def validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
from quick.toolguide.controller.ToolGuide import ToolGuideController
from quick.toolguide import ToolGuideConfig
if not (choices.queryGSuite and choices.refGSuite):
return ToolGuideController.getHtml(cls.toolId, [ToolGuideConfig.GSUITE_INPUT], choices.isBasic)
errorString = GeneralGuiTool._checkGSuiteFile(choices.queryGSuite)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteFile(choices.refGSuite)
if errorString:
return errorString
qGSuite = getGSuiteFromGalaxyTN(choices.queryGSuite)
errorString = GeneralGuiTool._checkGSuiteRequirements \
(qGSuite,
cls.GSUITE_ALLOWED_FILE_FORMATS,
cls.GSUITE_ALLOWED_LOCATIONS,
cls.GSUITE_ALLOWED_TRACK_TYPES,
cls.GSUITE_DISALLOWED_GENOMES)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteTrackListSize(qGSuite)
if errorString:
return errorString
refGSuite = getGSuiteFromGalaxyTN(choices.refGSuite)
errorString = GeneralGuiTool._checkGSuiteRequirements \
(refGSuite,
cls.GSUITE_ALLOWED_FILE_FORMATS,
cls.GSUITE_ALLOWED_LOCATIONS,
cls.GSUITE_ALLOWED_TRACK_TYPES,
cls.GSUITE_DISALLOWED_GENOMES)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteTrackListSize(refGSuite)
if errorString:
return errorString
errorString = cls._validateGenome(choices)
if errorString:
return errorString
errorString = cls.validateUserBins(choices)
if errorString:
return errorString
def getOptionsBoxGenome(prevChoices):
if not prevChoices.firstGSuite:
return
if not prevChoices.secondGSuite:
return
#it will be good to have box with selected genome instead of text
if prevChoices.firstGSuite and prevChoices.secondGSuite:
first = getGSuiteFromGalaxyTN(prevChoices.firstGSuite)
second = getGSuiteFromGalaxyTN(prevChoices.secondGSuite)
if first.genome or second.genome:
return first.genome
else:
attributeList1 = first.attributes
attributeList2 = second.attributes
retDict = OrderedDict()
for et in attributeList1:
retDict[et+' (first GSuite)'] = False
for et in attributeList2:
retDict[et+' (second GSuite)'] = False
return retDict
else:
return
def getOptionsBoxTfTracks(cls, prevChoices):
if prevChoices.sourceTfsDetails != cls.SELECT:
genome = prevChoices.genome
sourceTfs = prevChoices.sourceTfs
sourceTfsDetails = prevChoices.sourceTfsDetails
if sourceTfs == cls.SELECT:
return
elif sourceTfs == 'Hyperbrowser repository':
tfSourceTN = TfTrackNameMappings.getTfTrackNameMappings(
prevChoices.genome)[sourceTfsDetails]
subtypes = ProcTrackOptions.getSubtypes(
prevChoices.genome, tfSourceTN, True)
falses = ['False'] * len(subtypes)
return OrderedDict(zip(subtypes, falses))
elif sourceTfs == cls.REGIONS_FROM_HISTORY:
if isinstance(sourceTfsDetails, basestring):
galaxyTN = sourceTfsDetails.split(':')
if galaxyTN[
1] == "gsuite": #ExternalTrackManager.extractFileSuffixFromGalaxyTN(prevChoices.sourceTfsDetails, allowUnsupportedSuffixes=True) == "gsuite"
errorString = GeneralGuiTool._checkGSuiteFile(
sourceTfsDetails)
if not errorString:
gSuite = getGSuiteFromGalaxyTN(sourceTfsDetails)
sizeErrorString = GeneralGuiTool._checkGSuiteTrackListSize(
gSuite, 1, 1000)
if not sizeErrorString:
reqErrorString = GeneralGuiTool._checkGSuiteRequirements \
(gSuite,
AllTfsOfRegions.GSUITE_ALLOWED_FILE_FORMATS,
AllTfsOfRegions.GSUITE_ALLOWED_LOCATIONS,
AllTfsOfRegions.GSUITE_ALLOWED_TRACK_TYPES,
AllTfsOfRegions.GSUITE_DISALLOWED_GENOMES)
if not reqErrorString:
validity = 'Valid'
else:
return
else:
return
else:
return
if validity == 'Valid':
selectedTrackNames = []
gSuite = getGSuiteFromGalaxyTN(sourceTfsDetails)
for track in gSuite.allTracks():
selectedTrackNames.append(':'.join(
track.trackName))
falses = ['False'] * len(selectedTrackNames)
return OrderedDict(zip(selectedTrackNames, falses))
else:
tfTrackName = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(
genome, galaxyTN)
return [':'.join(tfTrackName)]
else:
return
else:
return
else:
return
def execute(cls, choices, galaxyFn=None, username=''):
basisTrackNameAsList = choices.basisTrack.split(':')
extractionOptions = dict(
GalaxyInterface.getTrackExtractionOptions(choices.genome,
basisTrackNameAsList))
extractionFormat = extractionOptions[
choices.extFormatLbl] if extractionOptions else None
gsuite = getGSuiteFromGalaxyTN(choices.gsuite)
outGSuite = GSuite()
for gsTrack in gsuite.allTracks():
# outputTrackFn = cls.extraGalaxyFn[gsTrack.title]
# print '<br>\n<br>\n output track filename: ', outputTrackFn
# print 'path: ', gsTrack.path
# print 'parsed uri: ', gsTrack._parsedUri
newTrackFileName = gsTrack.title + '.' + extractionFormat
outGalaxyFn = ExternalTrackManager.createGalaxyFilesFn(
galaxyFn, newTrackFileName)
ensurePathExists(outGalaxyFn)
uri = GalaxyGSuiteTrack.generateURI(galaxyFn,
extraFileName=newTrackFileName)
GalaxyInterface.parseExtFormatAndExtractTrackManyBins(
choices.genome, basisTrackNameAsList, gsTrack.suffix,
gsTrack.path, True, choices.extFormatLbl, outGalaxyFn)
outGSuite.addTrack(
GSuiteTrack(uri,
title=gsTrack.title,
fileFormat=gsTrack.fileFormat,
trackType=gsTrack.trackType,
genome=choices.genome,
attributes=gsTrack.attributes))
GSuiteComposer.composeToFile(outGSuite, galaxyFn)
def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
attrName = choices.attrName
outputGSuite = GSuite()
#Writes the information that has been changed to a new track but jumps over all the empty strings
for i, track in enumerate(gSuite.allTracks()):
if i < cls.MAX_NUM_OF_TRACKS:
newAttrValue = getattr(choices,
'selectAttribute%s' % ((i * 2) + 1))
if (attrName == TITLE_COL):
track.title = newAttrValue
else:
track.setAttribute(attrName, newAttrValue)
outputGSuite.addTrack(track)
#Creates the new GSuite
GSuiteComposer.composeToFile(outputGSuite, galaxyFn)
def getOptionsBoxGsuiteAttributeValues(cls, prevChoices):
if prevChoices.gsuite:
gSuite = getGSuiteFromGalaxyTN(prevChoices.gsuite)
return '__hidden__', [
track.getAttribute(prevChoices.attrName)
for track in gSuite.allTracks()
]
def execute(cls, choices, galaxyFn=None, username=''):
cls._setDebugModeIfSelected(choices)
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
if gSuite.genome != choices.genome:
gSuite.setGenomeOfAllTracks(choices.genome)
regSpec, binSpec = UserBinMixin.getRegsAndBinsSpec(choices)
paragraphs = []
paragraphs += generatePilotPageTwoParagraphs(gSuite,
galaxyFn,
regSpec=regSpec,
binSpec=binSpec)
paragraphs += generatePilotPageThreeParagraphs(gSuite,
galaxyFn,
regSpec=regSpec,
binSpec=binSpec)
core = HtmlCore()
core.begin()
core.divBegin(divId='results-page')
core.divBegin(divClass='results-section')
core.header('Similarity and uniqueness of tracks')
for prg in paragraphs:
core.paragraph(prg)
core.divEnd()
core.divEnd()
core.end()
print core
def execute(cls, choices, galaxyFn=None, username=''):
import time
start = time.clock()
# HTML settings
from gold.result.HtmlCore import HtmlCore
htmlCore = HtmlCore()
htmlCore.divBegin(style=cls.HTML_STYLE)
# Set debug environment
cls._setDebugModeIfSelected(choices)
# Analysis environment
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
analysisBins = GlobalBinSource(gSuite.genome)
# Print info about tool
cls.htmlClusterTitle(cls.getToolName(), htmlCore)
cls.htmlClusterSubtext(choices.corrStat, [cls.CORR_PEARSON, cls.CORR_SPEARMAN],
choices.linkageCriterion, htmlCore)
cls.htmlVectorExplanation(htmlCore)
corrDict, labels = cls.trackOverlapValuesCorrelation(analysisBins, gSuite)
if corrDict and labels:
cls.printCorrPlots(corrDict, labels, choices.corrStat, choices.linkageCriterion, galaxyFn, htmlCore)
cls.htmlClusterTime(str(time.clock() - start), htmlCore)
htmlCore.divEnd()
print htmlCore
def validateAndReturnErrors(choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
from gold.gsuite.GSuiteConstants import UNKNOWN, MULTIPLE
errorStr = GeneralGuiTool._checkGSuiteFile(choices.history)
if errorStr:
return errorStr
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
gSuite = getGSuiteFromGalaxyTN(choices.history)
if gSuite.numTracks() == 0:
return 'Please select a GSuite file with at least one track'
if not gSuite.isPreprocessed():
return 'Selected GSuite file is not preprocess. Please preprocess ' \
'the GSuite file before continuing the analysis.'
if gSuite.trackType in [UNKNOWN]:
return 'The track type of the GSuite file is not known. The track type ' \
'is needed for doing analysis.'
if gSuite.trackType in [MULTIPLE]:
return 'All tracks in the GSuite file needs to be of the same track ' \
'type. Multiple track types are not supported.'
def getOptionsBoxSelectRows(cls, prevChoices):
if prevChoices.history == None:
return
try:
gSuite = getGSuiteFromGalaxyTN(prevChoices.history)
rowIndicesStr = prevChoices.rowIndices
if rowIndicesStr:
selectedIndices = CommonFunctionsForTools.processIndicesString(
rowIndicesStr)
resDict = OrderedDict()
for i, trackTitle in enumerate(gSuite.allTrackTitles()):
if (i + 1) in selectedIndices:
resDict[cls.addIndexToTitle((i + 1),
trackTitle)] = True
else:
resDict[cls.addIndexToTitle((i + 1),
trackTitle)] = False
return resDict
# if selectedIndices:
# return
return OrderedDict([(cls.addIndexToTitle(
(i + 1),
x), True) for i, x in enumerate(gSuite.allTrackTitles())])
except:
pass
def execute(choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
regSpec, binSpec = UserBinMixin.getRegsAndBinsSpec(choices)
analysisBins = GalaxyInterface._getUserBinSource(regSpec,
binSpec,
genome=gSuite.genome)
gSuiteOverview = GSuiteOverview(gSuite)
coreHtml = HtmlCore()
coreHtml.begin()
coreHtml.append(
str(
getGSuiteOverviewHtmlCore(
gSuiteOverview.getGSuiteOverviewData(
analysisBins=analysisBins))))
coreHtml.end()
print coreHtml
def validateAndReturnErrors(cls, choices):
errMessage = GeneralGuiTool._checkGSuiteFile(choices.gsuite)
if errMessage:
return errMessage
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
errorString = GeneralGuiTool._checkGSuiteRequirements \
(gSuite,
cls.GSUITE_ALLOWED_FILE_FORMATS,
cls.GSUITE_ALLOWED_LOCATIONS,
cls.GSUITE_ALLOWED_TRACK_TYPES,
cls.GSUITE_DISALLOWED_GENOMES)
if errorString:
return errorString
errorStr = cls._validateGenome(choices)
if errorStr:
return errorStr
errorString = cls.validateUserBins(choices)
if errorString:
return errorString
errorString = cls._checkGSuiteTrackListSize(gSuite=gSuite, minSize=2)
if errorString:
return errorString
def execute(cls, choices, galaxyFn=None, username=''):
from quick.util.CommonFunctions import getFileSuffix
import gold.gsuite.GSuiteComposer as GSuiteComposer
from gold.gsuite.GSuite import GSuite
from gold.gsuite.GSuiteTrack import registerGSuiteTrackClass, GSuiteTrack, FileGSuiteTrack
registerGSuiteTrackClass(FileGSuiteTrack)
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
outGSuite = GSuite()
for track in gSuite.allTracks():
path = track.path
suffix = track.suffix if track.suffix != getFileSuffix(
path) else ''
uri = FileGSuiteTrack.generateURI(path=path, suffix=suffix)
newTrack = GSuiteTrack(uri,
title=track.title,
trackType=track.trackType,
genome=track.genome,
attributes=track.attributes)
outGSuite.addTrack(newTrack)
GSuiteComposer.composeToFile(outGSuite, galaxyFn)
def getOptionsBoxColors(cls, prevChoices):
if not prevChoices.refTrackCollection:
return
start = '<div style="float:left;width:50px; height:20px; margin-right:5px; background-color:rgb('
end = ')"></div>'
try:
refGSuite = getGSuiteFromGalaxyTN(prevChoices.refTrackCollection)
except Exception as e:
cls.exception = str(e)
return
maxSize = 10
size = refGSuite.numTracks()
if size > maxSize:
errorString = 'Selected GSuite must have at most %s tracks' %maxSize
errorString += '.<br /> Current number of tracks = ' + str(refGSuite.numTracks())
cls.exception = errorString
return
col = [['Track','Color']]
i=1
for trackTitle in refGSuite.allTrackTitles():
c=[]
c.append(trackTitle)
c.append(start + colorTab.getRGB(i) + end)
col.append(c)
i+=1
return col
def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
import gold.gsuite.GSuiteComposer as GSuiteComposer
from gold.gsuite.GSuite import GSuite
from gold.gsuite.GSuiteTrack import GSuiteTrack, GalaxyGSuiteTrack
from quick.application.UserBinSource import GlobalBinSource
from quick.extra.ProgressViewer import ProgressViewer
from quick.extra.TrackExtractor import TrackExtractor
genome = choices.genome
fullGenomeBins = GlobalBinSource(genome)
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
progressViewer = ProgressViewer(
[(cls.PROGRESS_PROCESS_DESCRIPTION, len(gSuite))], galaxyFn)
outGSuite = GSuite()
hiddenStorageFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'storage', datasetInfo=choices.gsuite)]
fileNameSet = set()
for track in gSuite.allTracks():
fileName = cls._getUniqueFileName(fileNameSet, track.trackName)
title = track.title
attributes = track.attributes
fi = cls._getFileFormatInfo(choices, gSuite, genome, track)
uri = GalaxyGSuiteTrack.generateURI(galaxyFn=hiddenStorageFn,
extraFileName=fileName,
suffix=fi.suffix)
gSuiteTrack = GSuiteTrack(uri,
title=title,
genome=genome,
attributes=attributes)
TrackExtractor.extractOneTrackManyRegsToOneFile(
track.trackName,
fullGenomeBins,
gSuiteTrack.path,
fileFormatName=fi.fileFormatName,
globalCoords=True,
asOriginal=fi.asOriginal,
allowOverlaps=fi.allowOverlaps)
outGSuite.addTrack(gSuiteTrack)
progressViewer.update()
primaryFn = cls.extraGalaxyFn[getGSuiteHistoryOutputName(
'primary', datasetInfo=choices.gsuite)]
GSuiteComposer.composeToFile(outGSuite, primaryFn)
def getOptionsBoxSecondGSuiteColumn(prevChoices):
if prevChoices.secondGSuite:
second = getGSuiteFromGalaxyTN(prevChoices.secondGSuite)
attributeList = [None] + second.attributes
return attributeList
else:
return
def execute(cls,choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
from gold.gsuite.GSuiteEditor import selectColumnsFromGSuite
from gold.gsuite.GSuiteConstants import TITLE_COL
from gold.gsuite.GSuiteComposer import composeToFile
gSuite = getGSuiteFromGalaxyTN(choices.history)
colList = [col for col,selected in choices.selectColumns.iteritems() if selected]
selectedAttributes = [col for col in colList if col != TITLE_COL]
selectTitle = TITLE_COL in colList
filteredGSuite = selectColumnsFromGSuite(gSuite, selectedAttributes,
selectTitle=selectTitle)
composeToFile(filteredGSuite, galaxyFn)
def validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
errorString = GeneralGuiTool._checkGSuiteFile(choices.history)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices.history)
errorString = cls._validateGenome(choices)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteRequirements(
gSuite, allowedLocations=cls.GSUITE_ALLOWED_LOCATIONS)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteTrackListSize(gSuite,
minSize=1)
if errorString:
return errorString
def getOptionsBoxFirstGSuiteColumn(prevChoices):
if prevChoices.firstGSuite:
first = getGSuiteFromGalaxyTN(prevChoices.firstGSuite)
attributeList = [None] + first.attributes
return attributeList
else:
return
def execute(cls, choices, galaxyFn=None, username=''):
"""
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results
page in Galaxy history. If getOutputFormat is anything else than
'html', the output should be written to the file with path galaxyFn.
If needed, StaticFile can be used to get a path where additional
files can be put (cls, e.g. generated image files). choices is a list
of selections made by web-user in each options box.
Mandatory unless isRedirectTool() returns True.
"""
choices_gsuite = choices.chooseTrackFiles
choices_randType = choices.randType
choices_randAlg = choices.randAlg
choices_numberOfTimesToRandomize = choices.numberOfTimesToRandomize
assert choices_gsuite is not None
genome = choices.genome
assert genome is not None
analysisBins = UserBinMixin.getUserBinSource(choices)
gsuite = getGSuiteFromGalaxyTN(choices_gsuite)
for i, gsTrack in enumerate(gsuite.allTracks()):
assert gsTrack.trackName is not None, "gsuite track %s has track name None" % gsTrack
ts = getFlatTracksTS(genome, choices_gsuite)
cls.run_on_extracted_variables(ts, analysisBins, choices_numberOfTimesToRandomize, choices_randAlg,
choices_randType, galaxyFn, genome)
def validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
errorStr = GeneralGuiTool._checkGSuiteFile(choices.history)
if errorStr:
return errorStr
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
gSuite = getGSuiteFromGalaxyTN(choices.history)
if gSuite.location == GSuiteConstants.REMOTE:
return 'All tracks in GSuite file are remote. ' \
'Please download the tracks of the GSuite file before preprocessing.'
errorStr = cls._validateGenome(choices)
if errorStr:
return errorStr
errorStr = cls._checkGSuiteRequirements(
gSuite,
allowedFileFormats=cls.GSUITE_ALLOWED_FILE_FORMATS,
allowedLocations=cls.GSUITE_ALLOWED_LOCATIONS)
if errorStr:
return errorStr
def execute(choices, galaxyFn=None, username=''):
gsuite = getGSuiteFromGalaxyTN(choices.gsuite)
bedRegions = choices.bedRegions
rp = RP(gsuite)
bedData = rp.openBedFile(bedRegions)
chrOrder, chrLength = rp.sortChrDict()
dataDict, dataDictLine, elementOrder, listResCopy, newDictRegions = rp.countMutations(
chrLength, bedData)
vg = visualizationGraphs()
tName = gsuite.allTrackTitles()
uniformDictList = OrderedDict() # expected values
observedDictList = OrderedDict() # observed values
seriesNameRegionUDL = OrderedDict()
seriesNameRegionODL = OrderedDict()
seriesNameRegion = OrderedDict()
GenerateDistributionOfPointsOfInterestTool.countRegionsForDistribution(
newDictRegions, observedDictList, rp, seriesNameRegion,
seriesNameRegionODL, seriesNameRegionUDL, tName, uniformDictList)
res = ''
for elK in uniformDictList.keys():
res += GenerateDistributionOfPointsOfInterestTool.drawDistribution(
elK, observedDictList, seriesNameRegion, seriesNameRegionODL,
seriesNameRegionUDL, uniformDictList, vg)
htmlCore = HtmlCore()
htmlCore.begin()
htmlCore.line(res)
htmlCore.end()
htmlCore.hideToggle(styleClass='debug')
print htmlCore
def validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are
not valid, an error text explaining the problem should be returned. The
GUI then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are
valid, the method should return None, which enables the execute button.
'''
errorString = cls._checkGSuiteFile(choices.gsuite)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
errorString = cls._checkGSuiteRequirements(
gSuite,
allowedLocations=cls.GSUITE_ALLOWED_LOCATIONS,
allowedFileFormats=cls.GSUITE_ALLOWED_FILE_TYPES,
allowedTrackTypes=cls.GSUITE_ALLOWED_TRACK_TYPES)
if errorString:
return errorString
errorString = cls._validateGenome(choices.genome)
if errorString:
return errorString
def getOptionsBoxRowIndices(cls, prevChoices):
if prevChoices.history == None:
return
gSuite = getGSuiteFromGalaxyTN(prevChoices.history)
return '1-%i' % (gSuite.numTracks() + 1)
def validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
errorStr = GeneralGuiTool._checkGSuiteFile(choices.history)
if errorStr:
return errorStr
gSuite = getGSuiteFromGalaxyTN(choices.history)
if gSuite.numTracks() == 0:
return 'Please select a GSuite file with at least one track'
errorStr = cls._checkGSuiteRequirements(
gSuite,
allowedFileFormats = cls.GSUITE_ALLOWED_FILE_FORMATS,
allowedLocations = cls.GSUITE_ALLOWED_LOCATIONS)
if errorStr:
return errorStr
if choices.operation:
if choices.operation == cls.NO_OPERATION_TEXT:
return 'Please select an operation to perform on the input tracks'
else:
try:
cls._runOperationOnExampleDataAndReturnOutput(choices)
except Exception as e:
return 'An error occured testing operation "%s": ' % choices.operation + str(e)
if choices.changeSuffix == 'Yes' and choices.suffix.strip() == '':
return 'Please select a file suffix'
def _validateGenome(cls, choices, validateBinaryTracksIfPresent=True):
from quick.multitrack.MultiTrackCommon import getGSuiteFromGalaxyTN
from quick.application.ProcTrackOptions import ProcTrackOptions
allGSuiteGalaxyTNs = [
getattr(choices, key) for key in cls.GSUITE_FILE_OPTIONS_BOX_KEYS
]
if all(allGSuiteGalaxyTNs):
if (not cls._allowGenomeOverride(choices)
) and cls._getNumUniquelySpecifiedGenomes(choices) > 1:
return cls.ERROR_GENOME_BUILD_MISMATCH + ', '.join(
cls._getGsuiteGenomes(choices))
errorStr = GeneralGuiTool._checkGenome(choices.genome)
if errorStr:
return errorStr
if not cls._allowMultipleGenomes(
choices) and choices.genome == GSuiteConstants.MULTIPLE:
return cls.ERROR_MULTIPLE_GENOMES_NOT_ALLOWED
if validateBinaryTracksIfPresent:
for galaxyTN in allGSuiteGalaxyTNs:
gSuite = getGSuiteFromGalaxyTN(galaxyTN)
if gSuite.fileFormat == GSuiteConstants.PREPROCESSED and gSuite.location == GSuiteConstants.LOCAL:
for gSuiteTrack in gSuite.allTracks():
if not ProcTrackOptions.isValidTrack(
choices.genome, gSuiteTrack.trackName,
True):
return cls.ERROR_PREPROCESSED_TRACK_INVALID % gSuiteTrack.title
def execute(cls, choices, galaxyFn=None, username=''):
import time
start = time.clock()
# HTML settings
from gold.result.HtmlCore import HtmlCore
htmlCore = HtmlCore()
htmlCore.divBegin(style=cls.HTML_STYLE)
# Set debug environment
cls._setDebugModeIfSelected(choices)
# Analysis environment
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
analysisBins = GlobalBinSource(gSuite.genome)
analysisSpec = AnalysisSpec(GeneticLociOverlapStat)
analysisSpec.addParameter('filterThreshold', int(choices.geneticLocus))
# Print tool information:
cls.htmlClusterTitle(cls.getToolName(), htmlCore)
cls.htmlClusterSubtext(choices.corrStat, [cls.CORR_PEARSON, cls.CORR_SPEARMAN],
choices.linkageCriterion, htmlCore)
cls.htmlVectorHandling(htmlCore)
# Get correlations
overlapMatrix, labels = cls.getOverlapMatrix(analysisBins, analysisSpec, gSuite)
corrDict = cls.getTriangularCorrMatrix(overlapMatrix)
cls.printCorrPlots(corrDict, labels, choices.corrStat, choices.linkageCriterion, galaxyFn, htmlCore)
cls.htmlClusterTime(str(time.clock() - start), htmlCore)
htmlCore.divEnd()
print htmlCore
def validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
errorStr = GeneralGuiTool._checkGSuiteFile(choices.history)
if errorStr:
return errorStr
gSuite = getGSuiteFromGalaxyTN(choices.history)
if choices.rowIndices:
try:
selectedIndices = CommonFunctionsForTools.processIndicesString(
choices.rowIndices)
maxIndex = max(selectedIndices)
if maxIndex > (gSuite.numTracks()):
return 'Selected row index %i is too high. GSuite contains %i tracks.' % (
maxIndex, gSuite.numTracks())
except:
return 'Please enter valid indices string (e.g. 1-10, 12, 14)'
if gSuite.numTracks() == 0:
return 'GSuite file contains no tracks'
def getOptionsBoxChangeFormat(cls, prevChoices):
if prevChoices.gsuite and prevChoices.genome:
gSuite = getGSuiteFromGalaxyTN(prevChoices.gsuite)
if cls._allTracksHasOriginalFormat(gSuite, prevChoices.genome):
return [cls.OUTPUT_FORMAT_ORIGINAL, cls.OUTPUT_FORMAT_OTHER]
else:
return [cls.OUTPUT_FORMAT_OTHER]
def execute(cls, choices, galaxyFn=None, username=''):
'''
Is called when execute-button is pushed by web-user. Should print
output as HTML to standard out, which will be directed to a results page
in Galaxy history. If getOutputFormat is anything else than HTML, the
output should be written to the file with path galaxyFn. If needed,
StaticFile can be used to get a path where additional files can be put
(e.g. generated image files). choices is a list of selections made by
web-user in each options box.
'''
gSuite = getGSuiteFromGalaxyTN(choices.history)
# titleList = []
# if choices.rowIndices:
# selectedIndices = CommonFunctionsForTools.processIndicesString(choices.rowIndices)
# titleList = [tt for i, tt in enumerate(gSuite.allTrackTitles()) if i in selectedIndices]
# else:
titleList = [
cls.removeIndexFromTitleName(title)
for title, selected in choices.selectRows.iteritems() if selected
]
filteredGSuite = selectRowsFromGSuiteByTitle(gSuite, titleList)
composeToFile(filteredGSuite, galaxyFn)
def getOptionsBoxAdditionalAttributes(cls, prevChoices):
galaxyGSName = getattr(prevChoices, cls.GSUITE_FILE_OPTIONS_BOX_KEY)
if galaxyGSName:
gsuite = getGSuiteFromGalaxyTN(galaxyGSName)
if gsuite.attributes:
return OrderedDict(
zip(gsuite.attributes, [False] * len(gsuite.attributes)))
def validateAndReturnErrors(cls, choices):
'''
Should validate the selected input parameters. If the parameters are not
valid, an error text explaining the problem should be returned. The GUI
then shows this text to the user (if not empty) and greys out the
execute button (even if the text is empty). If all parameters are valid,
the method should return None, which enables the execute button.
'''
errorString = GeneralGuiTool._checkGSuiteFile(choices.gsuite)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices.gsuite)
errorString = GeneralGuiTool._checkGSuiteRequirements \
(gSuite,
allowedLocations=GSuiteExportToHistoryTool.GSUITE_ALLOWED_LOCATIONS,
allowedFileFormats=GSuiteExportToHistoryTool.GSUITE_ALLOWED_FILE_FORMATS,
allowedTrackTypes=GSuiteExportToHistoryTool.GSUITE_ALLOWED_TRACK_TYPES)
if errorString:
return errorString
if choices.changeFormat == cls.OUTPUT_FORMAT_CONVERT and choices.outputFormat is None:
return 'There are no common supported file formats that all selected tracks can be converted to.'
def execute(cls, choices, galaxyFn=None, username=''):
from quick.webtools.clustering.GSuitePrimaryTrackModifier import GSuitePrimaryTrackModifier
# Set analysis environment
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
outGSuite = GSuite()
errorGSuite = GSuite()
progressViewer = ProgressViewer([('Manipulate tracks', gSuite.numTracks() + 24)],
cls.extraGalaxyFn[cls.HISTORY_PROGRESS_TITLE])
hiddenStorageFn = cls.extraGalaxyFn[cls.HISTORY_HIDDEN_TRACK_STORAGE]
# Get rsID map for the chosen reference genome
rsidMap = RsidMapper.createRsidMappingFromStaticFiles(progressViewer, choices.refGenome)
# Lift over all tracks
for track in gSuite.allTracks():
fileName = cls.getFilenameWithGTrackSuffix(track.path)
title = getTitleWithSuffixReplaced(track.title, 'gtrack')
try:
uri = GalaxyGSuiteTrack.generateURI(
galaxyFn=hiddenStorageFn,
extraFileName=fileName,
suffix='gtrack'
)
gSuiteTrack = GSuiteTrack(
uri,
title=title,
genome=track.genome,
trackType=track.trackType,
attributes=track.attributes
)
trackFn = gSuiteTrack.path
GSuitePrimaryTrackModifier.liftOverGTrack(track.path, trackFn, rsidMap)
outGSuite.addTrack(gSuiteTrack)
except Exception as e:
track.comment = 'An error occurred for the following track: ' + str(e)
errorGSuite.addTrack(track)
progressViewer.update()
# Update reference genome of all tracks and write to file
outGSuite.setGenomeOfAllTracks(choices.refGenome)
composeToFile(outGSuite, galaxyFn)
composeToFile(errorGSuite, cls.extraGalaxyFn[cls.HISTORY_ERROR_TITLE])
writeGSuiteHiddenTrackStorageHtml(hiddenStorageFn)
def execute(cls, choices, galaxyFn=None, username=''):
import time
start = time.clock()
# HTML settings
from gold.result.HtmlCore import HtmlCore
htmlCore = HtmlCore()
htmlCore.divBegin(style=cls.HTML_STYLE)
# Set debug environment
cls._setDebugModeIfSelected(choices)
# Print tool information
cls.htmlClusterTitle(choices.ldGraphMatching, htmlCore)
cls.htmlClusterSubtext(choices.distanceMeasure, cls.CLUSTER_LIST, choices.linkageCriterion, htmlCore)
htmlCore.line('Threshold of r<sup>2</sup>: ' + choices.rSquare)
# Analysis environment
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
analysisBins = GlobalBinSource(gSuite.genome)
graph = LDExpansions.createRSquareGraph(choices.ldGraphTrack, float(choices.rSquare))
tracks, labels = LDExpansions.generateTracksAndLabels(gSuite, analysisBins)
# Find distance/correlation matrices
size = gSuite.numTracks()
distDict = cls.createDistDict(cls.CLUSTER_LIST)
for i in range(0, size):
for j in range(i + 1, size):
track1 = tracks[i]
track2 = tracks[j]
cost_matrix = BipartiteMatching.generateCostMatrix(track1, track2, graph)
if choices.ldGraphMatching == LDBipartiteMatchingTool.LD_GREEDY:
count = BipartiteMatching.greedyBipartite(cost_matrix)
else:
count = BipartiteMatching.lapjvBipartite(cost_matrix)
cls.updateDistDict(distDict, count)
# Cluster and print plots
cls.printDistPlots(distDict, labels, choices.distanceMeasure, choices.linkageCriterion, galaxyFn, htmlCore)
cls.htmlClusterTime(str(time.clock() - start), htmlCore)
htmlCore.divEnd()
print htmlCore
def execute(cls, choices, galaxyFn=None, username=''):
from quick.webtools.clustering.CreateLDTrack import CreateLDTrack
from quick.webtools.clustering.RsidMapper import RsidMapper
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
outGSuite = GSuite()
errorGSuite = GSuite()
progressViewer = ProgressViewer([('Manipulate tracks', gSuite.numTracks() + 24)],
cls.extraGalaxyFn[cls.HISTORY_PROGRESS_TITLE])
ldDict = CreateLDTrack.getLDDict(float(choices.rsquare))
rsidDict = RsidMapper.createRsidMappingFromStaticFiles(progressViewer, choices.refGenome)
hiddenStorageFn = cls.extraGalaxyFn[cls.HISTORY_HIDDEN_TRACK_STORAGE]
for track in gSuite.allTracks():
fileName = cls.getFilenameWithGTrackSuffix(track.path)
title = getTitleWithSuffixReplaced(track.title, 'gtrack')
try:
uri = GalaxyGSuiteTrack.generateURI(
galaxyFn=hiddenStorageFn,
extraFileName=fileName,
suffix='gtrack'
)
gSuiteTrack = GSuiteTrack(
uri,
title=title,
genome=track.genome,
trackType='points',
attributes=track.attributes
)
trackFn = gSuiteTrack.path
CreateLDTrack.parseFileIntoPointTrack(track.path, trackFn, ldDict, rsidDict)
outGSuite.addTrack(gSuiteTrack)
except Exception as e:
track.comment = 'An error occurred for the following track: ' + str(e)
errorGSuite.addTrack(track)
progressViewer.update()
outGSuite.setGenomeOfAllTracks(choices.refGenome)
composeToFile(outGSuite, galaxyFn)
composeToFile(errorGSuite, cls.extraGalaxyFn[cls.HISTORY_ERROR_TITLE])
writeGSuiteHiddenTrackStorageHtml(hiddenStorageFn)
def validateGSuite(cls, choices):
errorString = cls._checkGSuiteFile(choices.gSuite)
if errorString:
return errorString
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
errorString = GeneralGuiTool._checkGSuiteRequirements(
gSuite,
allowedLocations=CommonClusteringFunctions.GSUITE_ALLOWED_LOCATIONS,
allowedFileFormats=CommonClusteringFunctions.GSUITE_ALLOWED_FILE_FORMATS,
allowedTrackTypes=CommonClusteringFunctions.GSUITE_ALLOWED_TRACK_TYPES)
if errorString:
return errorString
errorString = GeneralGuiTool._checkGSuiteTrackListSize(gSuite, 2)
if errorString:
return errorString
def execute(cls, choices, galaxyFn=None, username=''):
import time
start = time.clock()
# HTML settings
from gold.result.HtmlCore import HtmlCore
htmlCore = HtmlCore()
htmlCore.divBegin(style=cls.HTML_STYLE)
# Set debug environment
cls._setDebugModeIfSelected(choices)
# Print tool information
cls.htmlClusterTitle(cls.getToolName(), htmlCore)
cls.htmlClusterSubtext(choices.distanceMeasure, cls.CLUSTER_LIST, choices.linkageCriterion, htmlCore)
htmlCore.line('Threshold of r<sup>2</sup>: ' + choices.rSquare)
# Analysis environment
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
analysisBins = GlobalBinSource(gSuite.genome)
analysisSpec = AnalysisSpec(ExpandTrackAndMatchStat)
splitName = choices.ldTrack.split(":")
trackName = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(gSuite.genome, splitName)
linkedPointTrack = Track(trackName)
# Find distance/correlation matrix
labels = []
distDict = cls.createDistDict(cls.CLUSTER_LIST)
size = gSuite.numTracks()
for i in range(0, size):
gSuiteTrack1 = gSuite.getTrackFromIndex(i)
labels.append(gSuiteTrack1.title)
for j in range(i + 1, size):
gSuiteTrack2 = gSuite.getTrackFromIndex(j)
track1 = Track(gSuiteTrack1.trackName)
track2 = Track(gSuiteTrack2.trackName)
count = doAnalysis(analysisSpec, analysisBins, [track1, track2, linkedPointTrack]).getGlobalResult()
cls.updateDistDict(distDict, count)
# Cluster and print plots
cls.printDistPlots(distDict, labels, choices.distanceMeasure, choices.linkageCriterion, galaxyFn, htmlCore)
cls.htmlClusterTime(str(time.clock() - start), htmlCore)
htmlCore.divEnd()
print htmlCore
def validateAndReturnErrors(cls, choices=None):
errorStr = GeneralGuiTool._checkGSuiteFile(choices.gSuite)
if errorStr:
return errorStr
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
if gSuite.numTracks() == 0:
return 'Please select a GSuite file with at least one track'
errorStr = cls._checkGSuiteRequirements(
gSuite,
allowedFileFormats=cls.GSUITE_ALLOWED_FILE_FORMATS,
allowedLocations=cls.GSUITE_ALLOWED_LOCATIONS
)
if errorStr:
return errorStr
def execute(cls, choices, galaxyFn=None, username=''):
cls._setDebugModeIfSelected(choices)
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
analysisBins = GlobalBinSource(gSuite.genome)
core = HtmlCore()
core.divBegin(style=CommonClusteringFunctions.HTML_STYLE)
if choices.getEmpiricalCase == PrintingTool.PRINT_SNPS:
core.header(PrintingTool.PRINT_SNPS)
core.divider(True)
cls.printUniqueRsIDs(analysisBins, gSuite, core)
elif choices.getEmpiricalCase == PrintingTool.PRINT_DISEASE:
core.header(PrintingTool.PRINT_DISEASE)
core.divider(True)
cls.printDiseaseRsIDs(analysisBins, gSuite, core)
core.divEnd()
print core
def execute(cls, choices, galaxyFn=None, username=''):
from gold.description.AnalysisDefHandler import AnalysisSpec
from quick.statistic.UniquePointTrackStat import UniquePointTrackStat
from quick.application.UserBinSource import GlobalBinSource
cls._setDebugModeIfSelected(choices)
# Analysis environment
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
analysisBins = GlobalBinSource(gSuite.genome)
analysisSpec = AnalysisSpec(UniquePointTrackStat)
# Get unique rsids for whole GSuite
rsids = set()
for gSuiteTrack in gSuite.allTracks():
track = Track(gSuiteTrack.trackName)
result = doAnalysis(analysisSpec, analysisBins, [track]).getGlobalResult()
if 'Result' in result:
rsids.update(result['Result'])
# Create linked point track
cls.createLinkedPointTrack(rsids, str(choices.isUndirected), galaxyFn, float(choices.rsquare))
def execute(cls, choices, galaxyFn=None, username=''):
cls._setDebugModeIfSelected(choices)
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
analysisBins = GlobalBinSource(gSuite.genome)
htmlCore = HtmlCore()
htmlCore.divBegin(style=CommonClusteringFunctions.HTML_STYLE)
if choices.getEmpiricalCase == SNPStatsTool.SNP_COUNT:
htmlCore.bigHeader(SNPStatsTool.SNP_COUNT)
htmlCore.divider(True)
cls.getSNPFrequencyStats(analysisBins, gSuite, galaxyFn, htmlCore)
elif choices.getEmpiricalCase == SNPStatsTool.SNP_BETWEEN:
htmlCore.bigHeader(SNPStatsTool.SNP_BETWEEN)
htmlCore.divider(True)
cls.getDistancesBetween(analysisBins, gSuite, galaxyFn, htmlCore)
elif choices.getEmpiricalCase == SNPStatsTool.SNP_WITHIN:
htmlCore.bigHeader(SNPStatsTool.SNP_WITHIN)
htmlCore.divider(True)
cls.getDistancesWithin(analysisBins, gSuite, galaxyFn, htmlCore)
print htmlCore
def execute(cls, choices, galaxyFn=None, username=''):
import time
start = time.clock()
# HTML settings
from gold.result.HtmlCore import HtmlCore
htmlCore = HtmlCore()
htmlCore.divBegin(style=cls.HTML_STYLE)
# Set debug environment
cls._setDebugModeIfSelected(choices)
# Analysis environment
gSuite = getGSuiteFromGalaxyTN(choices.gSuite)
analysisBins = GlobalBinSource(gSuite.genome)
distDict = None
labels = None
# Print tool information:
cls.htmlClusterTitle(choices.vectorDef, htmlCore)
cls.htmlClusterSubtext(choices.distanceCorrMeasure, cls.CORR_DISTLIST, choices.linkageCriterion, htmlCore)
# Get distance / correlation matrixes
if choices.vectorDef == BinaryClusteringTool.COMP_DIRECT:
distDict, labels = cls.directVectorDistance(gSuite, analysisBins)
elif choices.vectorDef == BinaryClusteringTool.COMP_BINS:
distDict, labels = cls.microBinDistance(gSuite, analysisBins, choices)
# Print plots
if distDict and labels:
cls.printDistPlots(distDict, labels, choices.distanceCorrMeasure, choices.linkageCriterion, galaxyFn,
htmlCore)
cls.htmlClusterTime(str(time.clock() - start), htmlCore)
htmlCore.divEnd()
print htmlCore
