def process(self, **kw):
ext = kw.get('to') or 'sql'
outfile = self.temporary_path(ext=ext)
info = {'datatype': kw.get('datatype') or 'qualitative'}
convert(kw.get('infile'), outfile,
chrmeta=kw.get('assembly') or None, info=info)
self.new_file(outfile, 'converted_file')
return 1
def __call__(self, **kw):
ext = kw.get('to') or 'sql'
info = {'datatype': kw.get('datatype') or 'qualitative'}
infile = kw.get('infile')
fname = os.path.splitext(os.path.split(infile)[-1])[0]
outfile = self.temporary_path(fname=fname, ext=ext)
convert(infile, outfile,
chrmeta=kw.get('assembly') or None, info=info)
self.new_file(outfile, 'converted_file')
return self.display_time()
def __call__(self, **kw):
b2wargs = []
control = None
sample = kw.get("sample")
assert os.path.exists(str(sample)), "Bam file not found: '%s'." % sample
if kw.get('control'):
control = kw['control']
b2wargs = ["-c", str(control)]
assert os.path.exists(str(control)), "Control file not found: '%s'." % control
control = os.path.abspath(control)
sample = os.path.abspath(sample)
nreads = int(kw.get('normalization') or -1)
bamfile = track(sample, format='bam')
if nreads < 0:
if control is None:
nreads = len(set((t[4] for t in bamfile.read())))
else:
b2wargs += ["-r"]
merge_strands = int(kw.get('merge_strands') or -1)
read_extension = int(kw.get('read_extension') or -1)
output = self.temporary_path(fname='density_')
format = kw.get("format", "sql")
with execution(None) as ex:
files = bam_to_density(ex, sample, output,
nreads=nreads, merge=merge_strands,
read_extension=read_extension,
sql=True, args=b2wargs)
if merge_strands >= 0:
suffixes = ["merged"]
else:
suffixes = ["fwd", "rev"]
for n, x in enumerate(files):
tsql = track(x, format='sql', fields=['start', 'end', 'score'],
chrmeta=bamfile.chrmeta,
info={'datatype': 'quantitative'})
tsql.save()
if format == "sql":
outname = x
else:
outname = os.path.splitext(x)[0]+"."+format
convert(x, outname, mode="overwrite")
self.new_file(outname, 'density_'+suffixes[n])
return self.display_time()
