def __call__(self, **kw):
sample = track(kw['sample'],chrmeta="guess")
by_chrom = kw.get('by_chrom',False)
if isinstance(by_chrom, basestring):
by_chrom = (by_chrom.lower() in ['1', 'true', 't','on'])
outf = kw.get('output')
if outf not in output_list:
outf = output_list[0]
output = self.temporary_path(fname=sample.name+'_stats.'+outf)
if outf == 'txt':
out = open(output,"w")
else:
out = {}
if by_chrom:
chromlist = sample.chrmeta.keys()
else:
chromlist = [None]
for chrom in chromlist:
if outf == 'txt':
if chrom:
out.write("Chromosome %s\n--------------------\n"%chrom)
stats(sample,out=out,selection=chrom)
else:
out[chrom] = {}
stats(sample,out=out[chrom],selection=chrom)
if outf == 'txt' and chrom:
out.write("\n--------------------\n")
if outf == 'txt':
out.close()
self.new_file(output, 'stats')
else:
self._plot_pdf(output,out,sample.name)
self.new_file(output, 'pdf')
return self.display_time()
def __call__(self, **kw):
sample = track(kw['sample'],chrmeta="guess")
by_chrom = kw.get('by_chrom',False)
if isinstance(by_chrom, basestring):
by_chrom = (by_chrom.lower() in ['1', 'true', 't','on'])
outf = kw.get('output')
if outf not in output_list:
outf = output_list[0]
output = self.temporary_path(fname=sample.name+'_stats.'+outf)
if outf == 'txt':
out = open(output,"w")
else:
out = {}
if by_chrom:
chromlist = sample.chrmeta.keys()
else:
chromlist = [None]
for chrom in chromlist:
if outf == 'txt':
if chrom:
out.write("Chromosome %s\n--------------------\n"%chrom)
stats(sample,out=out,selection=chrom)
else:
out[chrom] = {}
stats(sample,out=out[chrom],selection=chrom)
if outf == 'txt' and chrom:
out.write("\n--------------------\n")
if outf == 'txt':
out.close()
self.new_file(output, 'stats')
else:
self._plot_pdf(output,out,sample.name)
self.new_file(output, 'pdf')
return self.display_time()
def stats(*args, **kw):
if len(args) < 1: raise Usage("No input file provided")
if kw['selection']:
if kw['selection'].count("{"):
jsonargs = json.loads(kw['selection'])
for k, v in jsonargs.iteritems():
if isinstance(v, basestring): jsonargs[k] = str(v)
kw['selection'] = dict(
(str(k), v) for k, v in jsonargs.iteritems())
elif kw['selection'].count(":"):
chr, coord = kw['selection'].split(':')
start, end = coord.split('-')
kw['selection'] = {
'chr': chr,
'start': (start, end),
'end': (start, end)
}
else:
kw['selection'] = str(kw['selection']).split(",")
fields = None
if kw['fields']:
fields = str(kw['fields']).split(",")
if kw['output'] is None:
output = sys.stdout
else:
output = open(kw['output'], 'w')
chrmeta = _get_chrmeta(**kw)
for infile in args:
intrack = track.track(infile, format=kw['format'], chrmeta=chrmeta)
if intrack.info:
fileinfo = ",".join(
["%s=%s" % (k, v) for k, v in intrack.info.iteritems()])
else:
fileinfo = 'None'
chromlist = ",".join(sorted(intrack.chrmeta.keys())) or "None"
fields = ",".join(intrack.fields)
output.write(\
"""*****************************************
File '%s' (%s):
Infos: %s
Chromosomes: %s
Fields: %s
*****************************************\n
""" %(os.path.basename(infile), intrack.format, fileinfo, chromlist, fields))
track.stats(intrack, out=output, **kw)
intrack.close()
output.close()
return 0
def stats(*args,**kw):
if len(args) < 1: raise Usage("No input file provided")
if kw['selection']:
if kw['selection'].count("{"):
jsonargs = json.loads(kw['selection'])
for k,v in jsonargs.iteritems():
if isinstance(v,basestring): jsonargs[k] = str(v)
kw['selection'] = dict((str(k),v) for k,v in jsonargs.iteritems())
elif kw['selection'].count(":"):
chr,coord = kw['selection'].split(':')
start,end = coord.split('-')
kw['selection'] = {'chr':chr,'start':(start,end),'end':(start,end)}
else:
kw['selection'] = str(kw['selection']).split(",")
fields = None
if kw['fields']:
fields = str(kw['fields']).split(",")
if kw['output'] is None:
output = sys.stdout
else:
output = open(kw['output'],'w')
chrmeta = _get_chrmeta(**kw)
for infile in args:
intrack = track.track(infile,format=kw['format'],chrmeta=chrmeta)
if intrack.info:
fileinfo = ",".join(["%s=%s" %(k,v) for k,v in intrack.info.iteritems()])
else: fileinfo = 'None'
chromlist = ",".join(sorted(intrack.chrmeta.keys())) or "None"
fields = ",".join(intrack.fields)
output.write(\
"""*****************************************
File '%s' (%s):
Infos: %s
Chromosomes: %s
Fields: %s
*****************************************\n
""" %(os.path.basename(infile), intrack.format, fileinfo, chromlist, fields))
track.stats(intrack,out=output,**kw)
intrack.close()
output.close()
return 0