last = seq[size - 1].split(']')
seq[size - 1] = last[0]
# print seq[size-1]
for i in range(0, size):
# print temp
temp.append(int(seq[i]))
# print temp
entries[key] = temp
for key in entries:
# print len(entries[key])
name = key.split(' ')
i = 0
allMed = []
while i < len(entries[key]) - k:
# for i in range(0, len(entries[key]) - k, k):
seq = entries[key]
frag = seq[i:i + k]
# print i, i+k, frag, len(frag)
med = aabpPyLib.findMedian(frag)
mean, std = aabpPyLib.meanStdDev(frag)
print name[0], med, std
allMed.append(med)
i += k
mean, std = aabpPyLib.meanStdDev(allMed)
print name[0], aabpPyLib.findMedian(aabpPyLib.findLowestQuartile(allMed))
#print entries
print 'Finished!'
# print seq[size-1]
for i in range(0, size):
# print temp
temp.append(int(seq[i]))
# print temp
entries[key] = temp
for key in entries:
# print len(entries[key])
name = key.split(' ')
i = 0
allMed = []
while i < len(entries[key]) - k:
# for i in range(0, len(entries[key]) - k, k):
seq = entries[key]
frag = seq[i:i+k]
# print i, i+k, frag, len(frag)
med = aabpPyLib.findMedian(frag)
mean, std = aabpPyLib.meanStdDev(frag)
print name[0], med, std
allMed.append(med)
i += k
mean, std = aabpPyLib.meanStdDev(allMed)
print name[0], aabpPyLib.findMedian(aabpPyLib.findLowestQuartile(allMed))
#print entries
print 'Finished!'
# Author: A. Black P.
# Usage: python getSeqCoverageReal.py inputGene.fa inputReads.fa output.txt
import makeRandomTestData, os, random, sys, aabpPyLib
infileGeneName = sys.argv[1]
infileReadsName = sys.argv[2]
outfile = open(sys.argv[3], 'w')
genes = makeRandomTestData.inputFastaSeq(infileGeneName)
geneId = genes.keys()[0]
print geneId, len(genes[geneId])
geneLength = len(genes[geneId])
Coverage = [0] * geneLength
reads = makeRandomTestData.inputFastaSeq(infileReadsName)
for key in reads.keys():
positionCut = key.split('Begin')
parts = positionCut[1].split('End')
print parts
for i in range(int(parts[0]), int(parts[1])):
Coverage[i] += 1
for i in range(0, geneLength):
outfile.write(str(Coverage[i]) + '\n')
median = aabpPyLib.findMedian(Coverage)
print median
print 'Finished!'
