Exemplo n.º 1
0
from bedtools import findBedAlignmentsByName
from rpkm import rpkm

if __name__ == "__main__":
	
	opts,args = getopt(sys.argv[1:],'')
	
	if len(args) < 3:
		print "bedRPKM.py alignment.bed uniqueLocations.bed totalAlignments"
		sys.exit()
	
	alignmentFile = args[0]
	uniqueFile = args[1]
	total = int(args[2])
	
	alignments = findBedAlignmentsByName(alignmentFile)
	pseudogenes = findBedAlignmentsByName(uniqueFile)
	
	for gene in alignments.keys():
		if gene in alignments and gene in pseudogenes:

			alignLine = alignments[gene][0]
			#find the beginning and end of the gene
			minStart,maxEnd = 987654321,0
			for line in alignments[gene]:
				if line.start < minStart:
					minStart = line.start
				if line.end > maxEnd:
					maxEnd = line.end
			chrom = alignLine.chrom
			count = sum([line.thickStart for line in alignments[gene]])#alignments[gene][0].thickStart
Exemplo n.º 2
0
opts,args = getopt.getopt(sys.argv[1:],'')
for opt,arg in opts:
	if opt == "-r":
		rpgenes = True
geneFile = args[0]
alignmentFile = args[1]

genes = []
"""
if not rpgenes:
	genes = pseudogenes.load_all()
else:
	genes = rpgenes.load_all()
"""
genes = bedtools.findBedAlignmentsByName(geneFile)
	
for k in genes.keys():
	
	total = 0
	mn = 987654321
	mx = 0
	for gene in genes[k]:
		if gene.start < mn:
			mn = gene.start
		if gene.end > mx:
			mx = gene.end
		alignments = samtools.findBamAlignments(alignmentFile,gene.chrom,gene.start,gene.end)
		for alignment in alignments:
			if alignment > 0:
				total+=1