import siRnaPredict
import cgSort
'''
si.predictSiRNA('small.peak.data', 'siDegradome.conf')
si.updateSmallExpression('small.degradome', 'siPeaks.conf')
si.exonOverlap('small.degradome.small')
'''
'''
cgSort.sortFileCG('small.degradome.small.degOverlap', 1, rev = True)
cgSort.sortFileCG('small.degradome.small.degOverlap', 2, rev = True)
'''
'''
f = open('/home/chrisgre/smallLibs/siRNA/small/SRR029124.fastq.clipped.mapped', 'r')
for i in range(0,100):
r = f.readline()
print r
read = siRnaPredict.readInfo(r)
print read.chrom, read.strand, read.start, read.end
print read.scores, read.mismatches
print read.returnMismatchPositions()
'''
directory = '/home/chrisgre/smallLibs/siRNA/small/sortedChroms'
siRnaPredict.markMismatches('small.degradome.small.degOverlap.clean',
directory)
import siRnaPredict
import cgSort
'''
si.predictSiRNA('small.peak.data', 'siDegradome.conf')
si.updateSmallExpression('small.degradome', 'siPeaks.conf')
si.exonOverlap('small.degradome.small')
'''
'''
cgSort.sortFileCG('small.degradome.small.degOverlap', 1, rev = True)
cgSort.sortFileCG('small.degradome.small.degOverlap', 2, rev = True)
'''
'''
f = open('/home/chrisgre/smallLibs/siRNA/small/SRR029124.fastq.clipped.mapped', 'r')
for i in range(0,100):
r = f.readline()
print r
read = siRnaPredict.readInfo(r)
print read.chrom, read.strand, read.start, read.end
print read.scores, read.mismatches
print read.returnMismatchPositions()
'''
directory = '/home/chrisgre/smallLibs/siRNA/small/sortedChroms'
siRnaPredict.markMismatches('small.degradome.small.degOverlap.clean', directory)
import siRnaPredict as si import cleanup import subprocess peakFName = 'small.peak.data' smallUpdateFN = 'small.degradome' cleanFN = 'small.degradome.small' exonUpdateFN = 'small.degradome.small.clean' mismatchFN = 'small.degradome.small.clean.degOverlap' clean2FN = 'small.degradome.small.clean.degOverlap.mismatch' sortFN = 'small.degradome.small.clean.degOverlap.mismatch.clean' smallDirectory = '/home/chrisgre/smallLibs/siRNA/small/sortedChroms' print 'Getting highest level, offset, middle level' si.predictSiRNA(peakFName, 'siDegradome.conf') print 'Getting small expression level' si.updateSmallExpression(smallUpdateFN, 'siPeaks.conf') print 'cleaning' cleanup.cleanup(cleanFN) print 'Getting transcript level' si.exonOverlap(exonUpdateFN) print 'Getting mismatch levels' si.markMismatches(mismatchFN, smallDirectory) print 'Cleaning up again, and sorting' cleanup.cleanup2(clean2FN) subprocess.Popen(['./sortIt.sh', sortFN], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
