[0].startswith('chr')), \
assert regParts[0] in GenomeInfo.getExtendedChrList(genome), \
"Region specification does not start with chromosome specification. Region specification: %s " % curRegSpec
chr = regParts[0]
try:
chrLen = GenomeInfo.getChrLen(genome, chr)
except Exception, e:
raise InvalidFormatError("Chromosome '%s' does not exist for genome '%s'" % (chr, genome))
if len(regParts)>1:
posParts = regParts[1]
assert '-' in posParts, \
"Position specification does not include character '-'. Region specification: %s " % curRegSpec
rawStart, rawEnd = posParts.split('-')
start = int(rawStart.replace('k','001').replace('m','000001'))
end = int(rawEnd.replace('k','000').replace('m','000000')) if rawEnd != '' else chrLen
assert start >= 1, \
"Start position is not positive. Region specification: %s " % curRegSpec
assert end >= start, \
"End position is not larger than start position. Region specification: %s " % curRegSpec
assert end <= chrLen, \
"End position is larger than chromosome size. Genome: %s. Chromosome size: %s. Region specification: %s" % (genome, chrLen, curRegSpec)
#-1 for conversion from 1-indexing to 0-indexing end-exclusive
start-=1
else:
start,end = 0, chrLen
regions.append( GenomeRegion(genome, chr, start, end) )
def parseRegSpec(regSpec, genome=None, includeExtraChrs=False):
from gtrackcore.track.core.GenomeRegion import GenomeRegion
from gtrackcore.metadata.GenomeInfo import GenomeInfo
class SimpleUserBinSource(list):
pass
regions = []
allRegSpecs = regSpec.strip().split(',')
for curRegSpec in allRegSpecs:
regParts = curRegSpec.strip().split(':')
if genome == None:
genome = regParts[0]
#assert GenomeInfo(genome).isInstalled(), "Specified genome is not installed: %s" % genome
if not (regParts[0] == '*'
or regParts[0] in GenomeInfo.getExtendedChrList(genome)):
#if (regParts[0]=='*' or regParts[0].startswith('chr')):
# if genome == None:
# genome = DEFAULT_GENOME
#else:
# assert genome is None or genome == regParts[0], \
assert regParts[0] == genome, \
"Region specification does not start with one of '*' or correct chromosome or genome name. Region specification: %s. Genome: %s" % (curRegSpec, genome)
#genome = regParts[0]
regParts = regParts[1:]
if regParts[0] == '*':
assert len(regParts) == 1, \
"Region specification starts with '*' but continues with ':'. Region specification: %s" % curRegSpec
assert len(allRegSpecs) == 1, \
"Region specification is '*', but is in a list with other region specifications: %s" % regSpec
chrList = GenomeInfo.getExtendedChrList(
genome) if includeExtraChrs else GenomeInfo.getChrList(genome)
for chr in chrList:
regions.append(
GenomeRegion(genome, chr, 0,
GenomeInfo.getChrLen(genome, chr)))
else:
#assert(regParts[0].startswith('chr')), \
assert regParts[0] in GenomeInfo.getExtendedChrList(genome), \
"Region specification does not start with chromosome specification. Region specification: %s " % curRegSpec
chr = regParts[0]
try:
chrLen = GenomeInfo.getChrLen(genome, chr)
except Exception, e:
raise InvalidFormatError(
"Chromosome '%s' does not exist for genome '%s'" %
(chr, genome))
if len(regParts) > 1:
posParts = regParts[1]
assert '-' in posParts, \
"Position specification does not include character '-'. Region specification: %s " % curRegSpec
rawStart, rawEnd = posParts.split('-')
start = int(
rawStart.replace('k', '001').replace('m', '000001'))
end = int(rawEnd.replace('k', '000').replace(
'm', '000000')) if rawEnd != '' else chrLen
assert start >= 1, \
"Start position is not positive. Region specification: %s " % curRegSpec
assert end >= start, \
"End position is not larger than start position. Region specification: %s " % curRegSpec
assert end <= chrLen, \
"End position is larger than chromosome size. Genome: %s. Chromosome size: %s. Region specification: %s" % (genome, chrLen, curRegSpec)
#-1 for conversion from 1-indexing to 0-indexing end-exclusive
start -= 1
else:
start, end = 0, chrLen
regions.append(GenomeRegion(genome, chr, start, end))
def __new__(cls, genome):
from gtrackcore.track.core.GenomeRegion import GenomeRegion
from gtrackcore.metadata.GenomeInfo import GenomeInfo
chrList = GenomeInfo.getChrList(genome)
if len(chrList) > 0:
return [GenomeRegion(genome, GenomeInfo.getChrList(genome)[0], 0, 1)]