Python splitRunの例

コード例 #1

ファイル: pipeline.updateAlignments.py プロジェクト: 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()

コード例 #2

ファイル: pipeline.updateAlignments.py プロジェクト: 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()

コード例 #3

ファイル: pipeline.updateAlignments.py プロジェクト: cgreer/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, '/home/chrisgre/scripts/endoClip/updateMismatchAndMiddleFlat.py', 'markMismatchedPairs', 'splitFN')
parClean(aFN, 5)
print timer.split()