コード例 #1
0
ファイル: mergeBamsE3.py プロジェクト: sirusb/uniformAnalysis
# TODO: Do we really need to track replicate numbers?

import os, sys
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.mergeBamStep import MergeBamStep

###############
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')
        MergeBamStep(ana).writeVersions(allLevels=True)  # Prints to stdout
    else:
        print "Can't locate " + settingsFile
    exit(0)

galaxyInputBamA = sys.argv[1]
repA = sys.argv[2]
galaxyInputBamB = sys.argv[3]
repB = sys.argv[4]
galaxyOutMergedBam = sys.argv[5]
genome = sys.argv[6]
expType = sys.argv[7]
anaId = sys.argv[8]

# No longer command line parameters:
コード例 #2
0
#                               <signalOutUniq[Minus]> [<signalOutUniqPlus>] <statsOutput> \
#                               <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]
コード例 #3
0
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]
コード例 #4
0
import os, sys
import json
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.hotspotStep import HotspotStep

###############
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')
        HotspotStep(ana).writeVersions(allLevels=True)  # Prints to stdout
    else:
        print "Can't locate " + settingsFile
    exit(0)

galaxyInputFile = sys.argv[1]
galaxyEvalFile = sys.argv[2]  # Look up paired, tagLength
galaxyOutputHot = sys.argv[3]
galaxyOutputPeaks = sys.argv[4]
galaxyOutputDensity = sys.argv[5]
fullOrSample = sys.argv[6]
genome = sys.argv[7]
expType = sys.argv[8]
repNo = sys.argv[9]
anaId = sys.argv[10]
コード例 #5
0
import os, sys
import json
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.fastqValidationStep import FastqValidationStep

###############
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')
        FastqValidationStep(ana).writeVersions(
            allLevels=True)  # Prints to stdout
    else:
        print "Can't locate " + settingsFile
    exit(0)

# Command line args:
galaxyInputFile = sys.argv[1]
galaxyOutputHtml = sys.argv[2]
galaxyOutputDir = sys.argv[3]
galaxyOutSummary = sys.argv[4]
genome = sys.argv[5]
expType = sys.argv[6]
repNo = sys.argv[7]
anaId = sys.argv[8]
コード例 #6
0
ファイル: bwaAlignE3.py プロジェクト: sirusb/uniformAnalysis
import os, sys
import json
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.bwaAlignmentStep import BwaAlignmentStep

###############
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'
        BwaAlignmentStep(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
galaxyOutputFile = sys.argv[4]
gender = sys.argv[5]
genome = sys.argv[6]
expType = sys.argv[7]
repNo = sys.argv[8]
コード例 #7
0
#  Usage: python(2.7) bamToBigWigE3,py <inputBam> <bamEvalFile> <readFilter> <strand> \
#                                      <galaxyOutSignal> <genome> <expType> <repNo> <analysisId>

import os, sys
import json
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.bamToBwStep import BamToBwStep

###############
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')
        BamToBwStep(ana).writeVersions(allLevels=True) # Prints to stdout
    else:
        print "Can't locate " + settingsFile
    exit(0)

galaxyInputFile     = sys.argv[1]
galaxyEvalFile      = sys.argv[2]
readFilter          = sys.argv[3]
strand              = sys.argv[4]
galaxyOutSignal     = sys.argv[5]
genome              = sys.argv[6]
expType             = sys.argv[7]
repNo               = sys.argv[8]
anaId               = sys.argv[9]
コード例 #8
0
#                                      <genome> <expType> <repNo> <analysisId>

import os, sys
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.bamEvaluateStep import BamEvaluateStep

###############
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')
        BamEvaluateStep(ana).writeVersions(allLevels=True)  # Prints to stdout
    else:
        print "Can't locate " + settingsFile
    exit(0)

galaxyInputFile = sys.argv[1]
galaxyOutBamEval = sys.argv[2]
genome = sys.argv[3]
expType = sys.argv[4]
repNo = sys.argv[5]
anaId = sys.argv[6]

# No longer command line parameters:
scriptPath = os.path.split(os.path.abspath(sys.argv[0]))[0]
galaxyPath = '/'.join(scriptPath.split('/')[:-2])