def check(*args,**kw):
if len(args) < 1: raise Usage("No input file provided")
if kw['output'] is None: output = sys.stdout
else: output = open(kw['output'],'w')
chrmeta = _get_chrmeta(**kw)
if kw['no_overlaps'] and not kw['sorted']:
output.write("--disjoint option was ignored: --sorted is required.\n")
for infile in args:
intrack = track.track(infile, format=kw['format'], chrmeta=chrmeta)
cf = track.check(intrack, output,
check_sorted=kw['sorted'],
check_noduplicates=kw['no_duplicates'],
check_positive=kw['positive'],
check_nooverlaps=kw['no_overlaps'])
if cf: output.write("File %s: file is correctly formatted.\n" % (infile,))
intrack.close()
return 0
def check(*args, **kw):
if len(args) < 1: raise Usage("No input file provided")
if kw['output'] is None: output = sys.stdout
else: output = open(kw['output'], 'w')
chrmeta = _get_chrmeta(**kw)
if kw['no_overlaps'] and not kw['sorted']:
output.write("--disjoint option was ignored: --sorted is required.\n")
for infile in args:
intrack = track.track(infile, format=kw['format'], chrmeta=chrmeta)
cf = track.check(intrack,
output,
check_sorted=kw['sorted'],
check_noduplicates=kw['no_duplicates'],
check_positive=kw['positive'],
check_nooverlaps=kw['no_overlaps'])
if cf:
output.write("File %s: file is correctly formatted.\n" %
(infile, ))
intrack.close()
return 0
def test_check(self):
self.assertTrue(check(self.bed))
# All sorted
tempfile = os.path.join(path, 'temp2.txt')
with open(tempfile, 'wb') as g:
g.writelines(["chrX\t1\t2\n", "chrX\t3\t4\n", "chrV\t1\t2\n"])
self.assertEqual(check(tempfile, check_sorted=True), True)
# Chromosomes unsorted
tempfile = os.path.join(path, 'temp3.txt')
with open(tempfile, 'wb') as g:
g.writelines(["chrX\t1\t2\n", "chrV\t1\t2\n", "chrX\t3\t4\n"])
self.assertEqual(check(tempfile, check_sorted=True), False)
# Starts unsorted
tempfile = os.path.join(path, 'temp4.txt')
with open(tempfile, 'wb') as g:
g.writelines(["chrX\t3\t4\n", "chrX\t1\t2\n", "chrV\t1\t2\n"])
self.assertEqual(check(tempfile, check_sorted=True), False)
# Ends unsorted
tempfile = os.path.join(path, 'temp5.txt')
with open(tempfile, 'wb') as g:
g.writelines(["chrX\t1\t4\n", "chrX\t1\t3\n", "chrV\t1\t2\n"])
self.assertEqual(check(tempfile, check_sorted=True), False)
# Duplicates
tempfile = os.path.join(path, 'temp5.txt')
with open(tempfile, 'wb') as g:
g.writelines(["chrX\t1\t4\n", "chrX\t1\t4\n", "chrV\t1\t2\n"])
self.assertEqual(check(tempfile, check_duplicates=True), False)
# Empty regions
tempfile = os.path.join(path, 'temp5.txt')
with open(tempfile, 'wb') as g:
g.writelines(["chrX\t1\t4\n", "chrX\t3\t3\n", "chrV\t1\t2\n"])
self.assertEqual(check(tempfile, check_zerosize=True), False)
def test_check(self):
self.assertTrue(check(self.bed))
# All sorted
tempfile = os.path.join(path,'temp2.txt')
with open(tempfile,'wb') as g:
g.writelines(["chrX\t1\t2\n", "chrX\t3\t4\n", "chrV\t1\t2\n"])
self.assertEqual(check(tempfile, check_sorted=True),True)
# Chromosomes unsorted
tempfile = os.path.join(path,'temp3.txt')
with open(tempfile,'wb') as g:
g.writelines(["chrX\t1\t2\n", "chrV\t1\t2\n", "chrX\t3\t4\n"])
self.assertEqual(check(tempfile, check_sorted=True),False)
# Starts unsorted
tempfile = os.path.join(path,'temp4.txt')
with open(tempfile,'wb') as g:
g.writelines(["chrX\t3\t4\n", "chrX\t1\t2\n", "chrV\t1\t2\n"])
self.assertEqual(check(tempfile, check_sorted=True),False)
# Ends unsorted
tempfile = os.path.join(path,'temp5.txt')
with open(tempfile,'wb') as g:
g.writelines(["chrX\t1\t4\n", "chrX\t1\t3\n", "chrV\t1\t2\n"])
self.assertEqual(check(tempfile, check_sorted=True),False)
# Duplicates
tempfile = os.path.join(path,'temp5.txt')
with open(tempfile,'wb') as g:
g.writelines(["chrX\t1\t4\n", "chrX\t1\t4\n", "chrV\t1\t2\n"])
self.assertEqual(check(tempfile, check_duplicates=True),False)
# Empty regions
tempfile = os.path.join(path,'temp5.txt')
with open(tempfile,'wb') as g:
g.writelines(["chrX\t1\t4\n", "chrX\t3\t3\n", "chrV\t1\t2\n"])
self.assertEqual(check(tempfile, check_zerosize=True),False)