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'
