def test_tool(tool_name):
"""Test motif prediction tools."""
params = {"background": bg_fa, "organism": "hg38", "width": 7}
print(__tools__)
if tool_name in [
"yamda", # not installable vio bioconda
"rpmcmc", # not installable via bioconda
"gadem", # sometimes crashes on invalid pointer
"jaspar",
"xxmotif", # takes too long
"trawler", # unpredictable, sometimes doesn't find the motif
"weeder", # doesn't work at the moment
"posmo", # motif doesn't predictably look like AP1
"dreme", # current dreme in bioconda is broken
]:
return
if platform.system() == "Darwin":
# No support for osx
if tool_name in ["amd", "hms", "improbizer", "motifsampler", "dinamo"]:
return
t = get_tool(tool_name)
print("Testing {}...".format(t))
(motifs, stderr, stdout) = t.run(fa, params)
print(motifs)
print(stderr)
print(stdout)
assert ap1_included(motifs)
def test_tools(self):
"""Test motif prediction tools."""
params = {
"background": self.bg_fa,
"organism": "hg38",
"width": 7,
}
for tool_name in sorted(__tools__):
if tool_name in [
"gadem", # sometimes crashes on invalid pointer
"jaspar",
"xxmotif", # takes too long
"trawler", # unpredictable, sometimes doesn't find the motif
]:
continue
if platform.system() == "Darwin":
# No support for osx
if tool_name in [
"amd",
"hms",
"improbizer",
"motifsampler",
"posmo",
"meme", # until the bioconda package is fixed
"memew", # until the bioconda package is fixed
]:
continue
t = get_tool(tool_name)
print("Testing {}...".format(t))
(motifs, stderr, stdout) = t.run(self.fa, params)
self.assertTrue(self.ap1_included(motifs))
def prediction(args):
tool = args.tool
infile = args.infile
outfile = args.outfile
paramfile = args.paramfile
t = get_tool(tool)
params = {}
if paramfile:
params = load(open(paramfile))
(motifs, stdout, stderr) = t.run(infile, params)
sys.stderr.write(stderr)
sys.stdout.write(stdout)
f = open(outfile, "w")
for m in motifs:
f.write("{0}\n".format(m.to_pfm()))
f.close()
def prediction(args):
tool = args.tool
infile = args.infile
outfile = args.outfile
paramfile = args.paramfile
t = get_tool(tool)
params = {}
if paramfile:
params = load(open(paramfile))
(motifs, stdout, stderr) = t.run(infile, params)
sys.stderr.write(stderr)
sys.stdout.write(stdout)
f = open(outfile, "w")
for m in motifs:
f.write("{0}\n".format(m.to_pfm()))
f.close()
def test_tools(self):
"""Test motif prediction tools."""
params = {
"background": self.bg_fa,
"organism": "hg38",
"width": 7,
}
for tool_name in sorted(__tools__):
if tool_name in [
"gadem", # sometimes crashes on invalid pointer
"jaspar",
"xxmotif", # takes too long
"trawler", # unpredictable, sometimes doesn't find the motif
"weeder", # doesn't work at the moment
"posmo", # motif doesn't predictably look like AP1
]:
continue
if platform.system() == "Darwin":
# No support for osx
if tool_name in [
"amd",
"hms",
"improbizer",
"motifsampler",
]:
continue
t = get_tool(tool_name)
print("Testing {}...".format(t))
(motifs, stderr, stdout) = t.run(self.fa, params)
print(motifs)
print(stderr)
print(stdout)
self.assertTrue(self.ap1_included(motifs))