本文整理汇总了Python中gimmemotifs.config.MotifConfig.set_gene_dir方法的典型用法代码示例。如果您正苦于以下问题：Python MotifConfig.set_gene_dir方法的具体用法？Python MotifConfig.set_gene_dir怎么用？Python MotifConfig.set_gene_dir使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类gimmemotifs.config.MotifConfig的用法示例。
在下文中一共展示了MotifConfig.set_gene_dir方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: run
# 需要导入模块: from gimmemotifs.config import MotifConfig [as 别名]
# 或者: from gimmemotifs.config.MotifConfig import set_gene_dir [as 别名]
def run(self):
from gimmemotifs.config import MotifConfig
cfg = MotifConfig(use_config=self.build_cfg)
data_dir = self.remove_nonsense(os.path.abspath(self.install_dir))
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'))
cfg.set_tools_dir(os.path.join(data_dir, 'gimmemotifs/tools'))
final_tools_dir = self.remove_nonsense(self.install_tools_dir)
for program in MOTIF_CLASSES:
m = eval(program)()
if cfg.is_configured(m.name):
bin = cfg.bin(m.name).replace(self.build_tools_dir, final_tools_dir)
dir = cfg.dir(m.name)
if dir:
dir = dir.replace(self.build_tools_dir, final_tools_dir)
cfg.set_program(m.name, {"bin":bin, "dir":dir})
dir = cfg.get_seqlogo()
dir = dir.replace(self.build_tools_dir, final_tools_dir)
cfg.set_seqlogo(dir)
# Use a user-specific configfile if any other installation scheme is used
# if os.path.abspath(self.install_dir) == "/usr/share":
config_file = os.path.join(self.install_dir, "gimmemotifs/%s" % CONFIG_NAME)
self.outfiles = [config_file]
if os.path.exists(config_file):
new_config = config_file + ".tmp"
dlog.info("INFO: Configfile %s already exists!" % config_file)
dlog.info("INFO: Will create %s, which contains the new config." % new_config)
dlog.info("INFO: If you want to use the newly generated config you can move %s to %s, otherwise you can delete %s.\n" % (new_config, config_file, new_config))
f = open(new_config, "wb")
cfg.write(f)
else:
dlog.info("writing configuration file %s" % config_file)
f = open(config_file, "wb")
cfg.write(f)
if os.path.abspath(self.install_dir) != "/usr/share":
dlog.info("PLEASE NOTE: GimmeMotifs is installed in a non-standard location.")
dlog.info("PLEASE NOTE: This is fine, but then every user should have a file called ~/.gimmemotifs.cfg")
dlog.info("PLEASE NOTE: The file %s is fully configured during install and can be used for that purpose." % config_file)示例2: run
# 需要导入模块: from gimmemotifs.config import MotifConfig [as 别名]
# 或者: from gimmemotifs.config.MotifConfig import set_gene_dir [as 别名]
def run(self):
from gimmemotifs.config import MotifConfig
cfg = MotifConfig(use_config=self.build_cfg)
data_dir = self.remove_nonsense(os.path.abspath(self.install_dir))
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'))
cfg.set_tools_dir(os.path.join(data_dir, 'gimmemotifs/tools'))
final_tools_dir = self.remove_nonsense(self.install_tools_dir)
for program in MOTIF_CLASSES:
m = eval(program)()
if cfg.is_configured(m.name):
bin = cfg.bin(m.name).replace(self.build_tools_dir, final_tools_dir)
dir = cfg.dir(m.name)
if dir:
dir = dir.replace(self.build_tools_dir, final_tools_dir)
cfg.set_program(m.name, {"bin":bin, "dir":dir})
dir = cfg.get_seqlogo()
dir = dir.replace(self.build_tools_dir, final_tools_dir)
cfg.set_seqlogo(dir)
# Use a user-specific configfile if any other installation scheme is used
# if os.path.abspath(self.install_dir) == "/usr/share":
config_file = os.path.join(self.install_dir, "gimmemotifs/%s" % CONFIG_NAME)
self.outfiles = [config_file]
if os.path.exists(config_file):
timestr = time.strftime("%Y%m%d-%H%M%S")
old_config = "{}.{}".format(config_file, timestr)
shutil.move(config_file, old_config)
dlog.info("INFO: Configfile %s already existed!", config_file)
dlog.info("INFO: This config has been saved as %s", old_config)
dlog.info("writing configuration file %s" % config_file)
f = open(config_file, "wb")
cfg.write(f)示例3: write_config
# 需要导入模块: from gimmemotifs.config import MotifConfig [as 别名]
# 或者: from gimmemotifs.config.MotifConfig import set_gene_dir [as 别名]
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