Example #1
0
def run(args):
    logging.basicConfig(level=logging.DEBUG) 
    fin=IO.fopen(args.input,"r")
    out=IO.fopen(args.output,"w")
    bam=DBI.init(args.bam,"bam");
    beds=[i for i in TableIO.parse(fin,"bed12")]
    beds.sort()
    bp=args.bp
    print("mapped:{}".format(bam.mapped))
    print("unmapped:{}".format(bam.unmapped))
    data={}
    for i,x in enumerate(iter_cluster(beds)):
        print("{}\t{}:{}-{}".format(i+1,x["chr"],x["start"]+1,x["stop"]))
        '''
        cds=[z.cds() for z in x["beds"] if z.cds()]
        utr3=[z.utr3() for z in x["beds"] if z.utr3()]
        utr5=[z.utr5() for z in x["beds"] if z.utr5()]
        '''
        
        coords = [ up_down_coordinate(gene,args.bp,args.bp) for gene in x["beds"] ]
        for j,y in enumerate(coords):
            data[y.id]={}
            data[y.id]["coord"]=y
            data[y.id]["values"]=[0.0 for l in range(y.cdna_length())];
        coord_beds = [ _translate(coord,bed) for coord,bed in itertools.izip(coords,x["beds"])]
        for j,read in enumerate(bam.query(method="bam1",chr=x["chr"],start=x["start"]-args.bp,stop=x["stop"]+args.bp,strand=args.strand)):
            NM=getNM(read)  # number of hits
            NC=0            # number of compatible 
            c_coords=[]
            for k,coord in enumerate(coords):
                if overlap(read,coord) and compatible(read,coord): # don't consider the reads extend out of coords.
                    NC+=1
                    c_coords.append(k)
            for k,c in enumerate(c_coords):
                coord=coords[c]
                if read.start < coord.start or read.stop > coord.stop:
                    start=max(read.start,coord.start)
                    stop=min(read.stop,coord.stop)
                    read=read._slice(start,stop)
                read_in_coord = _translate(coord,read)
                for l in xrange(read_in_coord.start,read_in_coord.stop):
                    data[coord.id]["values"][l]+=1.0/NC/NM
        for j,y in enumerate(coords):
            print(data[y.id]["coord"])
            print(data[y.id]["values"])

    '''
Example #2
0
def compatible_with_group(i,group):
    for j in group:
        if not compatible(i,j):
            return False
    return True