def locate_tool(tool, verbose=True):
tool = re.sub(r'[^a-zA-Z]','',tool)
m = eval(tool)()
tool_bin = which(m.cmd)
if tool_bin:
if verbose:
print "Found {} in {}".format(m.name, tool_bin)
return tool_bin
else:
print "Couldn't find {}".format(m.name)
def test5_motif_to_img(self):
""" Motif to img """
seqlogo = which("seqlogo")
if seqlogo:
m = Motif(self.pfm)
m.to_img("test/test.png", format="png", seqlogo=seqlogo)
self.assert_(os.path.exists("test/test.png"))
os.unlink("test/test.png")
else:
print "seqlogo not found, skipping."
def locate_tool(tool, verbose=True):
tool = re.sub(r'[^a-zA-Z]', '', tool)
m = eval(tool)()
tool_bin = which(m.cmd)
if tool_bin:
if verbose:
print "Found {} in {}".format(m.name, tool_bin)
return tool_bin
else:
print "Couldn't find {}".format(m.name)
def test5_motif_to_img(self):
""" Motif to img """
seqlogo = which("seqlogo")
if seqlogo:
m = Motif(self.pfm)
m.to_img("test/test.png", format="png", seqlogo=seqlogo)
self.assert_(os.path.exists("test/test.png"))
os.unlink("test/test.png")
else:
print "seqlogo not found, skipping."
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"
bin = ""
if 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 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", "")
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 == "trawler.pl":
cmd = "trawler/bin/trawler.pl"
bin = ""
if 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 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", "")
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 write_config(self):
from gimmemotifs.config import MotifConfig
cfg = MotifConfig(use_config="cfg/gimmemotifs.cfg.example")
data_dir = os.path.abspath(self.install_data)
cfg.set_template_dir(os.path.join(data_dir, 'gimmemotifs/templates'))
cfg.set_gene_dir(os.path.join(data_dir, 'gimmemotifs/genes'))
cfg.set_score_dir(os.path.join(data_dir, 'gimmemotifs/score_dists'))
cfg.set_index_dir(os.path.join(data_dir, 'gimmemotifs/genome_index'))
cfg.set_motif_dir(os.path.join(data_dir, 'gimmemotifs/motif_databases'))
cfg.set_bg_dir(os.path.join(data_dir, 'gimmemotifs/bg'))
print
print "Trying to locate motif programs"
MOTIF_CLASSES = ["MDmodule", "Meme", "Weeder", "Gadem", "MotifSampler", "Trawler", "Improbizer", "MoAn", "BioProspector"]
available = []
for program in MOTIF_CLASSES:
m = eval(program)()
cmd = m.cmd
bin = which(cmd)
if bin:
print "Found %s in %s" % (m.name, bin)
available.append(m.name)
dir = None
if program == "Weeder":
dir = bin.replace("weederTFBS.out","")
elif program == "Meme":
dir = bin.replace("bin/meme", "")
elif program == "Trawler":
dir = bin.replace("bin/trawler.pl", "")
cfg.set_program(m.name, {"bin":bin, "dir":dir})
else:
print "Couldn't find %s" % m.name
print
print "Trying to locate seqlogo"
bin = which("seqlogo")
if bin:
print "Found seqlogo in %s" % (bin)
cfg.set_seqlogo(bin)
else:
print "Couldn't find seqlogo"
print
DEFAULT_PARAMS["available_tools"] = ",".join(available)
DEFAULT_PARAMS["tools"] = ",".join(available)
cfg.set_default_params(DEFAULT_PARAMS)
# Use a user-specific configfile if any other installation scheme is used
if os.path.abspath(self.install_data) == "/usr/share":
config_file = "/usr/share/gimmemotifs/%s" % CONFIG_NAME
else:
config_file = os.path.expanduser("~/.%s" % CONFIG_NAME)
if os.path.exists(config_file):
new_config = config_file + ".tmp"
print "INFO: Configfile %s already exists!\n Will create %s, which contains the new config.\n If you want to use the newly generated config you can move %s to %s, otherwise you can delete %s.\n" % (config_file, new_config, new_config, config_file, new_config)
f = open(new_config, "wb")
cfg.write(f)
else:
print "Writing configuration file %s" % config_file
f = open(config_file, "wb")
cfg.write(f)
print "Edit %s to further configure GimmeMotifs." % config_file