def cli(logfile, outdir, ressep, table):
# Setup logger
logging.config.dictConfig({
"version": 1,
"disable_existing_loggers": False, # this fixes the problem
"formatters": {
"standard": {
"class": "logging.Formatter",
"format": "%(name)-12s %(levelname)-8s %(message)s",
},
"detailed": {
"class": "logging.Formatter",
"format":
"%(asctime)s %(name)-15s %(levelname)-8s %(message)s",
"datefmt": "%m-%d-%y %H:%M",
},
},
"handlers": {
"console": {
"class": "logging.StreamHandler",
"level": "INFO",
"formatter": "standard",
},
"file": {
"class": "logging.FileHandler",
"filename": logfile,
"level": "INFO",
"mode": "w",
"formatter": "detailed",
}
},
"root": {
"level": "INFO",
"handlers": ["console", "file"]
},
})
logger = logging.getLogger(__name__)
logger.info("Reading {}".format(table))
table_1 = paramtable.ParamTable(ressep=ressep)
table_1.from_file(table)
logger.info("{} read successfully.".format(table))
d_table = table_1.table.diff(axis=1).dropna(axis=1)
d_perres = table_1.per_residue.diff(axis=1).dropna(axis=1)
d_interactions = table_1.interactions.diff(axis=1).dropna(axis=1)
filename = path.join(outdir, "dframe_coupling.txt")
with open(filename, mode="wb") as output:
logger.info("Writing frame differences to {}".format(filename))
d_table = d_table.to_csv(
header=True,
index=True,
sep=native_str(" "),
float_format=native_str("%.4f"),
encoding="utf-8",
)
output.write(d_table.encode())
logger.info("Table written successfully.")
filename = path.join(outdir, "dframe_perres.txt")
with open(filename, mode="wb") as output:
logger.info(
"Writing per residue frame differences to {}".format(filename))
d_perres = d_perres.to_csv(
header=True,
index=True,
sep=native_str(" "),
float_format=native_str("%.4f"),
encoding="utf-8",
)
output.write(d_perres.encode())
logger.info("Table written successfully.")
filename = path.join(outdir, "dframe_interactions.txt")
with open(filename, mode="wb") as output:
logger.info(
"Writing residue-residue frame differences to {}".format(filename))
d_interactions = d_interactions.to_csv(
header=True,
index=True,
sep=native_str(" "),
float_format=native_str("%.4f"),
encoding="utf-8",
)
output.write(d_interactions.encode())
logger.info("Table written successfully.")
def cli(data_dir, logfile, outdir, prefix, tbltype, ressep, verbose, start, end, trimmed, trimcut):
pt = paramtable.ParamTable(
prefix=prefix,
tbltype=tbltype,
ressep=ressep,
datadir=data_dir,
start=start,
end=end,
trimmed=trimmed,
trimcut=trimcut
)
# Setup logger
logging.config.dictConfig({
"version": 1,
"disable_existing_loggers": False, # this fixes the problem
"formatters": {
"standard": {
"class": "logging.Formatter",
"format": "%(name)-12s %(levelname)-8s %(message)s",
},
"detailed": {
"class": "logging.Formatter",
"format":
"%(asctime)s %(name)-15s %(levelname)-8s %(message)s",
"datefmt": "%m-%d-%y %H:%M",
},
},
"handlers": {
"console": {
"class": "logging.StreamHandler",
"level": "INFO",
"formatter": "standard",
},
"file": {
"class": "logging.FileHandler",
"filename": logfile,
"level": "INFO",
"mode": "w",
"formatter": "detailed",
}
},
"root": {
"level": "INFO",
"handlers": ["console", "file"]
},
})
logger = logging.getLogger(__name__)
pt.run(verbose=verbose)
# Write the various tables to different files.
fn = path.join(outdir, filename(tbltype.lower(), ext="txt", keep=True))
pt.write(fn)
if tbltype == "Kb":
fn = path.join(outdir, filename("perres", ext="txt"))
with open(fn, mode="wb") as output:
logger.info("Writing per-residue data to {}.".format(fn))
table = pt.per_residue.to_csv(
header=True,
index=True,
sep=native_str(" "),
float_format=native_str("%.4f"),
encoding="utf-8",
)
output.write(table.encode())
logger.info("Table successfully written.")
fn = path.join(outdir, filename("interactions", ext="txt"))
with open(fn, mode="wb") as output:
logger.info("Writing interactions to {}.".format(fn))
table = pt.interactions.to_csv(
header=True,
index=True,
sep=native_str(" "),
float_format=native_str("%.4f"),
encoding="utf-8",
)
output.write(table.encode())
logger.info("Table successfully written.")
def cli(logfile, outdir, ressep, kb, b0):
# Setup logger
logging.config.dictConfig({
"version": 1,
"disable_existing_loggers": False, # this fixes the problem
"formatters": {
"standard": {
"class": "logging.Formatter",
"format": "%(name)-12s %(levelname)-8s %(message)s",
},
"detailed": {
"class": "logging.Formatter",
"format":
"%(asctime)s %(name)-15s %(levelname)-8s %(message)s",
"datefmt": "%m-%d-%y %H:%M",
},
},
"handlers": {
"console": {
"class": "logging.StreamHandler",
"level": "INFO",
"formatter": "standard",
},
"file": {
"class": "logging.FileHandler",
"filename": logfile,
"level": "INFO",
"mode": "w",
"formatter": "detailed",
}
},
"root": {
"level": "INFO",
"handlers": ["console", "file"]
},
})
logger = logging.getLogger(__name__)
resgrp = ['segidI', 'resI']
logger.info("Loading coupling strength table.")
kb_table = paramtable.ParamTable(ressep=ressep)
kb_table.from_file(kb)
kb_table = kb_table.table.copy(deep=True)
logger.info("Table loaded successfully.")
logger.info("Loading distance table.")
b0_table = paramtable.ParamTable(ressep=ressep)
b0_table.from_file(b0)
b0_table = b0_table.table.copy(deep=True)
logger.info("Table loaded successfully.")
idx = (kb_table == 0.0)
maxkb = np.maximum(kb_table[kb_table.columns[1:].values],
kb_table[kb_table.columns[:-1]].values)
maxkb[maxkb == 0.0] = np.NaN
kb_table = kb_table.diff(axis=1).dropna(axis=1) / maxkb
kb_table.columns = kb_table.columns.astype(np.int32) - 1
count = kb_table[kb_table.abs() > 0.].groupby(level=resgrp).count()
kb_table = kb_table.groupby(level=resgrp).sum() / count
kb_table.fillna(0., inplace=True)
# Calculate the r.m.s.d. of equilibrium distances between sites.
b0_table = b0_table.diff(axis=1).dropna(axis=1) / maxkb
b0_table[idx] = 0.0
b0_table = 0.5 * b0_table.pow(2).groupby(level=resgrp).sum()
b0_table = b0_table.apply(np.sqrt)
filename = path.join(outdir, "normed_kb.txt")
with open(filename, mode="wb") as output:
logger.info("Writing normed coupling strengths to {}".format(filename))
kb_table = kb_table.to_csv(
header=True,
index=True,
sep=native_str(" "),
float_format=native_str("%.4f"),
encoding="utf-8",
)
output.write(kb_table.encode())
logger.info("Table written successfully.")
filename = path.join(outdir, "normed_b0.txt")
with open(filename, mode="wb") as output:
logger.info("Writing normed distances to {}".format(filename))
b0_table = b0_table.to_csv(
header=True,
index=True,
sep=native_str(" "),
float_format=native_str("%.4f"),
encoding="utf-8",
)
output.write(b0_table.encode())
logger.info("Table written successfully.")