def plainRun(analysisDef, genome, track1Fn, track2Fn):
'''
Currently under development, not yet functioning.
Note that file names (track1Fn, track2Fn) must either be a valid .dat-file from a Galaxy system,
or be located in a path where the two deepest levels are numerical values above 1000, and unique between different runs by this tool'''
#GalaxyInterface.runManual(trackNames, analysisDef, regSpec, binSpec, genome, galaxyFn=None, trackNameIntensity=None, username='', \
#printResults=True, printProgress=True, printHtmlWarningMsgs=True, applyBoundaryFilter=False, printRunDescription=True, **kwArgs):
from quick.application.ExternalTrackManager import ExternalTrackManager
#fixme: is this correct?
assert all(
idPart > 1000
for idPart in ExternalTrackManager.extractIdFromGalaxyFn(track1Fn))
tn1 = ExternalTrackManager.constructGalaxyTnFromSuitedFn(track1Fn)
assert all(
idPart > 1000
for idPart in ExternalTrackManager.extractIdFromGalaxyFn(track2Fn))
tn2 = ExternalTrackManager.constructGalaxyTnFromSuitedFn(track2Fn)
from quick.application.GalaxyInterface import GalaxyInterface
userBinSource = GalaxyInterface._getUserBinSource('chrs', '*', genome, tn1,
tn2)
from gold.application.StatRunner import AnalysisDefJob
job = AnalysisDefJob(analysisDef, tn1, tn2, userBinSource)
result = job.run(printProgress=False)
return result
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()
