Exemplos de blankIDs em Python

Exemplo n.º 1

Arquivo: pipeline.k50SimulationFlat.py Projeto: combiochem/ResearchScripts

from checkExit import parClean


#files and init
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()

Exemplo n.º 2

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)

Exemplo n.º 3

Arquivo: pipeline.oRNABasicFlat.py Projeto: JasonAng/ResearchScripts

import updateContigsFlat 
import updateDuplicatesMultiTcc as udmt
import blankIDs


oRNAFN = sys.argv[1]
peakFN = sys.argv[2]
seqFN = sys.argv[3]
smallWigFN = sys.argv[4]

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

#initialize oRNA database
print 'make blank IDs'
blankIDs.blankIDs(seqFN, oRNAFN)
print 'sequence'
si.updateSequence(oRNAFN, seqFN)
print 'tcc'
si.updateTcc(oRNAFN, peakFN)
print 'entropy'
si.updateEntropy(oRNAFN)
#si.updateELevel(oRNAFN, '/home/chrisgre/smallLibs/siRNA/small/wigsk50')
si.updateELevel(oRNAFN, smallWigFN)

print 'contigs'
updateContigsFlat.updateTotalContig(oRNAFN)
updateContigsFlat.updateEndContig(oRNAFN)
print 'duplicates and mutlitcc'
udmt.updateSeqDuplicateMultiTcc(oRNAFN)
print timer.split()

Exemplo n.º 4

Arquivo: pipeline.oRNABasicFlat.py Projeto: sknyx/ResearchScripts

import sys
import updateContigsFlat
import updateDuplicatesMultiTcc as udmt
import blankIDs

oRNAFN = sys.argv[1]
peakFN = sys.argv[2]
seqFN = sys.argv[3]
smallWigFN = sys.argv[4]

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

#initialize oRNA database
print 'make blank IDs'
blankIDs.blankIDs(seqFN, oRNAFN)
print 'sequence'
si.updateSequence(oRNAFN, seqFN)
print 'tcc'
si.updateTcc(oRNAFN, peakFN)
print 'entropy'
si.updateEntropy(oRNAFN)
#si.updateELevel(oRNAFN, '/home/chrisgre/smallLibs/siRNA/small/wigsk50')
si.updateELevel(oRNAFN, smallWigFN)

print 'contigs'
updateContigsFlat.updateTotalContig(oRNAFN)
updateContigsFlat.updateEndContig(oRNAFN)
print 'duplicates and mutlitcc'
udmt.updateSeqDuplicateMultiTcc(oRNAFN)
print timer.split()