def test_bedSizeFilter_cmdline():
infn = 'inputfiles/multi.tracks.3.fields.bed'
outfn = tempfile.mktemp()
cmds = ' '.join([
'python',
'../bedSizeFilter.py',
'-i',
infn,
'-o',
outfn,
])
os.system(cmds)
assert open('inputfiles/expected.bedSizeFilter.0.bed').read() == open(
outfn).read()
# make sure minlen works
infile = open(infn)
outfile = open(outfn, 'w')
bedSizeFilter(infile, outfile, minlen=100, maxlen=None)
outfile.close()
assert open('inputfiles/expected.bedSizeFilter.1.bed').read() == open(
outfn).read()
# make sure minlen and maxlen work
infile = open(infn)
outfile = open(outfn, 'w')
bedSizeFilter(infile, outfile, minlen=10, maxlen=500)
outfile.close()
assert open('inputfiles/expected.bedSizeFilter.2.bed').read() == open(
outfn).read()
def test_bedSizeFilter_importing():
infn = 'inputfiles/multi.tracks.3.fields.bed'
outfn = tempfile.mktemp()
infile = open(infn)
outfile = open(outfn,'w')
bedSizeFilter(infile,outfile,minlen=None,maxlen=None)
outfile.close()
infile.close()
assert open('inputfiles/expected.bedSizeFilter.0.bed').read() == open(outfn).read()
def test_bedSizeFilter_importing():
infn = 'inputfiles/multi.tracks.3.fields.bed'
outfn = tempfile.mktemp()
infile = open(infn)
outfile = open(outfn, 'w')
bedSizeFilter(infile, outfile, minlen=None, maxlen=None)
outfile.close()
infile.close()
assert open('inputfiles/expected.bedSizeFilter.0.bed').read() == open(
outfn).read()
def test_bedSizeFilter_cmdline():
infn = 'inputfiles/multi.tracks.3.fields.bed'
outfn = tempfile.mktemp()
cmds = ' '.join(['python',
'../bedSizeFilter.py',
'-i', infn,
'-o', outfn,
])
os.system(cmds)
assert open('inputfiles/expected.bedSizeFilter.0.bed').read() == open(outfn).read()
# make sure minlen works
infile = open(infn)
outfile = open(outfn,'w')
bedSizeFilter(infile,outfile,minlen=100,maxlen=None)
outfile.close()
assert open('inputfiles/expected.bedSizeFilter.1.bed').read() == open(outfn).read()
# make sure minlen and maxlen work
infile = open(infn)
outfile = open(outfn,'w')
bedSizeFilter(infile,outfile,minlen=10,maxlen=500)
outfile.close()
assert open('inputfiles/expected.bedSizeFilter.2.bed').read() == open(outfn).read()