Ejemplos de parRun en Python

Ejemplo n.º 1

Archivo: pipeline.runLinkFiltered.py Proyecto: combiochem/ResearchScripts

import bioLibCG
import sys
from parRun import parRun
from checkExit import parClean
import subprocess

#fN and Init
oFN = sys.argv[1]
aFN = sys.argv[2] 
aFilteredFN = aFN  #+ '.filtered'

timer = bioLibCG.cgTimer()
timer.start()


#link oRNA to filteredTargets
print 'linking oRNA to filtered targets'
parRun(1, 'LOCAL', '/home/chrisgre/scripts/endoClip/siRnaPredictFlat.py', 'updateTargetIDsFiltered', oFN, aFilteredFN)
#parClean(oFN, 30)
print timer.split()

Ejemplo n.º 2

Archivo: pipeline.k50SimulationFlat.py Proyecto: combiochem/ResearchScripts

oFN = sys.argv[1]
aFN = sys.argv[2] 

seqFN = sys.argv[3] 
tFN = '/home/chrisgre/scripts/alignSeqs/dRNA.results.updated'

timer = bioLibCG.cgTimer()
timer.start()


#initialize oRNA
blankIDs.blankIDs(seqFN, oFN)

#initializing alignments
print '...appending T Info'
parRun(30, 3, '/home/chrisgre/scripts/alignSeqs/cgAlignmentFlat.py', 'appendTInfo', aFN, tFN)
parClean(aFN, 30)
print '...appending Tran Info'
parRun(30, 3, '/home/chrisgre/scripts/alignSeqs/cgAlignmentFlat.py', 'appendTranInfo', aFN, tFN)
parClean(aFN, 30)
print timer.split()


print '...updating paired interactions: centered mismatches and center expression'
parRun(30, 5, '/home/chrisgre/scripts/alignSeqs/updateMismatchAndMiddleFlat.py', 'markCenterExpression', aFN, '/home/chrisgre/smallLibs/siRNA/degradome/wigsk50')
parClean(aFN, 30)
print timer.split()
parRun(30, 3, '/home/chrisgre/scripts/alignSeqs/updateMismatchAndMiddleFlat.py', 'markMismatchedPairs', aFN)
parClean(aFN, 30)
print timer.split()

Ejemplo n.º 3

Archivo: pipeline.filterAlignments.py Proyecto: JasonAng/ResearchScripts

import bioLibCG
import sys
from parRun import parRun
from checkExit import parClean
import subprocess

#fN and Init
aFN = sys.argv[1] 
aFilteredFN = sys.argv[2]
cLevel = sys.argv[3]

timer = bioLibCG.cgTimer()
timer.start()

#filter targets
print 'filtering targets'
parRun(5, 3, '/home/chrisgre/scripts/endoClip/filteringFlat.py', 'filterTargetsInPlace', aFN, 'True', '1', '1', '.%s' % cLevel)
parClean(aFN, 5)
print timer.split()

#make db smaller
print 'truncating db'
subprocess.Popen(['/home/chrisgre/scripts/endoClip/truncate.filterAlignments.sh', aFN, aFilteredFN]).wait()
print timer.split()

Ejemplo n.º 4

import bioLibCG
import sys
from parRun import parRun
from checkExit import parClean
import subprocess
import blankIDs

#fN and Init
oFN = sys.argv[1]
aFN = sys.argv[2]
aFilteredFN = aFN  #+ '.filtered'
seqFN = sys.argv[3]

timer = bioLibCG.cgTimer()
timer.start()

#create oRNA file(simulated only)
blankIDs.copyIDs(seqFN, oFN)

#link oRNA to filteredTargets
print 'linking oRNA to filtered targets'
parRun(1, 'LOCAL', '/home/chrisgre/scripts/endoClip/siRnaPredictFlat.py',
       'updateTargetIDsFiltered', oFN, aFilteredFN)
#parClean(oFN, 30)
print timer.split()

Ejemplo n.º 5

Archivo: pipeline.updateAlignments.split.py Proyecto: JasonAng/ResearchScripts

import sys
import blankIDs
from parRun import parRun
from checkExit import parClean


#files and init
aFN = sys.argv[1] 
dFN = sys.argv[2]

timer = bioLibCG.cgTimer()
timer.start()


#initializing alignments
'''
print '...appending T Info'
parRun(50, 3, '/home/chrisgre/myLibs/cgAlignmentFlat.py', 'appendTInfoFlat', aFN, dFN)
parClean(aFN, 50)
print timer.split()
'''

print '...updating paired interactions: centered mismatches and center expression'
parRun(40, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markCenterExpression', aFN, '/home/chrisgre/smallLibs/siRNA/degradome/wigsk50')
parClean(aFN, 40)
print timer.split()

'''
parRun(50, 3, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markMismatchedPairs', aFN)
parClean(aFN, 50)
print timer.split()

Ejemplo n.º 6

Archivo: pipeline.updateAlignments.split.py Proyecto: sknyx/ResearchScripts

import bioLibCG
import sys
import blankIDs
from parRun import parRun
from checkExit import parClean

#files and init
aFN = sys.argv[1]
dFN = sys.argv[2]

timer = bioLibCG.cgTimer()
timer.start()

#initializing alignments
'''
print '...appending T Info'
parRun(50, 3, '/home/chrisgre/myLibs/cgAlignmentFlat.py', 'appendTInfoFlat', aFN, dFN)
parClean(aFN, 50)
print timer.split()
'''

print '...updating paired interactions: centered mismatches and center expression'
parRun(40, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py',
       'markCenterExpression', aFN,
       '/home/chrisgre/smallLibs/siRNA/degradome/wigsk50')
parClean(aFN, 40)
print timer.split()
'''
parRun(50, 3, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markMismatchedPairs', aFN)
parClean(aFN, 50)
print timer.split()

Ejemplo n.º 7

Archivo: pipeline.updateAlignments.py Proyecto: sknyx/ResearchScripts

import blankIDs
from parRun import parRun
from checkExit import parClean
from checkExit import parCleanSplit
from splitRun import splitRun

#files and init
aFN = sys.argv[1]
dFN = sys.argv[2]

timer = bioLibCG.cgTimer()
timer.start()

#initializing alignments
print '...appending T Info'
parRun(5, 3, '/home/chrisgre/myLibs/cgAlignmentFlat.py', 'appendTInfoFlat',
       aFN, dFN)
parCleanSplit(aFN, 5)
print timer.split()

print '...updating paired interactions:  center expression'
#splitRun(aFN, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markCenterExpression', 'splitFN', '/home/chrisgre/smallLibs/siRNA/degradome/wigsk50')
#splitRun(aFN, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markCenterExpression', 'splitFN', '/home/chrisgre/smallLibs/siRNA/degradome/HeLa/wigs.3t7n0m20k20b.contigFiltered')
splitRun(aFN, 5,
         '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py',
         'markCenterExpression', 'splitFN',
         '/home/chrisgre/data/Lab_Data/U87/result_primary/wigs.n0m20k20b')
parCleanSplit(aFN, 5)
print timer.split()

print '...updating paired interactions:  center mismatch'
splitRun(aFN, 3,

Ejemplo n.º 8

import bioLibCG
import sys
from parRun import parRun
from checkExit import parClean
import subprocess

#fN and Init
aFN = sys.argv[1]
aFilteredFN = sys.argv[2]
cLevel = sys.argv[3]

timer = bioLibCG.cgTimer()
timer.start()

#filter targets
print 'filtering targets'
parRun(5, 3, '/home/chrisgre/scripts/endoClip/filteringFlat.py',
       'filterTargetsInPlace', aFN, 'True', '1', '1', '.%s' % cLevel)
parClean(aFN, 5)
print timer.split()

#make db smaller
print 'truncating db'
subprocess.Popen([
    '/home/chrisgre/scripts/endoClip/truncate.filterAlignments.sh', aFN,
    aFilteredFN
]).wait()
print timer.split()

Ejemplo n.º 9

import updateDegPeaks as degPeaks
import sys
import blankIDs
from parRun import parRun
from checkExit import parClean


dRNAFN = sys.argv[1]
peakFN = sys.argv[2]
seqFN = sys.argv[3]

timer = bioLibCG.cgTimer()
timer.start()

#initialize oRNA database
print 'make blank IDs'
blankIDs.blankIDs(seqFN, dRNAFN)
print 'sequence'
degPeaks.updateSequence(dRNAFN, seqFN)
print 'tcc'
degPeaks.updateTcc(dRNAFN, peakFN)
print 'eLevel'
degPeaks.updateELevel(dRNAFN, '/home/chrisgre/smallLibs/siRNA/degradome/wigsk50')
print 'gSequence'
degPeaks.updateGSequence(dRNAFN)

print 'gScore'
parRun(50, 3, '/home/chrisgre/scripts/endoClip/updateDegPeaks.py', 'updateGScore', dRNAFN)
parClean(dRNAFN, 50)

Ejemplo n.º 10

Archivo: pipeline.updateAlignments.py Proyecto: JasonAng/ResearchScripts

import blankIDs
from parRun import parRun
from checkExit import parClean
from checkExit import parCleanSplit
from splitRun import splitRun

#files and init
aFN = sys.argv[1] 
dFN = sys.argv[2]

timer = bioLibCG.cgTimer()
timer.start()


#initializing alignments
print '...appending T Info'
parRun(5, 3, '/home/chrisgre/myLibs/cgAlignmentFlat.py', 'appendTInfoFlat', aFN, dFN)
parCleanSplit(aFN, 5)
print timer.split()

print '...updating paired interactions:  center expression'
#splitRun(aFN, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markCenterExpression', 'splitFN', '/home/chrisgre/smallLibs/siRNA/degradome/wigsk50')
splitRun(aFN, 5, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markCenterExpression', 'splitFN', '/home/chrisgre/smallLibs/siRNA/degradome/Bracken/wigs/kidney')
parCleanSplit(aFN, 5)
print timer.split()

print '...updating paired interactions:  center mismatch'
splitRun(aFN, 3, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markMismatchedPairs', 'splitFN')
parClean(aFN, 5)
print timer.split()

Ejemplo n.º 11

Archivo: pipeline.k50DataSimulation.py Proyecto: JasonAng/ResearchScripts

"""Also assumes that the results files have been made..."""
oFN = runName + "/oRNA.data"
aFN = runName + "/all.aligned.0.5.tabs"

seqFN = runName + "/oRNA.sequences"
tFN = runName + "/dRNA.results"

timer = bioLibCG.cgTimer()
timer.start()

# initialize oRNA
blankIDs.blankIDs(seqFN, oFN)

# initializing alignments
print "...appending T Info"
parRun(40, 3, "/home/chrisgre/scripts/alignSeqs/cgAlignmentFlat.py", "appendTInfo", aFN, tFN)
parClean(aFN, 40)
print "...appending Tran Info"
parRun(40, 3, "/home/chrisgre/scripts/alignSeqs/cgAlignmentFlat.py", "appendTranInfo", aFN, tFN)
parClean(aFN, 40)
print timer.split()


print "...updating paired interactions: centered mismatches and center expression"
parRun(
    30,
    4,
    "/home/chrisgre/scripts/alignSeqs/updateMismatchAndMiddleFlat.py",
    "markCenterExpression",
    aFN,
    "/home/chrisgre/smallLibs/siRNA/degradome/wigsk50",