def test5_motif_to_img(self):
""" Motif to img """
seqlogo = which("seqlogo")
if seqlogo:
m = Motif(self.pfm)
m.to_img("test/test.png", fmt="png", seqlogo=seqlogo)
self.assertTrue(os.path.exists("test/test.png"))
os.unlink("test/test.png")
else:
print("seqlogo not found, skipping.")
def test5_motif_to_img(self):
""" Motif to img """
seqlogo = which("seqlogo")
if seqlogo:
m = Motif(self.pfm)
m.to_img("test/test.png", fmt="png", seqlogo=seqlogo)
self.assertTrue(os.path.exists("test/test.png"))
os.unlink("test/test.png")
else:
print("seqlogo not found, skipping.")
def create_default_config(self):
logger.info("Creating new config.")
available_tools = []
self.config.read(self.default_config)
for m in MOTIF_CLASSES:
try:
exe = self.config.get(m, "bin")
mdir = self.config.get(m, "dir")
tool_dir = os.path.join(self.package_dir, mdir)
cmd = os.path.join(tool_dir, exe)
if which(cmd):
logger.info("Using included version of %s.", m)
available_tools.append(m)
else:
cmd = which(exe)
if cmd:
logger.info("Using system version of %s.", m)
self.set_program(m, {
"bin": cmd,
"dir": os.path.dirname(cmd)
})
available_tools.append(m)
else:
logger.warn(
"%s not found. To include it you will have to install it.",
m,
)
except configparser.NoSectionError:
logger.warn("{} not in config".format(m))
params = self.get_default_params()
params["available_tools"] = ",".join(available_tools)
self.set_default_params(params)
if not os.path.exists(CONFIG_DIR):
os.makedirs(CONFIG_DIR, exist_ok=True)
with open(self.user_config, "w") as f:
self.config.write(f)
logger.info("Configuration file: %s", self.user_config)
def create_default_config(self):
logger.info("Creating new config.")
available_tools = []
cfg = self.config.read(self.default_config)
for m in MOTIF_CLASSES:
try:
exe = self.config.get(m, "bin")
mdir = self.config.get(m, "dir")
tool_dir = os.path.join(self.package_dir, mdir)
cmd = os.path.join(tool_dir, exe)
if which(cmd):
logger.info("Using included version of %s.", m)
available_tools.append(m)
else:
cmd = which(exe)
if cmd:
logger.info("Using system version of %s.", m)
self.set_program(m,
{
"bin":cmd,
"dir":os.path.dirname(cmd)
}
)
available_tools.append(m)
else:
logger.warn("%s not found. To include it you will have to install it.", m)
except configparser.NoSectionError:
logger.warn("{} not in config".format(m))
params = self.get_default_params()
params['available_tools'] = ",".join(available_tools)
self.set_default_params(params)
if not os.path.exists(CONFIG_DIR):
os.makedirs(CONFIG_DIR, exist_ok=True)
with open(self.user_config, "w") as f:
self.config.write(f)
logger.info("Configuration file: %s", self.user_config)
def run(self):
if not os.path.exists(self.build_cfg):
os.mkdir(self.build_cfg)
from gimmemotifs.config import MotifConfig
cfg = MotifConfig(use_config="cfg/gimmemotifs.cfg.base")
dlog.info("locating motif programs")
available = []
for program in MOTIF_CLASSES:
# Get class
m = eval(program)()
cmd = m.cmd
### ugly, fixme :)
if cmd == "trawler.pl":
cmd = "trawler/bin/trawler.pl"
if cmd == "ChIPMunk.sh":
cmd = "ChIPMunk/ChIPMunk.sh"
if cmd == "hms":
cmd = "HMS/hms"
bin = ""
if cmd == "/bin/false":
# motif db
bin = "/bin/false"
elif os.path.exists(os.path.join(self.build_tools_dir, cmd)):
bin = os.path.join(self.build_tools_dir, cmd)
dlog.info("using included version of %s: %s" % (program, bin))
else:
### ugly, fixme :)
if cmd == "trawler/bin/trawler.pl":
cmd = "trawler.pl"
if cmd == "ChIPMunk/ChIPMunk.sh":
cmd = "ChIPMunk.sh"
if cmd == "HMS/hms":
cmd = "hms"
if program in MOTIF_BINS.keys():
dlog.info("could not find compiled version of %s" % program)
bin = which(cmd)
if bin:
dlog.info("using installed version of %s: %s" % (program, bin))
else:
dlog.info("not found: %s" % program)
### Some more ugly stuff
if bin:
dir = bin.replace(m.cmd,"")
if program == "Weeder":
dir = bin.replace("weederTFBS.out","")
elif program == "Meme":
dir = bin.replace("bin/meme.bin", "").replace("meme.bin", "")
elif program == "Trawler":
dir = bin.replace("bin/trawler.pl", "")
elif program == "ChIPMunk":
dir = bin.replace("ChIPMunk.sh", "")
available.append(m.name)
cfg.set_program(m.name, {"bin":bin, "dir":dir})
# Weblogo
bin = ""
seq_included = os.path.join(self.build_tools_dir, "seqlogo")
if os.path.exists(seq_included):
bin = seq_included
dlog.info("using included version of weblogo: %s" % seq_included)
else:
bin = which("seqlogo")
dlog.info("using installed version of seqlogo: %s" % (bin))
if bin:
cfg.set_seqlogo(bin)
else:
dlog.info("couldn't find seqlogo")
# Set the available tools in the config file
DEFAULT_PARAMS["available_tools"] = ",".join(available)
for tool in available:
if tool in LONG_RUNNING:
dlog.info("PLEASE NOTE: %s can take a very long time to run on large datasets. Therefore it is not added to the default tools. You can always enable it later, see documentation for details" % tool)
available.remove(tool)
DEFAULT_PARAMS["tools"] = ",".join(available)
cfg.set_default_params(DEFAULT_PARAMS)
# Write (temporary) config file
config_file = os.path.join(self.build_cfg, "%s" % CONFIG_NAME)
dlog.info("writing (temporary) configuration file: %s" % config_file)
f = open(config_file, "wb")
cfg.write(f)
f.close()
def run(self):
if not os.path.exists(self.build_cfg):
os.mkdir(self.build_cfg)
from gimmemotifs.config import MotifConfig
cfg = MotifConfig(use_config="cfg/gimmemotifs.cfg.base")
dlog.info("locating motif programs")
available = []
for program in MOTIF_CLASSES:
# Get class
m = eval(program)()
cmd = m.cmd
### ugly, fixme :)
if cmd == "ChIPMunk.sh":
cmd = "ChIPMunk/ChIPMunk.sh"
if cmd == "hms":
cmd = "HMS/hms"
bin = ""
if cmd == "/bin/false":
# motif db
bin = "/bin/false"
elif os.path.exists(os.path.join(self.build_tools_dir, cmd)):
bin = os.path.join(self.build_tools_dir, cmd)
dlog.info("using included version of %s: %s" % (program, bin))
else:
### ugly, fixme :)
if cmd == "ChIPMunk/ChIPMunk.sh":
cmd = "ChIPMunk.sh"
if cmd == "HMS/hms":
cmd = "hms"
if program in MOTIF_BINS.keys():
dlog.info("could not find compiled version of %s" %
program)
bin = which(cmd)
if bin:
dlog.info("using installed version of %s: %s" %
(program, bin))
else:
dlog.info("not found: %s" % program)
### Some more ugly stuff
if bin:
dir = bin.replace(m.cmd, "")
if program == "Weeder":
dir = bin.replace("weederTFBS.out", "")
elif program == "Meme":
dir = bin.replace("bin/meme.bin",
"").replace("meme.bin", "")
elif program == "ChIPMunk":
dir = bin.replace("ChIPMunk.sh", "")
available.append(m.name)
cfg.set_program(m.name, {
"bin": os.path.abspath(bin),
"dir": os.path.abspath(dir),
})
# Weblogo
bin = ""
seq_included = os.path.abspath(
os.path.join(self.build_tools_dir, "seqlogo"))
if os.path.exists(seq_included):
bin = seq_included
dlog.info("using included version of weblogo: %s" % seq_included)
else:
bin = which("seqlogo")
dlog.info("using installed version of seqlogo: %s" %
(os.path.abspath(bin)))
if bin:
cfg.set_seqlogo(os.path.abspath(bin))
else:
dlog.info("couldn't find seqlogo")
# Set the available tools in the config file
DEFAULT_PARAMS["available_tools"] = ",".join(available)
for tool in available:
if tool in LONG_RUNNING:
dlog.info(
"PLEASE NOTE: %s can take a very long time to run on large datasets. Therefore it is not added to the default tools. You can always enable it later, see documentation for details"
% tool)
available.remove(tool)
DEFAULT_PARAMS["tools"] = ",".join(available)
cfg.set_default_params(DEFAULT_PARAMS)
# Write (temporary) config file
config_file = os.path.join(self.build_cfg, "%s" % CONFIG_NAME)
dlog.info("writing (temporary) configuration file: %s" % config_file)
f = open(config_file, "w")
cfg.write(f)
f.close()
# TODO: fix this hack
my_cfg = open(config_file).read()
with open(config_file, "w") as f:
cwd = os.getcwd()
f.write(my_cfg.replace("/usr/share/gimmemotifs/", cwd + "/"))