def __call__(self, **kw):
# Set assembly
assembly_id = kw.get('assembly')
chrmeta = "guess"
if assembly_id:
assembly = genrep.Assembly(assembly_id)
chrmeta = assembly.chrmeta
# Set features track
features = track(kw['features'], chrmeta=chrmeta or None)
chrmeta = features.chrmeta
# Set filter track
filter = track(kw.get('filter'), chrmeta=chrmeta or None)
# Main
format = kw.get('format', features.format)
output = self.temporary_path(fname=features.name + '_filtered.' +
format)
tout = track(output,
format,
fields=filter.fields,
chrmeta=chrmeta,
info={'datatype': 'qualitative'})
for chrom in chrmeta:
tout.write(overlap(features.read(chrom), filter.read(chrom)),
chrom=chrom,
clip=True)
tout.close()
self.new_file(output, 'filtered')
return self.display_time()
def test_overlap(self):
s1 = [('chr',0,4,'n',1.), ('chr',7,12,'n',2.), ('chr',16,19,'n',3.), ('chr',22,27,'n',4.)]
s2 = [('chr',2,9,'m'), ('chr',13,14,'m'), ('chr',22,23,'m'), ('chr',26,27,'m')]
stream1 = fstream(s1, fields=['chr','start','end','name','score'])
stream2 = fstream(s2, fields=['chr','start','end','name'])
res = overlap(stream1,stream2)
expected = [('chr',0,4,'n',1.),('chr',7,12,'n',2.),('chr',22,27,'n',4.)]
self.assertListEqual(list(res),expected)
# Stranded
s1 = [('chr',0,3,'+'), ('chr',7,12,'+'), ('chr',16,19,'+'), ('chr',22,27,'+')]
s2 = [('chr',2,9,'+'), ('chr',13,14,'-'), ('chr',25,30,'-')]
stream1 = fstream(s1, fields=['chr','start','end','strand'])
stream2 = fstream(s2, fields=['chr','start','end','strand'])
res = overlap(stream1,stream2)
expected = [('chr',0,3,'+'),('chr',7,12,'+')]
self.assertListEqual(list(res),expected)
def test_overlap(self):
s1 = [('chr', 0, 4, 'n', 1.), ('chr', 7, 12, 'n', 2.),
('chr', 16, 19, 'n', 3.), ('chr', 22, 27, 'n', 4.)]
s2 = [('chr', 2, 9, 'm'), ('chr', 13, 14, 'm'), ('chr', 22, 23, 'm'),
('chr', 26, 27, 'm')]
stream1 = fstream(s1, fields=['chr', 'start', 'end', 'name', 'score'])
stream2 = fstream(s2, fields=['chr', 'start', 'end', 'name'])
res = overlap(stream1, stream2)
expected = [('chr', 0, 4, 'n', 1.), ('chr', 7, 12, 'n', 2.),
('chr', 22, 27, 'n', 4.)]
self.assertListEqual(list(res), expected)
# Stranded
s1 = [('chr', 0, 3, '+'), ('chr', 7, 12, '+'), ('chr', 16, 19, '+'),
('chr', 22, 27, '+')]
s2 = [('chr', 2, 9, '+'), ('chr', 13, 14, '-'), ('chr', 25, 30, '-')]
stream1 = fstream(s1, fields=['chr', 'start', 'end', 'strand'])
stream2 = fstream(s2, fields=['chr', 'start', 'end', 'strand'])
res = overlap(stream1, stream2)
expected = [('chr', 0, 3, '+'), ('chr', 7, 12, '+')]
self.assertListEqual(list(res), expected)
def __call__(self, **kw):
# Set assembly
assembly_id = kw.get('assembly')
chrmeta = "guess"
if assembly_id:
assembly = genrep.Assembly(assembly_id)
chrmeta = assembly.chrmeta
# Set features track
features = track(kw['features'], chrmeta=chrmeta or None )
chrmeta = features.chrmeta
# Set filter track
filter = track(kw.get('filter'), chrmeta=chrmeta or None)
# Main
format = kw.get('output',features.format)
output = self.temporary_path(fname=features.name+'_filtered.'+format)
tout = track(output, format, fields=filter.fields,
chrmeta=chrmeta, info={'datatype':'qualitative'})
for chrom in chrmeta:
tout.write(overlap(features.read(chrom),filter.read(chrom)), chrom=chrom,clip=True)
tout.close()
self.new_file(output, 'filtered')
return self.display_time()
