def test_select(self):
# by fields
stream = fstream([(10,12,0.5), (14,15,1.2)], fields=['start','end','score'])
res = list(select(stream,['score','end']))
expected = [(0.5,12),(1.2,15)]
self.assertListEqual(res,expected)
# by selection
stream = fstream([('a',10,12), ('a',14,15), ('b',16,19)], fields=['name','start','end'])
res = list(select(stream,None,{'name':['a','c']}))
expected = [('a',10,12),('a',14,15)]
self.assertListEqual(res,expected)
def test_select(self):
# by fields
stream = fstream([(10, 12, 0.5), (14, 15, 1.2)],
fields=['start', 'end', 'score'])
res = list(select(stream, ['score', 'end']))
expected = [(0.5, 12), (1.2, 15)]
self.assertListEqual(res, expected)
# by selection
stream = fstream([('a', 10, 12), ('a', 14, 15), ('b', 16, 19)],
fields=['name', 'start', 'end'])
res = list(select(stream, None, {'name': ['a', 'c']}))
expected = [('a', 10, 12), ('a', 14, 15)]
self.assertListEqual(res, expected)
def fimo(motifs,fasta,qval=True):
# Run Fimo
if qval:
options = "--max-stored-scores 1000000 --verbosity 1 --thresh 0.01 --qv-thresh"
else:
options = "--max-stored-scores 1000000 --verbosity 1 --thresh 0.000001"
cmd = "fimo " + options + " %s %s" % (motifs, fasta)
print "Running >>",cmd
os.system(cmd)
os.system("sort -k2,2n -k3,3n -k4,4n fimo_out/fimo.txt > fimo.txt")
# Bed output
t = track('fimo.txt', fields=["name","chr","start","end","strand","score","p-value","q-value","sequence"])
t.fields = ["name","chr","start","end","strand","a","score","q","sequence"]
s = t.read()
s = select(s,['chr','start','end','name','score','strand'])
s = apply(s,'chr',lambda x:x.split('|')[1])
s = sorted_stream(s)
s = cobble(s)
s = apply(s,'name',lambda x:'|'.join(list(set(x.split('|')))))
outname = 'fimo.bed'
bed = track(outname,fields=s.fields)
bed.make_header(name="TSS_motifs", description="Motifs +-XKb around TSS", mode='overwrite')
bed.write(s)
if os.path.exists("fimo_out"): shutil.rmtree("fimo_out")
def fimo(motifs, fasta, qval=True):
# Run Fimo
if qval:
options = "--max-stored-scores 1000000 --verbosity 1 --thresh 0.01 --qv-thresh"
else:
options = "--max-stored-scores 1000000 --verbosity 1 --thresh 0.000001"
cmd = "fimo " + options + " %s %s" % (motifs, fasta)
print "Running >>", cmd
os.system(cmd)
os.system("sort -k2,2n -k3,3n -k4,4n fimo_out/fimo.txt > fimo.txt")
# Bed output
t = track('fimo.txt',
fields=[
"name", "chr", "start", "end", "strand", "score", "p-value",
"q-value", "sequence"
])
t.fields = [
"name", "chr", "start", "end", "strand", "a", "score", "q", "sequence"
]
s = t.read()
s = select(s, ['chr', 'start', 'end', 'name', 'score', 'strand'])
s = apply(s, 'chr', lambda x: x.split('|')[1])
s = sorted_stream(s)
s = cobble(s)
s = apply(s, 'name', lambda x: '|'.join(list(set(x.split('|')))))
outname = 'fimo.bed'
bed = track(outname, fields=s.fields)
bed.make_header(name="TSS_motifs",
description="Motifs +-XKb around TSS",
mode='overwrite')
bed.write(s)
if os.path.exists("fimo_out"): shutil.rmtree("fimo_out")
