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 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.
'''
#print 'Executing...'
print GalaxyInterface.getHtmlBeginForRuns(galaxyFn)
print GalaxyInterface.getHtmlForToggles(withRunDescription=False)
genome = choices[1]
flankSize = int(choices[3])
if choices[4] == cls.REGIONS_FROM_HISTORY:
from quick.extra.tfbs.GeneTargetsOfTF import GeneTargetsOfRegions
regionsTn = choices[5].split(':')
GeneTargetsOfRegions.findGeneTargets(genome, regionsTn, flankSize,
flankSize, galaxyFn)
else:
tfSource = choices[4]
tfChoice = choices[5]
from quick.extra.tfbs.GeneTargetsOfTF import GeneTargetsOfTF
GeneTargetsOfTF.findGeneTargets(genome, tfSource, tfChoice,
flankSize, flankSize, galaxyFn)
print GalaxyInterface.getHtmlEndForRuns()
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 needed, can call _getStaticPath 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.
'''
#print 'choices: ', choices
genome = choices.genome
queryTrackStr = choices.history if choices.trackSource == 'history' else choices.track
queryTrack = queryTrackStr.split(':')
geneSource = choices.geneSource
upFlankSize = downFlankSize = int(choices.flank)
print GalaxyInterface.getHtmlBeginForRuns(galaxyFn)
print GalaxyInterface.getHtmlForToggles(withRunDescription=False)
geneIntersection = GeneIntersection(genome, geneSource, queryTrack,
galaxyFn)
geneIntersection.expandReferenceTrack(upFlankSize, downFlankSize)
expansionStr = ', after expansion,' if not (
upFlankSize == downFlankSize == 0) else ''
print '<p>There are %i %s-genes that%s intersect elements from your query track (%s).</p>' % \
(geneIntersection.getNumberOfIntersectedBins(), geneSource, expansionStr, prettyPrintTrackName(queryTrack))
idFileNamer = geneIntersection.getGeneIdStaticFileWithContent()
print '<p>', idFileNamer.getLoadToHistoryLink(
'Load to history the list',
'txt'), ' of all %s IDs intersecting query track.</p>' % (
geneSource)
regFileNamer = geneIntersection.getIntersectedRegionsStaticFileWithContent(
)
print '<p>', regFileNamer.getLoadToHistoryLink(
'Load to history a BED file',
'bed'), ' of all %s gene regions intersecting query track.</p>' % (
geneSource)
print GalaxyInterface.getHtmlEndForRuns()
def execute(cls, choices, galaxyFn=None, username=''):
cls._setDebugModeIfSelected(choices, galaxyFn)
with stdout_redirector(open(galaxyFn, "w", 0)):
core = HtmlCore()
core.append(GalaxyInterface.getHtmlBeginForRuns(galaxyFn))
core.append(
GalaxyInterface.getHtmlForToggles(withRunDescription=False))
core.styleInfoBegin(styleClass='debug')
core.paragraph(
'GalaxyInterface.startPreProcessing({}, {}, {})'.format(
choices.genome, choices.track, username))
print core
if choices.parsingError == cls.MOVE_TO_PARSING_ERROR_CHOICE:
finished = False
while not finished:
DebugConfig.PASS_ON_PREPROCESS_EXCEPTIONS = True
try:
GalaxyInterface.startPreProcessing(
choices.genome, choices.track, username)
finished = True
except (PreprocessWarning, PreprocessError) as e:
print e
match = re.search("trackName=\"([^\"]+)\"", str(e))
if match:
trackName = match.group(1).split(':')
PlainMover().parseFiles(choices.genome,
trackName,
direction='std_to_error')
else: # cls.DO_NOTHING_CHOICE
GalaxyInterface.startPreProcessing(choices.genome,
choices.track, username)
core = HtmlCore()
core.styleInfoEnd()
core.script('done = true;')
core.end()
print core
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.application.GalaxyInterface import GalaxyInterface
from proto.hyperbrowser.HtmlCore import HtmlCore
print GalaxyInterface.getHtmlBeginForRuns(galaxyFn)
print GalaxyInterface.getHtmlForToggles(withRunDescription=False)
print str(HtmlCore().styleInfoBegin(styleClass='debug'))
from quick.application.ExternalTrackManager import ExternalTrackManager
datasetId = ExternalTrackManager.extractIdFromGalaxyFn(ExternalTrackManager.extractFnFromGalaxyTN(choices[0]))[1]
#print datasetId
#print choices
##batchid = index for kjoering i batch. Ikke-batch-kjoering: 0
#batchid = 0
##mapId = Definer hva slags type innhold i Google map-bokser (naar du trykker). Innholdet er definert (hardkodet) i GoogleMapsInterface.py: getHtmlText() og getClusterHtmlText()
##Eks: encode_tf_vs_tf
if choices[1] != 'make new map id':
mapId = choices[1]
else:
mapId = choices[2]
from quick.application.ExternalTrackManager import ExternalTrackManager
histHtml = open(ExternalTrackManager.extractFnFromGalaxyTN(choices[0].split(':'))).read()
#rowTrackName = histHtml.split('<h3>TRACK 1</h3>')[-1].split('</b>')[1].split('\n')[0].strip()#.split(':')
#colTrackName = histHtml.split('<h3>TRACK 2</h3>')[-1].split('</b>')[1].split('\n')[0].strip()#.split(':')
from quick.application.GalaxyInterface import GalaxyInterface
batchLine = histHtml.split('<h3>CORRESPONDING BATCH COMMAND LINE</h3>')[-1].split('<p>')[1].split('/p')[0].strip()
genome = histHtml.split('<h3>GENOME</h3>')[-1].split('name:</b>')[1].split('<')[0].strip()
fullAccess = GalaxyInterface.userHasFullAccess(username)
from quick.batch.BatchRunner import BatchRunner
batchContents = BatchRunner.parseBatchLine(batchLine, genome, fullAccess)
rowTrackName = ':'.join(batchContents.cleanedTrackName1)
colTrackName = ':'.join(batchContents.cleanedTrackName2)
from quick.extra.CreateGoogleMapType import createMapType
createMapType(mapId, genome, rowTrackName, colTrackName, 'None', 'None', 'None')
from config.Config import HB_SOURCE_CODE_BASE_DIR
GMapInterfaceFn = HB_SOURCE_CODE_BASE_DIR+'/quick/extra/GoogleMapsInterface.py'
GMapInterfaceContent = open(GMapInterfaceFn).read()
replaceStr = "'%s', 'encode_gwas_vs_dhs'" % mapId
GMapInterfaceContent = GMapInterfaceContent.replace("'encode_gwas_vs_dhs'", replaceStr)
open(GMapInterfaceFn,'w').write(GMapInterfaceContent)
#title = navn paa Regulomet slik brukeren ser det, Eks: "ENCODE test, TFs vs TFs"
title = choices[3]
##name = navn paa katalog for google map: Eks: encode_test_tf_vs_tf
name = choices[4]
from quick.extra.CreateGoogleMap import GoogleMapCreator
from quick.extra.GoogleMapsInterface import Map
onMedSeqProd = False
#batchid
creator = GoogleMapCreator(name, datasetId, mapId, genome=genome)
creator.tile(onMedSeqProd)
creator.copyResultFiles()
creator.createResultShelves()
creator.createIndexFile(title, genome)
creator.fixPermissions()
print str(HtmlCore().styleInfoEnd())
map = Map(name)
row = []
row.append( str(HtmlCore().link(map.getPrettyName(), map.getUrl())) )
row.append( str(HtmlCore().link('Run description', map.getRunDescriptionUrl())) )
row.append( str(HtmlCore().link('Counts', map.getCountUrl())) )
row.append( str(HtmlCore().link('Effect size', map.getEffectSizeUrl())) )
row.append( str(HtmlCore().link('P-values', map.getPvalUrl())) )
core = HtmlCore()
core.tableHeader(None)
core.tableLine(row)
core.tableFooter()
print core
print GalaxyInterface.getHtmlEndForRuns()
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.
'''
genome = choices[0]
regSpec = '__chrs__'
binSpec = '*'
if choices[6] == 'Chromosome arms':
regSpec = '__chrArms__'
elif choices[6] == 'Track from history...':
#put in history bins support here
#print choices[4:]
regSpec = ExternalTrackManager.extractFileSuffixFromGalaxyTN(choices[7].split(':'))
binSpec = ExternalTrackManager.extractFnFromGalaxyTN(choices[7].split(':'))
#print 'regSpec, binSpec,', regSpec, binSpec
lineList, counter, tooManyBins = [], 0, False
for line in open(binSpec):
if line.strip() !='':
if counter == cls.MAX_NUM_ROWS:
tooManyBins = True
break
lineList.append(line)
counter+= 1 if line.strip()[0] !='#' else 0
if tooManyBins:
newHist = GalaxyRunSpecificFile(['newHistFile.%s' % regSpec], galaxyFn)
binSpec = newHist.getDiskPath(ensurePath=True)
open(binSpec, 'w').write(''.join(lineList))
print GalaxyInterface.getHtmlBeginForRuns(galaxyFn)
print GalaxyInterface.getHtmlForToggles(withRunDescription=False)
core = HtmlCore()
core.styleInfoBegin(styleClass='debug')
figImage = GalaxyRunSpecificFile(['VizTrackOnGenome.png'], galaxyFn)
#StaticImage(['VizTrackOnGenome.png'])
analysisDef = ' [normalizeRows=%s] [centerRows=%s] -> RawVisualizationDataStat' % \
(choices[4] == 'Scale to same size', choices[5] == 'Center')
if choices[1] == 'HyperBrowser repository':
trackName = choices[2].split(':')
else:
trackName = ExternalTrackManager.getPreProcessedTrackFromGalaxyTN(genome, choices[3].split(':'))
res = GalaxyInterface.runManual([trackName], analysisDef, regSpec, binSpec, genome, username=username, printResults=False, printHtmlWarningMsgs=False)
core.styleInfoEnd()
core.line('')
core.tableHeader(None)
#visPresenter = RawVisualizationPresenter(res, galaxyFn,'')#os.path.split()[0]
#htmlStreng = visPresenter.getReference('Result', fullImage=True)
rScript = cls.customRExecution(res, figImage.getDiskPath(ensurePath=True), '')
figUrl = figImage.getURL()
figLinkText ='<img src="%s" alt="Figure" height="%i" width="800"/>' % (figUrl, 20 *min(cls.MAX_NUM_ROWS, len(res)))
core.tableLine([figImage.getLink(figLinkText)])
rScriptGalaxyFile = GalaxyRunSpecificFile(['RScript.R'], galaxyFn)
with open(rScriptGalaxyFile.getDiskPath(ensurePath=True), 'w') as rScriptFile:
rScriptFile.write(rScript)
core.tableLine([rScriptGalaxyFile.getLink('R script')])
core.tableFooter()
print core
print GalaxyInterface.getHtmlEndForRuns()
