import os, sys import json from src.galaxyAnalysis import GalaxyAnalysis from src.steps.rsemStep import RsemStep ############### testOnly = False ############### if sys.argv[1] == '--version': settingsFile = os.path.split(os.path.abspath( sys.argv[0]))[0] + '/' + "settingsE3.txt" if os.path.isfile( settingsFile): # Unfortunately can't get xml arg for settings ana = GalaxyAnalysis(settingsFile, 'versions', 'hg19') ana.readType = 'paired' RsemStep(ana).writeVersions(allLevels=True) # Prints to stdout else: print "Can't locate " + settingsFile exit(0) # Command line args: galaxyBamInput = sys.argv[1] galaxyEvalFile = sys.argv[2] # Look up tagLength and encoding galaxyOutGenes = sys.argv[3] galaxyOutTrans = sys.argv[4] genome = sys.argv[5] expType = sys.argv[6] repNo = sys.argv[7] anaId = sys.argv[8]
except: pass # TODO Is this really an error? if isPaired != isPaired2: raise Exception("Evaluation files suggest that alignment and control files do not match.") # TODO: suffix needs to know whether this is being run on a sample! suffix = expType + "Rep" + repNo # Set up 'ana' so she can do all the work. If anaId matches another, then it's log is extended ana = GalaxyAnalysis(settingsFile, anaId, genome, expType) if testOnly: ana.dryRun = testOnly if isPaired: ana.readType = 'paired' else: ana.readType = 'single' # What step expects: # Inputs: 1 bam, pre-registered in analysis keyed as: 'alignment' + suffix + '.bam' # 1 bam control (optional), pre-registered keyed as: 'control' + suffix + '.bam' # Outputs: target narrowPeak peaks file, keyed as: 'peaks' + suffix + '.bigBed' # target density bigWig file, keyed as: 'density' + suffix + '.bigWig' # set up keys that join inputs through various file forwardings: bamInputKey = 'alignment' + suffix + '.bam' controlInputKey = 'control' + suffix + '.bam' peakKey = 'peaks' + suffix + '.bigBed' densityKey = 'density' + suffix + '.bigWig'
# <libId> <gender> <genome> <expType> <repNo> <analysisId> import os, sys import json from src.galaxyAnalysis import GalaxyAnalysis from src.steps.starAlignmentStep import StarAlignmentStep ############### testOnly = False ############### if sys.argv[1] == '--version': settingsFile = os.path.split( os.path.abspath( sys.argv[0] ) )[0] + '/' + "settingsE3.txt" if os.path.isfile( settingsFile ): # Unfortunately can't get xml arg for settings ana = GalaxyAnalysis(settingsFile, 'versions', 'hg19') ana.readType = 'paired' StarAlignmentStep(ana).writeVersions(allLevels=True) # Prints to stdout else: print "Can't locate " + settingsFile exit(0) # Command line args: pairedOrUnpaired = sys.argv[1] galaxyInputFile = sys.argv[2] galaxyEvalFile = sys.argv[3] # Look up tagLength and encoding galaxyGenoBamOutput = sys.argv[4] galaxyAnnoBamOutput = sys.argv[5] galaxyBwAllOut = sys.argv[6] galaxyBwUniqOut = sys.argv[7] galaxyStatsOut = sys.argv[8] libId = sys.argv[9]
pass # TODO Is this really an error? if isPaired != isPaired2: raise Exception( "Evaluation files suggest that alignment and control files do not match." ) # TODO: suffix needs to know whether this is being run on a sample! suffix = expType + "Rep" + repNo # Set up 'ana' so she can do all the work. If anaId matches another, then it's log is extended ana = GalaxyAnalysis(settingsFile, anaId, genome, expType) if testOnly: ana.dryRun = testOnly if isPaired: ana.readType = 'paired' else: ana.readType = 'single' # What step expects: # Inputs: 1 bam, pre-registered in analysis keyed as: 'alignment' + suffix + '.bam' # 1 bam control (optional), pre-registered keyed as: 'control' + suffix + '.bam' # Outputs: target narrowPeak peaks file, keyed as: 'peaks' + suffix + '.bigBed' # target density bigWig file, keyed as: 'density' + suffix + '.bigWig' # set up keys that join inputs through various file forwardings: bamInputKey = 'alignment' + suffix + '.bam' controlInputKey = 'control' + suffix + '.bam' peakKey = 'peaks' + suffix + '.bigBed' densityKey = 'density' + suffix + '.bigWig'