def rawsort(ifile,sort_ofile,gfile,format,step=10,suppress=False,buffer=None):
tm=time()
if format=='wig':
print('\nconverting',ifile,'...')
raw_ofile=sort_ofile[:-3]+'raw.wiq'
wg=Wig(file=ifile,gfile=gfile,step=step,suppress=suppress)
wg.ajust_size(gfile=gfile)
wg.save(file=raw_ofile,format="wiq",step=step,suppress=suppress)
print('time cost:',time()-tm)
tm=time()
else:raw_ofile=ifile
print('\nsorting',raw_ofile,'...')
temp=ifile[:-3]+'temp'
while os.path.isdir(temp):temp=temp+'.temp'
os.mkdir(temp)
if buffer!=None:cmd='sort -r -n -s -k1 -k2 -o '+sort_ofile+' --buffer-size '+str(buffer)+' --temporary-directory '+str(temp)+' '+raw_ofile
else:cmd='sort -r -n -s -k1 -k2 -o '+sort_ofile+' --temporary-directory '+str(temp)+' '+raw_ofile
os.system(cmd)
if format=='wig':
print('Removing ',raw_ofile,'...')
os.system('rm '+raw_ofile)
print('removing',temp)
os.system('rm '+str(temp)+' -r')
print('time cost:',time()-tm)
def rawsort(ifile,sort_ofile,gfile,format,step=10,suppress=False,buffer=None):
tm=time()
if format=='wig':
print '\nconverting',ifile,'...'
raw_ofile=sort_ofile[:-3]+'raw.wiq'
wg=Wig(file=ifile,gfile=gfile,step=step,suppress=suppress)
wg.ajust_size(gfile=gfile)
wg.save(file=raw_ofile,format="wiq",step=step,suppress=suppress)
print 'time cost:',time()-tm
tm=time()
else:raw_ofile=ifile
print '\nsorting',raw_ofile,'...'
temp=ifile[:-3]+'temp'
while os.path.isdir(temp):temp=temp+'.temp'
os.mkdir(temp)
if buffer!=None:cmd='sort -r -n -s -k1 -k2 -o '+sort_ofile+' --buffer-size '+str(buffer)+' --temporary-directory '+str(temp)+' '+raw_ofile
else:cmd='sort -r -n -s -k1 -k2 -o '+sort_ofile+' --temporary-directory '+str(temp)+' '+raw_ofile
os.system(cmd)
if format=='wig':
print 'Removing ',raw_ofile,'...'
os.system('rm '+raw_ofile)
print 'removing',temp
os.system('rm '+str(temp)+' -r')
print 'time cost:',time()-tm
def changevalue(ifile,
ref,
ofile,
gfile,
step=10,
suppress=False,
buffer=None):
from random import randint
if ifile != ref: print('\nnormalizing', ifile, '...')
else: print('\nsaving reference ...')
tm = time()
fi, fr = open(ifile), open(ref)
wg = Wig(step=step, gfile=gfile)
for line in fi:
col = line.split()
rcol = fr.readline().split()
if len(rcol) == 0: rcol = [0.0]
cr, pos, vl = col[2], int(col[3]) / step, float(rcol[0])
wg.data[cr][pos] = vl
n = 0
for line in fr:
n += 1
if n > 0:
print(
'Warning: the input genome size is smaller than the reference genome size by',
n, 'wiggle steps!')
wg.save(ofile, suppress=suppress)
print('time cost:', time() - tm)
def changevalue(ifile,ref,ofile,gfile,step=10,suppress=False,buffer=None):
from random import randint
if ifile!=ref:print '\nnormalizing',ifile,'...'
else:print '\nsaving reference ...'
tm=time()
fi,fr=open(ifile),open(ref)
wg=Wig(step=step,gfile=gfile)
for line in fi:
col=line.split()
rcol=fr.readline().split()
if len(rcol)==0:rcol=[0.0]
cr,pos,vl=col[2],int(col[3])/step,float(rcol[0])
wg.data[cr][pos]=vl
n=0
for line in fr:n+=1
if n>0:print 'Warning: the input genome size is smaller than the reference genome size by',n,'wiggle steps!'
wg.save(ofile,suppress=suppress)
print 'time cost:',time()-tm