def renameCollTrack(genome, oldTn, newTn):
oldPath = createCollectedPath(genome, oldTn)
if not os.path.exists(oldPath):
print '(TN did not exist in collTracks..)'
else:
print '(renaming track in collTracks..)'
newPath = createCollectedPath(genome, newTn)
if not ONLY_SIMULATION:
assert not os.path.exists(newPath), 'ERROR: Target path already exists: ' + newPath
ensurePathExists(newPath)
shutil.move(oldPath, newPath)
else:
print 'Would move %s to %s' % (oldPath, newPath)
def renameCollTrack(genome, oldTn, newTn):
oldPath = createCollectedPath(genome, oldTn)
if not os.path.exists(oldPath):
print '(TN did not exist in collTracks..)'
else:
print '(renaming track in collTracks..)'
newPath = createCollectedPath(genome, newTn)
if not ONLY_SIMULATION:
assert not os.path.exists(
newPath), 'ERROR: Target path already exists: ' + newPath
ensurePathExists(newPath)
shutil.move(oldPath, newPath)
else:
print 'Would move %s to %s' % (oldPath, newPath)
def writeTrackData(choices, genome, tn):
from gold.util.RandomUtil import random
from gold.util.CommonFunctions import createCollectedPath
from quick.util.CommonFunctions import ensurePathExists
trackFn = createCollectedPath(genome, tn,
'simulatedTracks.category.bed')
ensurePathExists(trackFn)
trackFile = open(trackFn, 'w')
#determinePossibilities
numPossiblePositions = int(choices[2])
spacingBetweenPositions = 1e3
possiblePositions = [
i * spacingBetweenPositions
for i in range(1, int(numPossiblePositions))
]
numHighProbPositions = int(choices[3])
highProbPossiblePositions = possiblePositions[0:numHighProbPositions]
lowProbPossiblePositions = possiblePositions[numHighProbPositions:]
largestPossiblePosition = possiblePositions[-1]
print 'largestPossiblePosition: ', largestPossiblePosition / 1e6, 'M'
assert largestPossiblePosition < 1.5e8 #just due to hardcoded analysis region below..
sizePerPosition = 591 #empirical across all VDR binding sites..
print 'Total BpCoverage: ', len(possiblePositions) * sizePerPosition
#make samples
numExperiments = int(choices[0])
proportionFromHighProbPositions = float(choices[4])
fixedNumFromHighProbPositions = int(choices[5])
#numPositionsPerExperiment = [3000]*9
numPositionsPerExperiment = [
int(x) for x in choices[1].split(',')
] #[3073, 7118, 5290, 3059, 4051, 1021, 200, 610, 573]
for experimentIndex in range(numExperiments):
#sampledPositions = random.sample(possiblePositions, numPositionsPerExperiment[experimentIndex])
numHighProbSamples = int(numPositionsPerExperiment[experimentIndex]
* proportionFromHighProbPositions
) + fixedNumFromHighProbPositions
numLowProbSamples = numPositionsPerExperiment[
experimentIndex] - numHighProbSamples
print 'numHighProbSamples: %i, out of numHighProbPossiblePositions: %i' % (
numHighProbSamples, len(highProbPossiblePositions))
sampledPositions = random.sample(highProbPossiblePositions, numHighProbSamples ) \
+ random.sample(lowProbPossiblePositions, numLowProbSamples )
sampledSegments = [(position, position + sizePerPosition)
for position in sampledPositions]
for seg in sampledSegments:
trackFile.write('\t'.join([
'chr1',
'%i' % seg[0],
'%i' % seg[1],
'T%i' % experimentIndex
]) + '\n')
trackFile.close()
def execute(cls, choices, galaxyFn=None, username=''):
from gold.util.RandomUtil import random
outputFile = open(galaxyFn, 'w')
genome = choices[0]
histItem = choices[2]
trackItem = choices[3]
chromRegsPath = GenomeInfo.getChrRegsFn(genome)
chrSizeDict = dict([(chrom, GenomeInfo.getChrLen(genome, chrom))
for chrom in GenomeInfo.getChrList(genome)])
geSource = headLinesStr = None
if choices[1] == 'history':
trackType = choices[2].split(':')[1]
username = ''.join(
[chr(random.randint(97, 122)) for i in range(6)])
tempFn = createCollectedPath(
genome, [],
username + '_'.join([str(v) for v in time.localtime()[:6]]) +
'.' + trackType)
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(
choices[2].split(':'))
open(tempFn, 'w').write(open(fnSource, 'r').read())
if trackType in ['valued.bed', 'category.bed', 'bed']:
geSource = GenomeElementSorter(
BedGenomeElementSource(tempFn, genome=genome)).__iter__()
#elif trackType == 'gtrack':
# geSource = GenomeElementSorter(GtrackGenomeElementSource(tempFn, genome=genome)).__iter__()
# headLinesStr = geSource.getHeaderLines().replace('##','\n##')
cls.WriteExpandedElementsToFile(geSource,
chrSizeDict,
outputFile,
headLinesStr,
writeHeaderFlag=True)
os.remove(tempFn)
else:
writeHeaderFlag = True
for chrom in GenomeInfo.getChrList(genome):
gRegion = GenomeRegion(genome, chrom, 0, chrSizeDict[chrom])
plTrack = PlainTrack(trackItem.split(':'))
geSource = GenomeElementTvWrapper(
plTrack.getTrackView(gRegion)).__iter__()
cls.WriteExpandedElementsToFile(geSource, chrSizeDict,
outputFile, headLinesStr,
writeHeaderFlag)
writeHeaderFlag = False
outputFile.close()
def createChromosomeFile(genome, chromNames, referToCollected=False):
"""genome chromNames"""
# python quick/extra/CustomFuncCatalog.py CreateChromosomeFile mm9 'chr1, chr2, ...'"
chrList = chromNames.replace(' ','').split(',')
if referToCollected:
from gold.util.CommonFunctions import createCollectedPath
basePath = createCollectedPath(genome, GenomeInfo.getChrTrackName(genome))
else:
basePath = gcf.createOrigPath(genome, GenomeInfo.getChrTrackName(genome))
# Why is this file a category.bed file?
outFn = basePath + os.sep + 'chromosomes.category.bed'
qcf.ensurePathExists(outFn)
print 'Creating: ' + outFn
outFile = open(outFn, 'w')
for chr in chrList:
outFile.write('\t'.join([chr, '0', str(GenomeInfo.getChrLen(genome, chr)), chr]) + os.linesep)
outFile.close()
def execute(cls, choices, galaxyFn=None, username=''):
outputFile = open(galaxyFn, 'w')
genome = choices[0]
histItem = choices[2]
trackItem = choices[3]
chromRegsPath = GenomeInfo.getChrRegsFn(genome)
chrSizeDict = dict([ ( chrom, GenomeInfo.getChrLen(genome, chrom)) for chrom in GenomeInfo.getChrList(genome)])
geSource = headLinesStr = None
if choices[1] == 'History':
trackType = choices[2].split(':')[1]
username = ''.join([chr(random.randint(97,122)) for i in range(6)])
tempFn = createCollectedPath(genome, [], username+'_'.join([str(v) for v in time.localtime()[:6]])+'.'+trackType)
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(choices[2].split(':'))
open(tempFn,'w').write(open(fnSource,'r').read())
if trackType in ['marked.bed', 'category.bed', 'bed']:
geSource = GenomeElementSorter(BedGenomeElementSource(tempFn, genome=genome)).__iter__()
elif trackType == 'gtrack':
geSource = GenomeElementSorter(GtrackGenomeElementSource(tempFn, genome=genome)).__iter__()
headLinesStr = geSource.getHeaderLines().replace('##','\n##')
cls.WriteExpandedElementsToFile(geSource, chrSizeDict, outputFile, headLinesStr, writeHeaderFlag=True)
os.remove(tempFn)
else:
writeHeaderFlag = True
for chrom in GenomeInfo.getChrList(genome):
gRegion = GenomeRegion(genome, chrom, 0, chrSizeDict[chrom])
plTrack = PlainTrack(trackItem.split(':'))
geSource = GenomeElementTvWrapper(plTrack.getTrackView(gRegion)).__iter__()
cls.WriteExpandedElementsToFile(geSource, chrSizeDict, outputFile, headLinesStr, writeHeaderFlag)
writeHeaderFlag = False
outputFile.close()
def getCollectedPathGFF(cls, abbrv):
return createCollectedPath(abbrv, GenomeInfo.getGenomeAnnotationsTrackName(abbrv), 'genome_annotations.gff')
def getBasePathGFF(cls, abbrv):
return createCollectedPath(abbrv, GenomeInfo.getGenomeAnnotationsTrackName(abbrv))
def getBasePathSequence(cls, abbrv):
return createCollectedPath(abbrv, GenomeInfo.getSequenceTrackName(abbrv))
def getTableData(self, genome, trackName):
webObject, paramForm = self._getWebPageAndForm( self._makeUrlstreng(self._sessionId, 'hgta_outputType', trackName[-1]) )
response = mechanize.urlopen(paramForm.click('hgta_doTopSubmit'))
fn = createCollectedPath(genome, trackName, 'fromUcsc.'+trackName[-1])
ensurePathExists(fn)
open(fn,'w').write(response.read())
def getTableData(self, genome, trackName):
webObject, paramForm = self._getWebPageAndForm( self._makeUrlstreng(self._sessionId, 'hgta_outputType', trackName[-1]) )
response = mechanize.urlopen(paramForm.click('hgta_doTopSubmit'))
fn = createCollectedPath(genome, trackName, 'fromUcsc.'+trackName[-1])
ensurePathExists(fn)
open(fn,'w').write(response.read())
