本文整理汇总了Python中gimmemotifs.config.MotifConfig.get_seqlogo方法的典型用法代码示例。如果您正苦于以下问题：Python MotifConfig.get_seqlogo方法的具体用法？Python MotifConfig.get_seqlogo怎么用？Python MotifConfig.get_seqlogo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.get_seqlogo方法的4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 get_seqlogo [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 get_seqlogo [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: Motif
# 需要导入模块: from gimmemotifs.config import MotifConfig [as 别名]
# 或者: from gimmemotifs.config.MotifConfig import get_seqlogo [as 别名]
class Motif(object):
PSEUDO_PFM_COUNT = 1000 # Jaspar mean
PSEUDO_PWM = 1e-6
def __init__(self, pfm=None):
if pfm is None:
pfm = []
if len(pfm) > 0:
if np.sum(pfm[0]) > 2:
self.pfm = [list(x) for x in pfm]
self.pwm = self.pfm_to_pwm(pfm)
else:
self.pwm = [list(x) for x in pfm]
self.pfm = [[n * self.PSEUDO_PFM_COUNT for n in col] for col in pfm]
else:
self.pwm = []
self.pfm = []
self.seqs = []
self.consensus = ""
self.id = ""
self.config = MotifConfig()
self.seqlogo = self.config.get_seqlogo()
self.nucs = "ACGT"
self.iupac_rev = {
'CG': 'S',
'AG': 'R',
'AT': 'W',
'CT': 'Y',
'GT': 'K',
'AC': 'M',
'CGT': 'B',
'ACT': 'H',
'AGT': 'D',
'ACG': 'V'
}
self.iupac = {
'A':['A'],
'C':['C'],
'G':['G'],
'T':['T'],
'S':['C','G'],
'R':['A','G'],
'W':['A','T'],
'Y':['C','T'],
'K':['G','T'],
'M':['A','C'],
'B':['C','G','T'],
'H':['A','C','T'],
'D':['A','G','T'],
'V':['A','C','G'],
'N':['A','C','G','T']
}
self.iupac_pwm = {
'A':[1, 0, 0, 0],
'C':[0, 1, 0, 0],
'G':[0, 0, 1, 0],
'T':[0, 0, 0, 1],
'S':[0, 0.5, 0.5, 0],
'R':[0.5, 0, 0.5, 0],
'W':[0.5, 0, 0, 0.5],
'Y':[0, 0.5, 0, 0.5],
'K':[0, 0, 0.5, 0.5],
'M':[0.5, 0.5, 0, 0],
'B':[0, 0.33, 0.33, 0.33],
'H':[0.33, 0.33, 0, 0.33],
'D':[0.33, 0, 0.33, 0.33],
'V':[0.33, 0.33, 0.33, 0],
'N':[0.25, 0.25, 0.25, 0.25]
}
def __getitem__(self, x):
m = Motif()
if self.pwm:
m.pwm = self.pwm[x]
if self.pfm:
m.pfm = self.pfm[x]
if self.seqs:
m.seqs = [seq[x] for seq in self.seqs]
if self.consensus:
m.consensus = self.consensus[x]
return m
def __len__(self):
return len(self.to_consensus())
def __repr__(self):
return "%s\t%s" % (self.id, self.to_consensus())
def information_content(self):
ic = 0
for row in self.pwm:
ic += 2.0 + np.sum([row[x] * log(row[x])/log(2) for x in range(4) if row[x] > 0])
return ic
def pwm_min_score(self):
#.........这里部分代码省略.........
示例4: Motif
# 需要导入模块: from gimmemotifs.config import MotifConfig [as 别名]
# 或者: from gimmemotifs.config.MotifConfig import get_seqlogo [as 别名]
class Motif(object):
"""
Representation of a transcription factor binding motif.
Examples
--------
>>> motif = Motif([[0,1,0,0], [0.5,0,0,0.5], [0,0,1,0]])
>>> print(motif.to_pwm())
>
0 1 0 0
0.5 0 0 0.5
0 0 1 0
>>> print(motif.to_consensus())
CwG
"""
PSEUDO_PFM_COUNT = 1000 # Jaspar mean
PSEUDO_PWM = 1e-6
G = 0.25
Z = 0.01
def __init__(self, pfm=None):
if pfm is None:
pfm = []
if len(pfm) > 0:
if np.sum(pfm[0]) > 2:
self.pfm = [list(x) for x in pfm]
self.pwm = self.pfm_to_pwm(pfm)
else:
self.pwm = [list(x) for x in pfm]
self.pfm = [[n * self.PSEUDO_PFM_COUNT for n in col] for col in pfm]
self.logodds = [[np.log(n / self.G + self.Z) for n in col] for col in self.pwm]
else:
self.pwm = []
self.pfm = []
self.wiggled_pwm = None
self.factors = {DIRECT_NAME:[], INDIRECT_NAME:[]}
self.seqs = []
self.consensus = ""
self.min_score = None
self.max_score = None
self.id = ""
self.config = MotifConfig()
self.seqlogo = self.config.get_seqlogo()
self.nucs = "ACGT"
self.iupac_rev = {
'CG': 'S',
'AG': 'R',
'AT': 'W',
'CT': 'Y',
'GT': 'K',
'AC': 'M',
'CGT': 'B',
'ACT': 'H',
'AGT': 'D',
'ACG': 'V'
}
self.iupac = {
'A':['A'],
'C':['C'],
'G':['G'],
'T':['T'],
'S':['C','G'],
'R':['A','G'],
'W':['A','T'],
'Y':['C','T'],
'K':['G','T'],
'M':['A','C'],
'B':['C','G','T'],
'H':['A','C','T'],
'D':['A','G','T'],
'V':['A','C','G'],
'N':['A','C','G','T']
}
self.iupac_pwm = {
'A':[1, 0, 0, 0],
'C':[0, 1, 0, 0],
'G':[0, 0, 1, 0],
'T':[0, 0, 0, 1],
'S':[0, 0.5, 0.5, 0],
'R':[0.5, 0, 0.5, 0],
'W':[0.5, 0, 0, 0.5],
'Y':[0, 0.5, 0, 0.5],
'K':[0, 0, 0.5, 0.5],
'M':[0.5, 0.5, 0, 0],
'B':[0, 0.33, 0.33, 0.33],
'H':[0.33, 0.33, 0, 0.33],
'D':[0.33, 0, 0.33, 0.33],
'V':[0.33, 0.33, 0.33, 0],
'N':[0.25, 0.25, 0.25, 0.25]
}
#.........这里部分代码省略.........