Python parClean Exemples

Exemple #1

Fichier : pipeline.k50SimulationFlat.py Projet : combiochem/ResearchScripts

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()

print 'Linking oRNA to Targets'

Exemple #2

Fichier : pipeline.filterAlignments.py Projet : 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()

Exemple #3

Fichier : pipeline.k50DataSimulation.py Projet : sknyx/ResearchScripts

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')
parClean(aFN, 30)
print timer.split()
parRun(50, 3,
       '/home/chrisgre/scripts/alignSeqs/updateMismatchAndMiddleFlat.py',

Exemple #4

Fichier : pipeline.updateAlignments.split.py Projet : sknyx/ResearchScripts

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()
'''

Exemple #5

Fichier : pipeline.updateAlignments.split.py Projet : JasonAng/ResearchScripts

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()
'''

Exemple #6

Fichier : pipeline.updateAlignments.py Projet : sknyx/ResearchScripts

#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,
         '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py',
         'markMismatchedPairs', 'splitFN')
parClean(aFN, 5)
print timer.split()

Exemple #7

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)

Exemple #8

Fichier : pipeline.k50DataSimulation.py Projet : JasonAng/ResearchScripts

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",
)